U.S. patent application number 17/197536 was filed with the patent office on 2021-08-05 for guayule with increased rubber production and yield.
The applicant listed for this patent is The United States of America, as represented by the Secretary of Agriculture, The United States of America, as represented by the Secretary of Agriculture. Invention is credited to Colleen M. McMahan, Dante Placido.
Application Number | 20210238619 17/197536 |
Document ID | / |
Family ID | 1000005450864 |
Filed Date | 2021-08-05 |
United States Patent
Application |
20210238619 |
Kind Code |
A1 |
McMahan; Colleen M. ; et
al. |
August 5, 2021 |
GUAYULE WITH INCREASED RUBBER PRODUCTION AND YIELD
Abstract
Altered guayule that produce more rubber than the amount of
rubber produced by non-altered guayule are provided. The
alterations may include (i) a reduction in amount of functional
PaAos produced by the altered guayule, (ii) an increase in amount
of a transcription factor produced by the altered guayule, (iii) an
increase in amount of salicylic acid within the altered guayule,
(iv) exposure of the altered guayule to cold temperature, and (v) a
combination thereof. Methods of producing the altered guayule and
methods of increasing the amount of rubber produced by a guayule
are also provided.
Inventors: |
McMahan; Colleen M.;
(Sausalito, CA) ; Placido; Dante; (Oakland,
CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
The United States of America, as represented by the Secretary of
Agriculture |
Washington |
DC |
US |
|
|
Family ID: |
1000005450864 |
Appl. No.: |
17/197536 |
Filed: |
March 10, 2021 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
15975851 |
May 10, 2018 |
10982219 |
|
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17197536 |
|
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62504762 |
May 11, 2017 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12N 15/8218 20130101;
C08L 7/02 20130101; C12N 15/1137 20130101; C12N 9/88 20130101; C12N
15/8261 20130101; C12Y 402/01092 20130101; C12N 2310/11 20130101;
C12N 15/8251 20130101; C12N 2310/14 20130101; C07K 14/415 20130101;
C12N 15/8243 20130101 |
International
Class: |
C12N 15/82 20060101
C12N015/82; C12N 15/113 20060101 C12N015/113; C12N 9/88 20060101
C12N009/88; C07K 14/415 20060101 C07K014/415 |
Claims
1. An altered guayule, parts and progeny thereof, that produces
more rubber than an amount of rubber produced by a non-altered
guayule comprising an alteration that causes said altered guayule
to produce an increased amount of rubber, said alteration being an
increase in amount of salicylic acid within said altered guayule;
wherein said alteration causes said altered guayule to produce more
rubber than said amount of rubber produced by said non-altered
guayule.
2. The altered guayule of claim 1, wherein said increase in said
amount of salicylic acid within said altered guayule comprises
administering salicylic acid to a guayule to generate said altered
guayule; and wherein said salicylic acid causes said altered
guayule to produce more rubber than said amount of rubber produced
by said non-altered guayule.
3. A germplasm of said altered guayule of claim 1, wherein said
germplasm comprises said alteration.
4. A seed of said altered guayule of claim 1, wherein said seed
comprises said alteration.
5. A method for increasing an amount of rubber produced by an
altered guayule compared to an amount of rubber produced by a
non-altered guayule, said method comprising an alteration, the
alteration being increasing the amount of salicylic acid within
said altered guayule, wherein said alteration causes said altered
guayule to produce more rubber than said amount of rubber produced
by said non-altered guayule.
6. The method of claim 5, wherein said increasing said amount of
salicylic acid within said altered guayule comprises administering
salicylic acid to said guayule to generate said altered guayule;
and wherein said salicylic acid causes said altered guayule to
produce more rubber than said amount of rubber produced by said
non-altered guayule.
8. The method of claim 5, further comprising exposing said altered
guayule to between approximately 7.degree. C. and approximately
15.degree. C. for approximately 8 hours per day.
9. An altered guayule produced by the method of claim 5, wherein
said altered guayule comprises said alteration and produces more
rubber than the amount of rubber produced by a non-altered
guayule.
10. An altered seed of an altered guayule produced by the method of
claim 5, wherein said altered seed comprises said alteration.
Description
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This patent application claims priority to U.S. patent
application Ser. No. 15/975,851, filed May 10, 2018, which itself
claims priority to U.S. Provisional Patent Application 62/504,762
filed on May 11, 2017, contents of which are expressly incorporated
by reference herein.
BACKGROUND OF THE INVENTION
Sequence Listing
[0002] The Sequence Listing submitted via EFS-Web as ASCII
compliant text file format (.txt) filed on Mar. 10, 2021, named
"SequenceListing", (created on May 9, 2018, 50 KB), is incorporated
herein by reference. This Sequence Listing serves as paper copy of
the Sequence Listing required by 37 C.F.R. .sctn. 1.821(c) and the
Sequence Listing in computer-readable form (CRF) required by 37
C.F.R. .sctn. 1.821(e). A statement under 37 C.F.R. .sctn. 1.821(f)
is not necessary.
Field of the Invention
[0003] This invention relates to altered guayule plants that grow
larger and produce more rubber than non-altered guayule plants,
when grown under the same conditions. The altered guayule contain
the cDNA sequence of Parthenium argentatum Allene oxide synthase
(PaAos) in the reverse complement orientation under control of a
heterologous promoter which reduces the production of PaAos via
RNAi. Other types of genetic alternations can be made in guayule to
reduce the functionality of PaAos. Methods of increasing rubber
yield in guayule via reducing PaAos translation and/or reducing the
amount of functional PaAos in plants are also included.
Description of Related Art
[0004] Natural rubber is synthesized by more than 2,500 plant
species (Cornish, et al., J. Nat. Rubber Research 8:275-285 (1993);
Cornish, K., Phytochemistry 57:1123-1134 (2001)). Rubber is
produced by these plants as a secondary metabolite with no clear
indication of its function in plant cells. Possible reasons on why
these species synthesize rubber are to defend themselves against
pathogens and insect attacks, repair tissue damages caused by
mechanical wounding and protect cell damage induced by
environmental stresses (Demel, et al., Biochim. Biophys. Acta.
1375:36-42 (1998); Tangpakdee and Tanaka, J. Rubber Res. 1:14
(1998); Vereyken, et al., Biochim. Biophys. Acta, 1510:307-320
(2001); Kim, et al., Plant Cell Physiol., 412-414 (2003) and
references therein; Konno, K., Phytochemistry, 1510-1530 (2011);
and Sarkar, J., Rubber Science, 228-237 (2013)). According to a
2014 market report, the rubber that these plants produce accounted
for $16.5 billion in trade worldwide
(rubberworld.com/RWmarket_report.asp). Even more so, the end
products made from natural rubber, including tires for the
transportation industry, sports equipment, medical devices, and
more, are indispensable in our everyday life. The Hevea tree is the
main source of natural rubber but concerns exist as it is limited
geographically to tropical climates, mainly in Southeast Asia, is
susceptible to diseases, and produces rubber that causes allergic
reactions. Clearly, an alternative source for the production of
natural rubber is very important to reduce economic risk and
safeguard human health.
[0005] One plant known to be a promising source of natural rubber
is guayule (Parthenium argentatum, Gray), a desert shrub native to
the southwestern United States and northern Mexico (Mooibroek and
Cornish, Appl. Microbio. and Biochem. 53:355-365 (2000); van Beilen
and Poirier, Critical Reviews Biotech. 27:217-231 (2007)). The
majority of rubber synthesis in guayule occurs during the cold
season. Guayule synthesizes rubber within subcellular organelles
called rubber particles (Archer and Audley, Bot. J. Linnean Soc.
94:181-196 (1987)) stored in the parenchyma cells of stembark
tissues (Gilliland, M.v., Protoplasma, 169-177 (1984)); Macrae, S.
G., Plant Physiol., 1027-1032 (1986)). Natural rubber synthesis is
initiated by the action of allylic pyrophosphates initiators
(Cornish and Siler, J. Plant Physiol., 301-305 (1995)), usually
farnesyl pyrophosphate (FPP). Then, the monomer
isopentenyl-pyrophosphate (IPP), produced by the mevalonic acid
pathway (MEV) in the cytosol and the methylerythritol phosphate
(MEP) pathway in the plastid (Mooibroek and Cornish (2000); van
Beilen and Poirier, TRENDS in Biotech., 522-529 (2007)) elongates
the rubber chain. Rubber synthesis is mediated by rubber
transferases requiring magnesium ions as cofactor (Da Costa, et
al., Phytochemistry 67(15): 1621-1628 (2006)).
[0006] The proposed model for the structure of rubber particles
consists mostly of hydrophobic cis-polyisoprene units (natural
rubber) encapsulated inside a protein and phospholipid surface
monolayer (Nawamawat, et al., Colloids and Surfaces A:
Physicochemical and Engineering Aspects, 390:157-166 (2011);
Sansatsadeekul, et al., J. Biosci. and Bioeng, 111:628-634 (2011)).
The phospholipids serve to stabilize and solubilize the otherwise
insoluble (rubber) product. Guayule rubber particles include
several proteins (Whalen, et al., Development of crops to produce
industrially useful natural rubber. Chapter 23 in Isoprenoid
Synthesis in Plants and Microorganisms: New Concepts and
Experimental Approaches, Bach and Rohmer (eds.), DOI
10.1007/978-1-4614-4063-5_23, Springer Science+Business Media NY,
329-345 (2013)) of which Aos has been found to be the most abundant
(Backhaus, et al., Phytochemistry 30:2493-2497 (1991)). Aos is
well-known as an enzyme in the jasmonic acid biosynthetic pathway
(Harms, et al., Plant Cell, 1645-1654 (1995); Wang, et al., Plant
Mol. Biol., 783-793 (1999); Schaller, F., J. Exper. Botany, 11-23
(2001)). The role of Aos in rubber biosynthesis, and the reason for
the abundance of Aos protein on guayule rubber particle surfaces,
is not known (Whalen, et al. (2013)).
[0007] The need exists for a method to increase rubber production
in altered guayule compared to rubber production amounts in
non-altered guayule in order to improve the commercial
attractiveness of using guayule rubber as a replacement of
synthetic rubber and Hevea rubber. Further, a need exists for
increasing the rubber yield per acre obtained from altered guayule
compared to the rubber yield per acre obtained from non-altered
guayule. This greater rubber yield results from the altered guayule
being larger in size than non-altered guayule of similar age. A
need also exists for altered guayule that produce more rubber than
the amount of rubber produced by non-altered guayule. A need also
exists for altered guayule that have a larger size than similarly
aged non-altered guayule because the altered guayule that are
larger than the non-altered guayule will possess more tissue for
storage of rubber and thus generate greater rubber yield per acre
than the rubber yield per acre of non-altered guayule.
BRIEF SUMMARY OF THE INVENTION
[0008] It is an object of this invention to have an altered guayule
(and progeny and parts thereof) that produces more rubber than the
amount of rubber produced by a non-altered guayule. It is a further
object of this invention that the alteration causes the altered
guayule to produce a reduced amount of functional Parthenium
argentatum Allene oxide synthase (PaAos) compared the amount of
functional PaAos produced by non-altered guayule. It is another
object of this invention that the reduced amount of functional
PaAos causes more rubber to be produced by the altered guayule
compared to the amount of rubber produced by non-altered guayule.
It is another object of this invention that the reduced amount of
functional PaAos causes the altered guayule to grow larger in size
compared to the size of similarly aged non-altered guayule, and the
larger sized altered guayule has an increased rubber yield per acre
than the rubber yield per acre of similarly aged non-altered
guayule. It is another object of this invention to have an altered
guayule that produces a greater rubber yield per acre than the
rubber yield per acre produced by a similarly aged non-altered
guayule. It is a further object of this invention to have
germplasm, pollen, flowers, seeds, stems, leaves, roots, cells,
etc., of the altered guayule.
[0009] It is an object of this invention that the altered guayule
contains an alteration in PaAos functionality. It is another object
of this invention that the altered guayule contains an expression
vector which further contains a heterologous promoter operably
linked to a polynucleotide encoding PaAos anti-sense RNA and/or
PaAos dsRNA and/or one or more guayule transcription factors,
PaWRKY3-like (SEQ ID NOs: 39 and 40 and a sequence at least 95%
identical thereof), PaWRKY71-like (SEQ ID NOs: 41 and 42 and a
sequence at least 95% identical thereof), and/or PaMYBS3-like (SEQ
ID NOs: 43 and 44 and a sequence at least 95% identical thereof),
for overexpression of one or more of the transcription factors
and/or the anti-sense RNA or dsRNA. It is further object of this
invention that salicylic acid (SA) and/or PaAos dsRNA is
administered to a non-altered guayule to make an altered guayule
that produces more rubber than a non-altered guayule. It is another
object that an altered guayule (containing one or more of the
following: one or more expression vectors encoding PaAos anti-sense
RNA, PaAos dsRNA (SEQ ID NO: 45), PaWRKY3-like, PaWRKY71-like,
and/or PaMYBS3-like) is also treated with one or more of SA, PaAos
dsRNA, and/or cold temperature (between approximately 7.degree. C.
and approximately 15.degree. C. for approximately 8 hours per day),
thereby causing the altered guayule to produce more rubber than is
produced by a non-altered guayule and have great rubber yield per
acre than non-altered guayule. It is a further object of this
invention to have methods for creating the altered guayule. It is a
further object of this invention to have altered guayule and parts
thereof created by those methods.
[0010] It is an object of this invention that PaAos anti-sense RNA
has a sequence that is the reverse complementary sequence of PaAos
(SEQ ID NOs: 9, 12, or 14 or a sequence at least 95% identical
thereof or any PaAos sequence in any guayule cultivar) or a
fragment thereof (e.g., SEQ ID NO: 11 or a sequence at least 95%
identical thereof, or any 19 contiguous nucleotides of SEQ ID NOs:
9, 12, or 14 or a sequence at least 95% identical thereof or any
PaAos sequence in any guayule cultivar), such that the PaAos
anti-sense RNA silences PaAos via RNAi in the altered guayule. It
is another object of this invention that the dsRNA (either produced
by the altered guayule or administered to the altered guayule) is
at least 19 nucleotides long and contains a sense region selected
from a portion of SEQ ID NO: 11 or a sequence at least 95%
identical thereof, or any 19 contiguous nucleotides of SEQ ID NOs:
9, 12, or 14 or a sequence at least 95% identical thereof or any
PaAos sequence in any guayule cultivar, or SEQ ID NO: 45), such
that the dsRNA silences PaAos in the altered guayule which causes
the altered guayule to produce more rubber than the amount of
rubber produced by a non-altered guayule.
[0011] It is an object of this invention to have a method for
increasing the amount of rubber produced by an altered guayule
compared to the amount of rubber produced by a non-altered guayule.
It is a further object that the method involves making one of the
genetic alteration described supra in a non-altered guayule cell to
produce a genetically altered guayule cell, such that the genetic
alteration causes the genetically altered guayule to produce a
reduced amount of functional PaAos compared the amount of
functional PaAos produced by non-altered guayule cell and/or to
produce an increased amount of one or more transcription factors
(PaWRKY3-like, PaWRKY71-like, and/or PaMYBS3-like) compared to the
amount of the one or more transcription factors produced by a
non-altered guayule; selecting for a genetically altered guayule
cell that produces (i) a reduced amount of functional PaAos
compared to the amount of functional PaAos produced by a
non-altered guayule cell and/or (ii) an increased amount of
PaWRKY3-like, PaWRKY71-like, and/or PaMYBS3-like compared to the
amount of PaWRKY3-like, PaWRKY71-like, and/or PaMYBS3-like produced
by a non-altered guayule; and growing the selected genetically
altered guayule cell into a genetically altered guayule that
produces more rubber than the non-altered guayule. It is a further
object of this invention that the lower amount of functional PaAos
produced and/or increased amount of PaWRKY3-like, PaWRKY71-like,
and/or PaMYBS3-like produced results in an increase in the amount
of rubber produced by the genetically altered guayule compared to
the amount of rubber produced by a non-altered guayule. It is
another object of this invention that the genetically altered
guayule is exposed to a temperature between approximately 7.degree.
C. and approximately 15.degree. C. for approximately 8 hours per
day and/or exposed to salicylic acid and/or exposed to PaAos dsRNA
which results in a synergistic increase in the amount of rubber
produced by the genetically altered guayule. Another object of this
invention is to have a genetically altered guayule made using these
methods and the progeny thereof. It is a further object of this
invention to have germplasm, pollen, flowers, seeds, stems, leaves,
roots, cells, etc., of these genetically altered guayule.
[0012] It is an object of this invention to have a method for
increasing the amount of rubber produced by an altered guayule
compared to the amount of rubber produced by a non-altered guayule.
It is another object of this invention that the alteration induces
RNAi to silence PaAos expression which is generated by transforming
a non-altered guayule cell with an expression vector containing a
heterologous promoter operably linked to a polynucleotide encoding
PaAos anti-sense RNA. The polynucleotide can also encode a sequence
complementary to PaAos anti-sense RNA sequence so that dsRNA is
formed.
[0013] It is a further object of this invention to have a method
for increasing the amount of rubber produced by an altered guayule
compared to the amount of rubber produced by a non-altered guayule
by administering salicylic acid (SA) and/or a PaAos dsRNA solution
to a non-altered guayule to produce an altered guayule. The SA
and/or PaAos dsRNA enter the altered guayule and cause the altered
guayule to produce an increased amount of rubber compared to the
amount of rubber produced by the non-altered guayule. It is another
object of this invention that the PaAos dsRNA has a sequence of at
least 19 contiguous nucleotides of the sequence of PaAos, at least
19 contiguous nucleotides of the reverse complementary sequence of
PaAos, SEQ ID NO: 11 (or a sequence at least 95% identical
thereof), and/or at least 19 contiguous nucleotides of SEQ ID NO:
11; or SEQ ID NO: 45. It is another object of this invention that
an SA solution can have a concentration between approximately 0.1
nM to approximately 100 nM of SA. It is another object of this
invention that the SA and/or PaAos dsRNA solution is administered
to the plant by (i) spraying onto the plant, (ii) applying to soil
surrounding the plant, (iii) applying to a root of plant and/or
(iv) applying to irrigation water which is applied to soil
surrounding the plant. It is another object of this invention that
one can optionally expose the altered guayule to a temperature
between approximately 7.degree. C. and approximately 15.degree. C.
for approximately 8 hours per day which results in a synergistic
increase in the amount of rubber produced by the altered guayule
compared to a non-altered guayule exposed to the same
temperatures.
BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS
[0014] FIG. 1 shows the design of the plasmids used in Example 1
for the overexpression of PaAos (pND6-Aos), silencing of PaAos
(pND6-AosiL), and for the control plasmid (pND6). Each expression
vector features the NPTII gene to confer kanamycin resistance for
selection, and the control plasmid contains the GUS
(.beta.-glucuronidase) reporter gene instead of PaAos or a portion
of PaAos in reverse complementary orientation. Thus, one can use a
histochemical GUS staining assay (the chromogenic substrate X-Gluc
(C.sub.14H.sub.13BrCINO.sub.7)) as a visual indicator of
transformed tissues with the negative control plasmid.
[0015] FIG. 2 shows the primers used in the qRT-PCR, PCR reaction
conditions, and the expected amplicon product size to determine RNA
expression in the genetically altered guayule Amplicon (mRNA
product) PaAos.sub.OE is derived from plants transformed with
pND6-Aos (Aos overexpression). Amplicon (mRNA product)
PaAos.sub.RNAi is derived from plants transformed with pND6-AosiL
(Aos silencing). Amplicon (mRNA product) 18S is from 18S ribosome
RNA. Amplicon (mRNA product) PaAos is for wild-type guayule plants
with intact PaAos gene.
[0016] FIG. 3 provides size and weight measurements of the four
types of guayule plants grown under different conditions in growth
chambers. Plants are initially transferred to soil from tissue
culture media and grown under greenhouse conditions for one month.
Following, plants are moved to controlled-temperature growth
chamber conditions under 27.degree. C. (16 h)/25.degree. C. (8 h)
and at 27.degree. C. (16 h)/10.degree. C. (8 h). The four type of
guayule plants are wild-type (G7-11.1 and G7-11.2), guayule
transformed with the empty expression vector pND6 (pND6-10,
pND6-12, pND6-35), guayule transformed with pND6-AosiL for
silencing PaAos via RNAi (pND6-AosiL.sub.7-2, pND6-AosiL.sub.8-1,
pND6-AosiL.sub.9-16, pND6-AosiL.sub.12-1,), and guayule transformed
with pND6-Aos to overexpress PaAos (pND6-Aos.sub.4-1,
pND6-Aos.sub.4-2, pND6-Aos.sub.5-1, pND6-Aos.sub.7-1,) at 2 months
old. G7-11 is a breeder's nomenclature for what later became the
USDA publicly released guayule Germplasm line AZ-2 (Reg. No. GP-9;
PI 599676). The biomass of the shoot (leaves plus stems) and root
are weighed in 2 months old guayule plants grown in growth chambers
under 27.degree. C. (16 h)/25.degree. C. (8 h) and at 27.degree. C.
(16 h)/10.degree. C. (8 h). The asterisks, (*), (**) and (***),
indicate significant difference in comparison to (non-altered)
G7-11 at p >0.05, 0.005 and 0.0005, respectively.
[0017] FIG. 4 shows SPAD values indicating leaf chlorophyll
concentration ("SPAD units") for wild-type guayule (G7-11), guayule
transformed with the empty expression vector (pND6); guayule
transformed with pND6-Aos (Oe), and guayule transformed with
pND6-AosiL (RNAi) grown at 27.degree. C. (16 h)/25.degree. C. (8 h)
or 27.degree. C. (16 h)/10.degree. C. (8 h).
[0018] FIG. 5 shows the number of branches and stem diameter of 2
months old genetically altered guayule (pND6-AosiL and pND6-Aos
lines), non-altered guayule (G7-11) and empty vector control
guayule (pND6) plants grown in growth chambers at 27.degree. C. (16
h)/25.degree. C. (8 h) or at 27.degree. C. (16 h)/10.degree. C. (8
h). pND6-AosiL genotypes have larger number of stems than the
non-altered and empty vector controls. Additionally, the mature
stembark tissues in pND6-AosiL have significantly thicker diameter
(ranging from 35% to 54%) under both 27.degree. C. (16
h)/25.degree. C. (8 h) and 27.degree. C. (16 h)/10.degree. C. (8
h).
[0019] FIG. 6 shows results from gel permeation chromatography for
elution of cyclohexane extractables from transformed and
non-altered guayule plant lines. The natural rubber molecular
weight is calculated using Astra software for three pND6-AosiL
transformed guayule plants, three pND6-Aos transformed guayule
plants, two pND6 transformed guayule plants, and non-altered
guayule G7-11. The error bars represent 3 different plants with 3
technical replicates.
[0020] FIG. 7 shows the rubber content of SA (0 nM, 10 nM, and 100
nM) treated guayule G7-11 plants.
[0021] FIG. 8 shows PaAOS relative expression and rubber content
analyzed by ASE in one month old soil-grown guayule G7-11 plants
treated with salicylic acid for 2 months and grown in greenhouse
settings.
[0022] FIG. 9A, FIG. 9B, and FIG. 9C show single nucleotide
polymorphisms (SNP) in PaAos coding sequence for guayule cultivars
W6 549 ("W6549"; SEQ ID NO: 12), G7-11 (SEQ ID NO: 9), and PI
478652 ("478652"; SEQ ID NO: 14). The SNPs are contained in
boxes.
[0023] FIG. 10 shows an alignment of PaAos amino acid sequences
obtained from guayule cultivars W6 549 ("W6549"; SEQ ID NO: 13), PI
478652 ("478652"; SEQ ID NO: 15) and G7-11 (SEQ ID NO: 10). The
boxes highlight the different amino acids against the
cultivars.
[0024] FIG. 11A, FIG. 11B, and FIG. 11C provide PaAos promoter's
sequence (SEQ ID NO: 26) and indicates sequences that are putative
binding sites of the indicated transcription factors.
[0025] FIG. 12 provides the names and sequences of various primers,
their annealing temperatures and amplicon size.
[0026] FIGS. 13A-13C show the relative expression of WRKY3-like
(FIG. 13A), WRKY71-like (FIG. 13B), and MYBS3-like (FIG. 13C) in
non-altered guayule, genetically altered guayule with PaAos
silenced, and genetically altered guayule with PaAos
overexpressed.
DETAILED DESCRIPTION OF THE INVENTION
[0027] This invention involves a novel and unexpected method of
increasing natural rubber yield in guayule plants by manipulating
the expression of PaAos and/or reducing the amount of functional
PaAos and/or reducing PaAos' functionality present in guayule. By
altering the expression of PaAos and/or reducing the amount of
functional PaAos and/or reducing PaAos' functionality, one also
reduces the amount of functional PaAos in rubber particles. The
rubber yield per acre is increased because the genetically altered
guayule is also larger than non-altered guayule and has more tissue
in which to store rubber. Genetically altered guayule that express
the reverse complement of PaAos have reduced amounts of PaAos in
the rubber particles via RNAi. Because these genetically altered
guayule plants produce less PaAos, they also have altered amounts
of various hormones that are produced in the biosynthetic pathway
for which PaAos is one enzyme. In particular, the amount of
jasmonic acid, abscisic acid, gibberellin A.sub.20, gibberellin
A.sub.1, and gibberellin A.sub.3 are decreased in the RNAi
genetically altered guayule while the amount of salicylic acid (SA)
is increased, compared to non-genetically altered guayule. Using
RNAi technology to reduce the amount of PaAos in the plant, these
genetically altered guayule unexpectedly and surprisingly have
increased amount of rubber compared to non-altered guayule plants
AND more biomass which increases the rubber yield. One optionally
exposes the genetically altered guayule to cold temperature
(between approximately 7.degree. C. and approximately 15.degree. C.
or between approximately 10.degree. C. and approximately 15.degree.
C.; approximately 8 hours per day) which, surprisingly and
unexpectedly, acts synergistically with the reduced PaAos
transcription (and/or reduced amount of functional PaAos) to
increase the amount of rubber production even greater than to the
amount produced by non-altered guayule. Methods of enhancing rubber
yield via suppression of PaAos expression via RNAi and similar
technologies, and markers for the identification of such guayule
with altered PaAos are provided. For the purposes of this
invention, the terms "function", "functional", and "functionality"
include any activity that the protein or other compound possesses.
A protein/compound may have enzymatic activity, binding activity,
transporting activity, structural activity, etc.
[0028] As mentioned above, one embodiment of this invention
involves using RNAi to reduce production of PaAos which causes an
increase in rubber production and biomass of the genetically
altered guayule. In another embodiment, the invention involves
altering the genomic PaAos sequence such that no functional PaAos
is produced (a "null" mutation), or that the encoded protein has
reduced functionality compared to the activity of non-modified
PaAos. When no functional PaAos is produced or when PaAos with
reduced functionality is produced, then it is understood that the
altered guayule produces "a reduced amount of functional PaAos".
Such altered guayule producing a reduced amount of functional PaAos
is another embodiment of this invention. In yet another embodiment,
the invention involves increasing the amount of SA in guayule which
results in increased amount of rubber being produced compared to
the amount of rubber produced in guayule which does not have
increased amount of SA. One embodiment involves administering an
effective amount of SA to a non-altered guayule, which causes the
treated guayule to reduce PaAos expression and/or reduce the amount
of functional PaAos, and thus increases the amount of rubber
produced by the treated guayule compared to the amount of rubber
produced by a non-altered guayule.
[0029] Another embodiment of this invention involves an altered
guayule producing more rubber than the amount of rubber produced by
a non-altered guayule. In one embodiment, the altered guayule
overexpresses one or more transcription factors (PaWRKY3-like,
PaWRKY71-like, and/or PaMYBS3-like) using an expression vector that
contains a heterologous promoter operably linked to the coding
sequences of one or more of these transcription factors (SEQ ID
NOs: 39 and 40, 41 and 42, and/or 43 and 44, or a sequence at least
95% identical thereof for PaWRKY3-like, PaWRKY71-like, and/or
PaMYBS3-like, respectively). In another embodiment, the altered
guayule contains an expression vector that produces PaAos dsRNA or
anti-sense RNA so that less amount of PaAos is produced by the
altered guayule. In another embodiment, the altered guayule
contains a mutated PaAos and the altered guayule produces PaAos
with reduced or no functionality, compared to the functionality of
PaAos in a non-altered guayule. In yet another embodiment, any of
these genetic alterations are present in the guayule. In yet
another embodiment, one optionally subjects any of the altered
guayule to cold temperatures and/or administers SA to the altered
guayule and/or administers dsRNA for PaAos to the altered guayule
to increase rubber production in the altered guayule compared to
the amount of rubber produced by a non-altered guayule.
[0030] Because this invention involves production of genetically
altered plants and involves recombinant DNA techniques, the
following definitions are provided to assist in describing this
invention. The terms "isolated", "purified", or "biologically pure"
as used herein, refer to material that is substantially or
essentially free from components that normally accompany the
material in its native state or when the material is produced. In
an exemplary embodiment, purity and homogeneity are determined
using analytical chemistry techniques such as polyacrylamide gel
electrophoresis or high performance liquid chromatography. A
nucleic acid or particular bacteria that are the predominant
species present in a preparation is substantially purified. In an
exemplary embodiment, the term "purified" denotes that a nucleic
acid or protein that gives rise to essentially one band in an
electrophoretic gel. Typically, isolated nucleic acids or proteins
have a level of purity expressed as a range. The lower end of the
range of purity for the component is about 60%, about 70% or about
80% and the upper end of the range of purity is about 70%, about
80%, about 90% or more than about 90%.
[0031] The term "gene" refers to a DNA sequence involved in
producing a RNA or polypeptide or precursor thereof. The
polypeptide or RNA is encoded by a full-length coding sequence
(cds) or by intron-interrupted portions of the coding sequence,
such as exon sequences. In one embodiment of this invention, the
gene involved is Parthenium argentatum allene oxide synthase (PaAos
or Aos). PaAos cDNA and amino acid sequence is found in GenBank
accession number X78166.2 which is cultivar G7-11
(wild-type/non-altered) (USDA publicly released guayule Germplasm
line AZ-2 (Reg. No. GP-9; PI 599676)). The cDNA sequence is in SEQ
ID NO: 9; the protein sequence is in SEQ ID NO: 10. SEQ ID NO: 12
is the cDNA sequence for PaAos and SEQ ID NO: 13 is the amino acid
sequence for PaAos in guayule W6549 cultivar. SEQ ID NO: 14 is the
cDNA sequence for PaAos and SEQ ID NO: 15 is the amino acid
sequence for PaAos in guayule 478652 cultivar. In one embodiment,
the reverse complementary sequence of PaAos (negative strand) (or a
sequence that is at least 95% identical) is operably linked to a
heterologous promoter to produce RNA have a complementary sequence
to the mRNA made from PaAos (SEQ ID NOs: 9, 12, or 14 or the
sequence present any other cultivar) (positive strand). In one
embodiment, one uses the sequence in SEQ ID NO: 11 (or a sequence
that is at least 95% identical) as a portion of the reverse
complement polynucleotide of PaAos, or use SEQ ID NO: 45. In
another embodiment, DNA encoding one or more of the transcription
factors PaWRKY3-like (SEQ ID NOs: 39 and 40 or a sequence at least
95% identical thereof), PaWRKY71-like (SEQ ID NOs: 41 and 42 or a
sequence at least 95% identical thereof), and PaMYBS3-like (SEQ ID
NOs: 43 and 43 or a sequence at least 95% identical thereof) are
overexpressed in an altered guayule.
[0032] The term "nucleic acid" as used herein, refers to a polymer
of ribonucleotides or deoxyribonucleotides. Typically, "nucleic
acid" polymers occur in either single- or double-stranded form, but
are also known to form structures comprising three or more strands.
The term "nucleic acid" includes naturally occurring nucleic acid
polymers as well as nucleic acids comprising known nucleotide
analogs or modified backbone residues or linkages, which are
synthetic, naturally occurring, and non-naturally occurring, which
have similar binding properties as the reference nucleic acid, and
which are metabolized in a manner similar to the reference
nucleotides. Exemplary analogs include, without limitation,
phosphorothioates, phosphoramidates, methyl phosphonates,
chiral-methyl phosphonates, 2-O-methyl ribonucleotides,
peptide-nucleic acids (PNAs). "DNA", "RNA", "polynucleotides",
"polynucleotide sequence", "oligonucleotide", "nucleotide",
"nucleic acid", "nucleic acid molecule", "nucleic acid sequence",
"nucleic acid fragment", and "isolated nucleic acid fragment" are
used interchangeably herein.
[0033] For nucleic acids, sizes are given in either kilobases (kb)
or base pairs (bp), or nucleotides (nt). Estimates are typically
derived from agarose or acrylamide gel electrophoresis, from
sequenced nucleic acids, or from published DNA sequences. For
proteins, sizes are given in kiloDaltons (kDa) or amino acid
residue numbers. Proteins sizes are estimated from gel
electrophoresis, from sequenced proteins, from derived amino acid
sequences, or from published protein sequences.
[0034] Unless otherwise indicated, a particular nucleic acid
sequence for each amino acid substitution (alteration) also
implicitly encompasses conservatively modified variants thereof
(e.g., degenerate codon substitutions), the complementary (or
complement) sequence, and the reverse complement sequence, as well
as the sequence explicitly indicated. Specifically, degenerate
codon substitutions may be achieved by generating sequences in
which the third position of one or more selected (or all) codons is
substituted with mixed-base and/or deoxyinosine residues (see e.g.,
Batzer et al., Nucleic Acid Res. 19:5081 (1991); Ohtsuka et al., J.
Biol. Chem. 260:2605-2608 (1985); and Rossolini et al., Mol. Cell.
Probes 8:91-98(1994)). Because of the degeneracy of nucleic acid
codons, one can use various different polynucleotides to encode
identical polypeptides. Table 1, infra, contains information about
which nucleic acid codons encode which amino acids and is useful
for determining the possible nucleotide substitutions that are
included in this invention.
TABLE-US-00001 TABLE 1 Amino acid Nucleic acid codons Amino acid
Nucleic acid codons Ala/A GCT, GCC, GCA, GCG Leu/L TTA, TTG, CTT,
CTC, CTA, CTG Arg/R CGT, CGC, CGA, CGG, AGA, AGG Lys/K AAA, AAG
Asn/N AAT, AAC Met/M ATG Asp/D GAT, GAC Phe/F TTT, TTC Cys/C TGT,
TGC Pro/P CCT, CCC, CCA, CCG Gln/Q CAA, CAG Ser/S TCT, TCC, TCA,
TCG, AGT, AGC Glu/E GAA, GAG Thr/T ACT, ACC, ACA, ACG Gly/G GGT,
GGC, GGA, GGG Trp/W TGG His/H CAT, CAC Tyr/Y TAT, TAC Ile/I ATT,
ATC, ATA Val/V GTT, GTC, GTA, GTG Stop TAA, TGA, TAG
[0035] In addition to the degenerate nature of the nucleotide
codons which encode amino acids, alterations in a polynucleotide
that result in the production of a chemically equivalent amino acid
at a given site, but do not affect the functional properties of the
encoded polypeptide, are well known in the art. "Conservative amino
acid substitutions" are those substitutions that are predicted to
interfere least with the properties of the reference polypeptide.
In other words, conservative amino acid substitutions substantially
conserve the structure and the function of the reference protein.
Thus, a codon for the amino acid alanine, a hydrophobic amino acid,
may be substituted by a codon encoding another less hydrophobic
residue, such as glycine, or a more hydrophobic residue, such as
valine, leucine, or isoleucine. Similarly, changes which result in
substitution of one negatively charged residue for another, such as
aspartic acid for glutamic acid, or one positively charged residue
for another, such as lysine for arginine or histidine, is also
expected to produce a functionally equivalent protein or
polypeptide. Table 2 provides a list of exemplary conservative
amino acid substitutions. Conservative amino acid substitutions
generally maintain (a) the structure of the polypeptide backbone in
the area of the substitution, for example, as a beta sheet or alpha
helical conformation, (b) the charge or hydrophobicity of the
molecule at the site of the substitution, and/or (c) the bulk of
the side chain. In another embodiment, groups of amino acids that
are conservative substitutions for each other are (i) alanine (Ala
or A), serine (Ser or S), and threonine (Thr or T); (ii) aspartic
acid (Asp or D) and glutamic acid (Glu or E); (iii) asparagine (Asn
or N) and glutamine (Gln or Q); (iv) arginine (Arg or R) and lysine
(Lys or K); (v) isoleucine (Ile or I), leucine (Leu or L),
methionine (Met or M), and valine (Val or V); and (vi)
phenylalanine (Phe or F), tyrosine (Tyr or Y), and tryptophan (Trp
or W). See, Creighton, Proteins, W.H. Freeman and Co. (1984),
contents of which are expressly incorporated herein. In yet another
embodiment, amino acid(s) that are conservative substitutes for one
amino acid are grouped by the following characteristics: aliphatic
amino acids (alanine, glycine, isoleucine, leucine, and valine);
hydroxyl or sulfur containing amino acids (cysteine, serine,
methionine, and threonine); cyclic (proline); aromatic
(phenylalanine, tryptophan, and tyrosine); basic (arginine,
histidine, and lysine); acidic (aspartate and glutamate); and
uncharged (asparagine and glutamine).
TABLE-US-00002 TABLE 2 Amino Acid Conservative Substitute Ala Gly,
Ser Arg His, Lys Asn Asp, Gln, His Asp Asn, Glu Cys Ala, Ser Gln
Asn, Glu, His Glu Asp, Gln, His Gly Ala His Asn, Arg, Gln, Glu Ile
Leu, Val Leu Ile, Val Lys Arg, Gln, Glu Met Ile, Leu Phe His, Leu,
Met, Trp, Tyr Ser Cys, Thr Thr Ser, Val Trp Phe, Tyr Tyr His, Phe,
Trp Val Ile, Leu, Thr
[0036] The term "primer" refers to an oligonucleotide which may act
as a point of initiation of DNA extension. A primer may occur
naturally, as in a purified restriction digest, or may be produced
synthetically.
[0037] A primer is selected to be "substantially complementary" to
a strand of specific sequence of the template. A primer must be
sufficiently complementary to hybridize with a template strand for
primer elongation to occur. A primer sequence need not reflect the
exact sequence of the template. For example, a non-complementary
nucleotide fragment may be attached to the 5' end of the primer,
with the remainder of the primer sequence being substantially
complementary to the strand. Non-complementary bases or longer
sequences can be interspersed into the primer, provided that the
primer sequence is sufficiently complementary with the sequence of
the template to hybridize and thereby form a template primer
complex for synthesis of the extension product of the primer.
[0038] "dsRNA" refers to double-stranded RNA that contains a sense
region and an antisense region of a selected target gene (or
sequences with high sequence identity thereto so that gene
silencing occurs), as well as any smaller double-stranded RNAs
formed therefrom by RNAse or Dicer activity. Such dsRNA may include
portions of single-stranded RNA, but contains at least 18 base
pairs of dsRNA. A dsRNA after been processed by Dicer generates
siRNAs (18-25 bp in length) that are double-strand, and could
contain ends with 2 nucleotide overhangs, which will be
single-stranded. It is predicted that usually siRNA around 19 nt in
length (or, alternatively, between 17 and 27 nt in length), will be
incorporated into RISC. In one embodiment, the sense region and the
antisense region of a dsRNA are on the same strand of RNA and are
separated by a linker. In this embodiment, when the sense region
and the antisense region anneal together, the dsRNA contains a loop
which is the linker. One promoter operably linked to the DNA or RNA
encoding both the sense region and the antisense region is used to
produce the one RNA molecule containing both the sense region and
the anti-sense region. In another embodiment, the sense region and
the antisense region are present on two distinct strands of RNA (a
sense strand and the anti-sense strand which is complementary to
the sense strand) which anneal together to form the dsRNA. In this
embodiment, a promoter is operably linked to each strand of DNA or
RNA; where one DNA or RNA strand encodes the RNA containing the
sense region and the other strand of DNA or RNA encodes the RNA
containing the anti-sense region. In this embodiment, the promoter
on each strand may be the same as or different from the promoter on
the other strand. After the RNAs are transcribed, two RNA strands
anneal together because the sense region and the anti-sense region
are complementary to each other, thus forming the dsRNA. In yet
another embodiment, one strand of DNA or RNA can encode both the
sense region and the anti-sense region of the dsRNA. However, the
DNA or RNA coding each region are separated from each other so that
two promoters are necessary to transcribe each region. That is, the
DNA or RNA encoding the anti-sense region and the DNA or RNA
encoding the sense region are operably linked to their own
promoter. Again, the two promoters may be the same promoter or
different promoters. In one embodiment, the promoter can be a T7
RNA polymerase promoter. Other promoters are well-known in the art
and can be used (see discussion infra). While many embodiments of
this invention use DNA to encode the sense region and/or anti-sense
region, as described infra, it is possible to use a recombinant RNA
virus to produce the dsRNA described herein. In such cases, a virus
has had its genome altered so that the infected cell produces one
of the sequences of PaAos described herein or the reverse
complement thereof or both.
[0039] Active dsRNA molecules have worked when they were as long as
1,000 bp, and should work when even longer. For the purposes of the
inventions described herein, any siRNA having at least 19 nt length
derived fromPaAos, or the reverse complement sequence thereof and
that are specific to PaAos. In one embodiment, the dsRNA may be any
16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,
33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 55, 60, or longer
contiguous nucleotides, up and including the full-length of PaAos
cDNA (SEQ ID NOs: 9, 12, and/or 14 or a sequence at least 95%
identity thereof or the sequence of any other PaAos). In another
embodiment, the reverse complement sequence of PaAos is SEQ ID NO:
11 or a sequence at least 95% identity thereof, or SEQ ID NO: 45.
In alternative embodiments, the dsRNA ranges in length between 16
bp and 30 bp, between 16 bp and 25 bp, between 18 and 30 bp, and
between 19 bp and 28 bp. In yet another embodiment, RNA forms that
are created by RNAse III family (Dicer or Dicer-like ribonuclease)
or Dicer activity that are longer dsRNA are within the scope of
this invention.
[0040] One uses computer programs to predict dsRNA sequences that
will be effective in reducing production of the desired
gene/protein (in this embodiment PaAos and PaAos). Information
about such computer programs are be found on the following two
websites: genelink com/siRNA/RNAiwhatis.asp; and
rnaiweb.com/RNAi/RNAi_Web_Resources/RNAi_Tools_Software/Online_siRNA_Desi-
gn_Tools/inde x.html. Using such computer programs, one can obtain
sequences that differ from SEQ ID NO: 11 which can be used to
generate dsRNA via binding to PaAos mRNA. Alternatively, one can
determine an appropriate sequence to test using the methodologies
described in Preuss, S. and Pikaard, C. S. (2003) Targeted gene
silencing in plants using RNA interference, in RNA interference
(RNAi)-Nuts and Bolts of siRNA Technology (Engelke, D., Ed.), pp
23-36, DNA Press, LLC.
[0041] siRNA may be synthetically made, expressed and secreted
directly from a transformed cell, or microbe, or generated from a
longer dsRNA by enzymatic activity. These siRNAs may be blunt-ended
or have 1 bp to 4 bp overlapping ends of various nucleotide
combinations. Also modified microRNAs comprising a portion of PaAos
and its reverse complementary sequence are included herein as
dsRNAs. In one embodiment of the invention, the dsRNA is expressed
in a plant to be protected, or expressed in microorganisms which
can be endemic organisms of the plant (microbes, virus,
phytoplasma, viroids, fungal, protists) or free-living microbes
(yeasts, bacteria, protists, fungi) any of which are delivered,
alive, dead or processed, via root treatments, or foliar sprayed on
plants, or injected into plants, which are to be protected.
Alternatively, the microorganism can be a transgenic organism
endemic to the plant and deliver dsRNA to the plant. See, e.g.,
Subhas, et al. (2014) J. Biotech. 176:42-49 for an example of virus
induced gene silencing using Citrus tristeza virus. See, also,
Tenllado, et al. (2003) BMC Biotechnol 3:3 for an example of a
crude extract of a bacterial cell culture containing dsRNA that
protects plants against viral infections.
[0042] In one embodiment, a dsRNA solution is administered to the
guayule plant. A dsRNA solution contains one or more of the dsRNAs
discussed herein and an agriculturally acceptable carrier. An
agriculturally acceptable carrier can be water, one or more
liposomes, one or more lipids, one or more surfactants, one or more
proteins, one or more peptides, one or more nanotubes, chitin,
and/or one or more inactivated microorganisms that encapsulate the
dsRNA. See WO 2003/004644 for examples of other agriculturally
acceptable carriers, contents of which are expressly incorporated
herein. The dsRNA solution may also contain one or more sugars,
compounds that assist in preventing dsRNA degradation, translaminar
chemicals, chemical brighteners, clays, minerals, and/or
fertilizers. One can spray the dsRNA solution on plants (leaves,
branches, trunk, exposed roots, etc.). One can apply the dsRNA
solution to the soil around the plant so that the plant's roots
absorb the dsRNA solution and transport it to other parts of the
plants. Alternatively, one or more roots can be placed in a
container which contains the dsRNA solution so that those roots
absorb the dsRNA solution. The dsRNA solution can also be injected
into the plant. As such, the dsRNA solution may be in a spray dsRNA
solution, a drenching dsRNA solution, or an injectable dsRNA
solution. The dsRNA may also be mixed into irrigation water which
is then administered to the plants. The plant's roots will absorb
the dsRNA in the irrigation water, resulting in RNAi. Other types
of solutions are known in the art.
[0043] In another embodiment, one administers dsRNA and salicylic
acid to a non-altered guayule or to a guayule with a genetic
alteration (such as overexpressing one or more of the transcription
factors PaWRKY3-like, PaWRKY71-like, and/or PaMYBS3-like) to
increase rubber production which would yield more rubber than the
amount of rubber produced by a non-altered guayule, under the same
conditions. The dsRNA and salicylic acid are administered
concurrently or sequentially. They can be administered via
irrigation water, by administering the dsRNA and/or salicylic acid
to the soil around the plant, by placing a root of the plant into a
container holding the dsRNA and/or salicylic acid, spraying the
dsRNA and/or salicylic acid onto the plant, or a combination
thereof. For example, the dsRNA could be sprayed onto the plant
while the salicylic acid is added to the irrigation water and
applied to the soil around the plant. Root drenching with dsRNA
and/or salicylic acid is yet another embodiment. In yet another
embodiment, one administers the dsRNA and salicylic acid to the
plant prior to or when the temperature is cold (between
approximately 7.degree. C. and approximately 15.degree. C. or
between approximately 10.degree. C. and approximately 15.degree.
C.; for approximately 8 hours per day). The treated guayule will
produce more rubber than the amount of rubber produced by the
untreated guayule.
[0044] Oligonucleotides and polynucleotides that are not
commercially available can be chemically synthesized e.g.,
according to the solid phase phosphoramidite triester method first
described by Beaucage and Caruthers, Tetrahedron Letts.
22:1859-1862 (1981), or using an automated synthesizer, as
described in Van Devanter et al., Nucleic Acids Res. 12:6159-6168
(1984). Other methods for synthesizing oligonucleotides and
polynucleotides are known in the art. Purification of
oligonucleotides is by either native acrylamide gel electrophoresis
or by anion-exchange HPLC as described in Pearson & Reanier, J.
Chrom. 255:137-149 (1983).
[0045] The terms "identical" or percent "identity", in the context
of two or more polynucleotides or polypeptide sequences, refer to
two or more sequences or sub-sequences that are the same or have a
specified percentage of nucleotides or amino acids (respectively)
that are the same (e.g., 80%, 85% identity, 90% identity, 99%, or
100% identity), when compared and aligned for maximum
correspondence over a designated region as measured using a
sequence comparison algorithm or by manual alignment and visual
inspection.
[0046] The phrase "high percent identical" or "high percent
identity", in the context of two polynucleotides or polypeptides,
refers to two or more sequences or sub-sequences that have at least
about 80%, identity, at least about 81%, 82%, 83%, 84%, 85%, 86%,
87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or
100% nucleotide or amino acid identity, when compared and aligned
for maximum correspondence, as measured using a sequence comparison
algorithm or by visual inspection. In an exemplary embodiment, a
high percent identity exists over a region of the sequences that is
at least about 16 nucleotides or amino acids in length. In another
exemplary embodiment, a high percent identity exists over a region
of the sequences that is at least about 50 nucleotides or amino
acids in length. In still another exemplary embodiment, a high
percent identity exists over a region of the sequences that is at
least about 100 nucleotides or amino acids or more in length. In
one exemplary embodiment, the sequences are high percent identical
over the entire length of the polynucleotide or polypeptide
sequences.
[0047] For sequence comparison, typically one sequence acts as a
reference sequence, to which test sequences are compared. When
using a sequence comparison algorithm, test and reference sequences
are entered into a computer, subsequence coordinates are
designated, if necessary, and sequence algorithm program parameters
are designated. Default program parameters may be used, or
alternative parameters designated. The sequence comparison
algorithm then calculates the percent sequence identities for the
test sequences relative to the reference sequence, based on the
program parameters. Methods of alignment of sequences for
comparison are well-known in the art. Optimal alignment of
sequences for comparison is conducted, e.g., by the local homology
algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981),
by the homology alignment algorithm of Needleman & Wunsch, J.
Mol. Biol. 48:443 (1970), by the search for similarity method of
Pearson & Lipman, Proc. Natl. Acad. Sci. USA 85:2444 (1988), by
computerized implementations of various algorithms (GAP, BESTFIT,
FASTA, and TFASTA in the Wisconsin Genetics Software Package,
Genetics Computer Group, 575 Science Dr., Madison, Wis.), and/or by
manual alignment and visual inspection (see, e.g., Ausubel et al.
(eds.), Current Protocols in Molecular Biology, 1995
supplement).
[0048] The "complement" of a particular polynucleotide sequence is
that nucleotide sequence which would be capable of forming a
double-stranded DNA or RNA molecule with the represented nucleotide
sequence, and which is derived from the represented nucleotide
sequence by replacing the nucleotides by their complementary
nucleotide according to Chargaff's rules (A<>T; G<>C)
and reading in the 5' to 3' direction, i.e., in opposite direction
of the represented nucleotide sequence (reverse complement).
[0049] In one embodiment of the invention, sense and antisense RNAs
and dsRNA can be separately expressed in-vitro or in-vivo. In-vivo
production of sense and antisense RNAs may use different chimeric
polynucleotide constructs using the same or different promoters or
using an expression vector containing two convergent promoters in
opposite orientation. The sense and antisense RNAs which are formed
(e.g., in the same host cells or synthesized) then combine to form
dsRNA. To be clear, whenever reference is made herein to a dsRNA
chimeric or fusion polynucleotide or a dsRNA molecule, that such
dsRNA formed (e.g., in plant cells) from sense and antisense RNA
produced separately is also included. Also, synthetically made
dsRNA and self-annealing RNA strands are included herein when the
sense and antisense strands are present together.
[0050] As used herein, the term "promoter" refers to a
polynucleotide that, in its native state, is located upstream or 5'
to a translational start codon of an open reading frame (or
protein-coding region) and that is involved in recognition and
binding of RNA polymerase and other proteins (trans-acting
transcription factors) to initiate transcription. A "plant
promoter" is a native or non-native promoter that is functional in
plant cells, even if the promoter is present in a microorganism
that infects plants or a microorganism that does not infect plants.
The promoters that are predominately functional in a specific
tissue or set of tissues are considered "tissue-specific
promoters". A plant promoter can be used as a 5' regulatory element
for modulating expression of a particularly desired polynucleotide
(heterologous polynucleotide) operably linked thereto. When
operably linked to a transcribable polynucleotide, a promoter
typically causes the transcribable polynucleotide to be transcribed
in a manner that is similar to that of which the promoter is
normally associated.
[0051] Plant promoters include promoters produced through the
manipulation of known promoters to produce artificial, chimeric, or
hybrid promoters. Such promoters can also combine cis-elements from
one or more promoters, for example, by adding a heterologous
regulatory element to an active promoter with its own partial or
complete regulatory elements. The term "cis-element" refers to a
cis-acting transcriptional regulatory element that confers an
aspect of the overall control of gene expression. A cis-element may
function to bind transcription factors, trans-acting protein
factors that regulate transcription. Some cis-elements bind more
than one transcription factor, and transcription factors may
interact with different affinities with more than one
cis-element.
[0052] The term "vector" refers to DNA, RNA, a protein, or
polypeptide that are to be introduced into a host cell or organism.
The polynucleotides, protein, and polypeptide which are to be
introduced into a host may be therapeutic or prophylactic in
nature; may encode or be an antigen; may be regulatory in nature;
etc. There are various types of vectors including viruses, viroids,
plasmids, bacteriophages, cosmids, and bacteria.
[0053] An expression vector is nucleic acid capable of replicating
in a selected host cell or organism. An expression vector can
replicate as an autonomous structure, or alternatively integrate,
in whole or in part, into the host cell chromosomes or the nucleic
acids of an organelle, or it is used as a shuttle for delivering
foreign DNA to cells, and thus replicate along with the host cell
genome. Thus, an expression vector are polynucleotides capable of
replicating in a selected host cell, organelle, or organism, e.g.,
a plasmid, virus, artificial chromosome, nucleic acid fragment, and
for which certain genes on the expression vector (including genes
of interest) are transcribed and translated into a polypeptide or
protein within the cell, organelle or organism; or any suitable
construct known in the art, which comprises an "expression
cassette". In contrast, as described in the examples herein, a
"cassette" is a polynucleotide containing a section of an
expression vector. The use of the cassettes assists in the assembly
of the expression vectors. An expression vector is a replicon, such
as plasmid, phage, virus, chimeric virus, or cosmid, and which
contains the desired polynucleotide sequence operably linked to the
expression control sequence(s).
[0054] A heterologous polynucleotide sequence is operably linked to
one or more transcription regulatory elements (e.g., promoter,
terminator and, optionally, enhancer) such that the transcription
regulatory elements control and regulate the transcription and/or
translation of that heterologous polynucleotide sequence. A
cassette has the heterologous polynucleotide operably linked to one
or more transcription regulatory elements. As used herein, the term
"operably linked" refers to a first polynucleotide, such as a
promoter, connected with a second transcribable polynucleotide,
such as a gene of interest, where the polynucleotides are arranged
such that the first polynucleotide affects the transcription of the
second polynucleotide. In some embodiments, the two polynucleotide
molecules are part of a single contiguous polynucleotide. In other
embodiments, the two polynucleotides are adjacent. For example, a
promoter is operably linked to a gene of interest if the promoter
regulates or mediates transcription of the gene of interest in a
cell. Similarly, a terminator is operably linked to the
polynucleotide of interest if the terminator regulates or mediates
transcription of the polynucleotide of interest, and, in
particular, the termination of transcription. Constructs of the
present invention would typically contain a promoter operably
linked to a transcribable polynucleotide operably linked to a
terminator.
[0055] The term "recombinant" when used with reference, e.g., to a
cell, or nucleic acid, protein, or vector, indicates that the cell,
organism, nucleic acid, protein or vector, has been altered by the
introduction of a heterologous nucleic acid or protein or the
alteration of a native nucleic acid or protein, or that the cell is
derived from a cell so altered. Thus, for example, recombinant
cells may express genes/polynucleotides that are not found within
the native (non-recombinant or non-altered or wild-type) form of
the cell or express native genes in an otherwise abnormal
amount--over-expressed, under-expressed or not expressed at
all--compared to the non-altered cell or organism. In particular,
one alters the genomic DNA of a non-altered plant by molecular
biology techniques that are well-known to one of ordinary skill in
the art and generate a recombinant plant.
[0056] The terms "transgenic", "transformed", "transformation", and
"transfection" are similar in meaning to "recombinant".
"Transformation", "transgenic", and "transfection" refer to the
transfer of a polynucleotide into a host organism or into a cell.
Such a transfer of polynucleotides may result in genetically stable
inheritance of the polynucleotides or in the polynucleotides
remaining extra-chromosomally (not integrated into the chromosome
of the cell). Genetically stable inheritance may potentially
require the transgenic organism or cell to be subjected for a
period of time to one or more conditions which require the
transcription of some or all of the transferred polynucleotide in
order for the transgenic organism or cell to live and/or grow.
Polynucleotides that are transformed into a cell but are not
integrated into the host's chromosome remain as an expression
vector within the cell. One may need to grow the cell under certain
growth or environmental conditions in order for the expression
vector to remain in the cell or the cell's progeny. Further, for
expression to occur the organism or cell may need to be kept under
certain conditions. Genetically altered organisms or cells
containing the recombinant polynucleotide are referred to as
"transgenic" or "transformed" organisms or cells or simply as
"transformants", as well as recombinant organisms or cells.
[0057] A genetically altered organism is any organism with any
changes to its genetic material involving the invention described
herein, whether in the nucleus or cytoplasm (organelle). As such, a
genetically altered organism may be a recombinant or transformed
organism. A genetically altered organism may also be an organism
that was subjected to one or more mutagens or the progeny of an
organism that was subjected to one or more mutagens and has
mutations in its DNA caused by the one or more mutagens, as
compared to the wild-type organism (i.e., organism not subjected to
the mutagens) or the non-altered organism (i.e., one that contains
alterations that are not the subject matter of this invention).
Also, an organism that has been bred to incorporate a mutation into
its genetic material is a genetically altered organism.
[0058] The term "altered" means that a change occurred compared to
the "non-altered" item. However, a "non-altered" item could contain
changes that are induced by man, but those changes are not the
subject matter of the inventions described herein. For example, a
non-altered guayule contains none of the described genetic changes
nor has been treated with any of the described external substance,
but may contain pre-existing changes which are not part of this
invention. An altered guayule (which also is a genetically altered
guayule) may contain a non-native expression vector that produces
dsRNA or anti-sense RNA involving PaAOS or another gene and/or
produces one or more transcription factors described herein or
another gene. An altered guayule is also one which has been treated
with a substance, such as dsRNA or salicylic acid (SA). An altered
guayule may also have both types of changes.
[0059] Transformation and generation of genetically altered
monocotyledonous and dicotyledonous plant cells is well known in
the art. See, e.g., Weising, et al., Ann. Rev. Genet. 22:421-477
(1988); U.S. Pat. No. 5,679,558; Agrobacterium Protocols, ed:
Gartland, Humana Press Inc. (1995); and Wang, et al. Acta Hort.
461:401-408 (1998). A method to generate genetically altered
guayule is described in U.S. Pat. No. 9,018,449 (Dong &
Cornish) and in Dong, et al., Plant Cell Reports 25:26-34 (2006). A
method to generate transplastomic guayule is provided in U.S.
Patent Application Publication 2014/0325699, the contents of which
are expressly incorporated herein. The choice of method varies with
the type of plant to be transformed, the particular application,
and/or the desired result. The appropriate transformation technique
is readily chosen by the skilled practitioner.
[0060] A polynucleotide encoding PaAos (SEQ ID NOs: 9, 12 and/or
14), the reverse complement of PaAos, or a portion thereof (e.g.,
SEQ ID NO: 11), operably linked to one or two appropriate
promoters, can be stably inserted in a conventional manner into the
genome (cytoplasmic genome or nucleic genome) of a single plant
cell, and the altered plant cell can be used in a conventional
manner to produce a genetically altered plant that produces the
dsRNA of this invention. In this regard, a disarmed Ti-plasmid,
containing the polynucleotide of this invention, in Agrobacterium
tumefaciens can be used to genetically alter the plant cell, and
thereafter, a genetically altered plant can be regenerated from the
genetically altered plant cell using the procedures described in
the art, for example, in EP 0 116 718, EP 0 270 822, WO 84/02913
and EP 0 242 246. Plant regeneration from cultured protoplasts is
described in Evans et al., Protoplasts Isolation and Culture, in
Handbook of Plant Cell Culture, pp. 124-176, MacMillan Publishing
Company, New York, 1983; and Binding, Regeneration of Plants, in
Plant Protoplasts, pp. 21-73, CRC Press, Boca Raton, 1985.
Regeneration can also be obtained from plant callus, explants,
organs, or parts thereof. Such regeneration techniques are
described generally in Klee, et al., Ann. Rev. of Plant Phys.
38:467-486 (1987). Similarly, a polynucleotide encoding
PaWRKY3-like, PaWRKY71-like, and/or PaMYBS3-like (the genomic
sequence or coding sequence) may be incorporated into altered
guayule.
[0061] Preferred Ti-plasmid vectors each contain the
polynucleotides described herein between the border sequences, or
at least located to the left of the right border sequence, of the
T-DNA of the Ti-plasmid. Of course, other types of vectors may be
used to transform the plant cell, using procedures such as direct
gene transfer (as described, for example in EP 0 233 247), pollen
mediated transformation (as described, for example in EP 0 270 356,
WO 85/01856, and U.S. Pat. No. 4,684,611), plant RNA virus-mediated
transformation (as described, for example in EP 0 067 553 and U.S.
Pat. No. 4,407,956), liposome-mediated transformation (as
described, for example in U.S. Pat. No. 4,536,475), and other
methods such as the methods for transforming certain lines of corn
(e.g., U.S. Pat. No. 6,140,553; Fromm, et al., Bio/Technology
8:833-839 (1990); Gordon-Kamm, et al., The Plant Cell 2:603-618
(1990) and rice (Shimamoto, et al., Nature 338:274-276 (1989);
Datta et al., Bio/Technology 8:736-740 (1990)) and the method for
transforming monocots generally (WO 92/09696). For cotton
transformation, the method described in WO 2000/71733 can be used.
For soybean transformation, reference is made to methods known in
the art, e.g., Hinchee, et al. (Bio/Technology 6:915 (1988)) and
Christou, et al. (Trends Biotechnology 8:145 (1990)) or the method
of WO 00/42207.
[0062] The resulting genetically altered plant can be used in a
conventional plant breeding scheme to produce more genetically
altered plants with the same characteristics or to introduce the
polynucleotide into other varieties of the same or related plant
species. Seeds, which are obtained from the genetically altered
plants, contain the expression vector as a stable genomic insert.
Altered plants include plants having or derived from root stocks of
altered plants containing the expression vector. Hence, any
non-altered grafted plant parts inserted on a genetically altered
plant or plant part are included in the invention.
[0063] For a genetically altered plant that produces dsRNA, one
constructs an expression vector or cassette (made from DNA) that
encodes, at a minimum, a first promoter and the dsRNA sequence of
interest such that the promoter sequence is 5' (upstream) to and
operably linked to the dsRNA sequence. The expression vector or
cassette may optionally contain a second promoter (same as or
different from the first promoter) upstream and operably linked to
the reverse complementary sequence of the dsRNA sequence such that
two strands of RNA that are complementary to each other are
produced. Alternatively, the expression vector or cassette can
contain one promoter operably linked to both the dsRNA sequence
(sense strand) in question and the complement or reverse complement
of the dsRNA sequence (anti-sense strand) in question, such that
the transcribed RNA bends on itself and the two desires sequences
anneal. Alternatively, a second expression vector or cassette (made
from DNA) may encode, at a minimum, a second promoter (same as or
different from the promoter) operably linked to the reverse
complementary sequence of the dsRNA such that two strands of
complementary RNA are produced in the plant. The expression
vector(s) or cassette(s) is/are inserted in a plant cell genome
(nuclear or cytoplasmic). The promoter(s) used should be a
promoter(s) that is/are active in a plant and is/are heterologous
to PaAos (not normally driving the transcription of RNA of genomic
PaAos). Of course, the expression vector or cassette may have other
transcription regulatory elements, such as enhancers, terminators,
etc.
[0064] Promoters (and more specifically, heterologous promoters for
PaAos, the reverse complement of PaAos, and the transcription
factors) that are active in plants are well-known in the field.
Such promoters may be constitutive, inducible, and/or
tissue-specific. Non-limiting examples of constitutive plant
promoters include 35S promoters of the cauliflower mosaic virus
(CaMV) (e.g., of isolates CM 1841 (Gardner, et al., Nucleic Acids
Research 9:2871-2887 (1981)), CabbB-S (Franck, et al., Cell
21:285-294 (1980)) and CabbB-JI (Hull and Howell, Virology
86:482-493 (1987))), ubiquitin promoter (e.g., the maize ubiquitin
promoter of Christensen, et al., Plant Mol. Biol. 18:675-689
(1992)), gos2 promoter (de Pater, et al., The Plant J. 2:834-844
(1992)), emu promoter (Last, et al., Theor. Appl. Genet. 81:581-588
(1990)), actin promoter (see, e.g., An, et al., The Plant J. 10:107
(1996)) and Zhang, et al., The Plant Cell 3:1155-1165 (1991));
Cassava vein mosaic virus promoters (see, e.g., WO 97/48819 and
Verdaguer, et al., Plant Mol. Biol. 37:1055-1067 (1998)), the pPLEX
series of promoters from Subterranean Clover Stunt Virus (WO
96/06932, particularly the S4 or S7 promoter), alcohol
dehydrogenase promoter (e.g., pAdhlS (GenBank accession numbers
X04049, X00581)), and the TR 1' promoter and the TR2' promoter
which drive the expression of the 1' and 2' genes, respectively, of
the T-DNA (Velten, et al., EMBO J. 3:2723-2730 (1984)).
Tissue-specific promoters are promoters that direct a greater level
of transcriptional expression in some cells or tissues of the plant
than in other cells or tissue. Non-limiting examples of
tissue-specific promoters include the phosphoenolpyruvate
carboxylase (PEP or PPC1) promoter (Pathirana, et al., Plant J.
12:293-304 (1997), and Kausch, et al., Plant Mol. Biol. 45(1):1-15
(2001)), chlorophyll A/B binding protein (CAB) promoter (Bansal, et
al., Proc. Natl. Acad. Sci. USA 89(8):3654-8 (1992)), small subunit
of ribulose-1,5-bisphosphate carboxylase (ssRBCS) promoter (Bansal,
et al., Proc. Natl. Acad. Sci. USA 89(8):3654-8 (1992)), senescence
activated promoter (SEE1) (Robson, et al., Plant Biotechnol. J.
2(2):101-12 (2004)), and sorghum leaf primoridia specific promoter
(RS2) (GenBank Accession No. EI979305.1). These promoters (PPC1,
CAB, ssRBCS, SSE1, and RS2) are all active in the aerial part of a
plant. Further, the PPC1 promoter is a strong promoter for
expression in vascular tissue. Some examples of phloem specific
promoters are the sucrose synthase-1 promoters (CsSUS 1p and CsSUS
1p-2) (Singer et al., Planta 234:623-637 (2011)) and the phloem
protein-2 promoter (CsPP2) (Miyata et al., Plant Cell Report
31(11):2005-2013 (2012)) from Citrus sinensis. Alternatively, a
plant-expressible promoter may also be a wound-inducible promoter,
such as the promoter of the pea cell wall invertase gene (Zhang, et
al., Plant Physiol. 112:1111-1117 (1996)).
[0065] Other types of RNA polymerase promoters that may be used are
promoters from microorganisms, such as, but not limited to the
bacteriophage T7 RNA polymerase promoter, yeast Galactose (GAL1)
promoter, yeast glyceraldehyde-3-phosphate dehydrogenase (GAP)
promoter, yeast Alcohol Oxidase (AOX) promoter.
[0066] Other elements used to increase transcription expression in
plant cells include, but are not limited to, an intron (e.g., hsp70
intron) at the 5' end or 3' end of the chimeric gene, or in the
coding sequence of the chimeric dsRNA gene (such as, between the
region encoding the sense and antisense portion of the dsRNA),
promoter enhancer elements, duplicated or triplicated promoter
regions, 5' leader sequences different from the chimeric gene or
different from an endogenous (plant host) gene leader sequence, 3'
untranslated sequences different from the chimeric gene or
different from an endogenous (plant host) 3' untranslated
sequence.
[0067] The expression vector or cassette could contain suitable 3'
untranslated transcription regulation sequences (i.e., transcript
formation and polyadenylation sequences). Potential polyadenylation
and transcript formation sequences include those sequences in the
nopaline synthase gene (Depicker, et al., J. Molec. Appl. Genetics
1:561-573 (1982)), the octopine synthase gene (Gielen, et al., EMBO
J. 3:835-845 (1984)), the SCSV or the Malic enzyme terminators
(Schunmann, et al., Plant Functional Biology 30:453-460 (2003)),
and the T-DNA gene 7 (Velten and Schell, Nucleic Acids Research
13:6981-6998 (1985)).
[0068] The term "plant" includes whole plants, plant organs,
progeny of whole plants or plant organs, embryos, somatic embryos,
embryo-like structures, protocorms, protocorm-like bodies (PLBs),
and suspensions of plant cells. Plant organs comprise, e.g., shoot
vegetative organs/structures (e.g., leaves, stems and tubers),
roots, flowers and floral organs/structures (e.g., bracts, sepals,
petals, stamens, carpels, anthers and ovules), seed (including
embryo, endosperm, and seed coat) and fruit (the mature ovary),
plant tissue (e.g., vascular tissue, ground tissue, and the like)
and cells (e.g., guard cells, egg cells, trichomes and the like).
The class of plants that can be used in the method of the invention
is generally as broad as the class of higher and lower plants
amenable to the molecular biology and plant breeding techniques
described herein, specifically angiosperms (monocotyledonous
(monocots) and dicotyledonous (dicots) plants). It includes plants
of a variety of ploidy levels, including aneuploid, polyploid,
diploid, haploid and hemizygous. The genetically altered plants
described herein are guayule plants.
[0069] Rubber yield may be expressed as a product of rubber content
(% rubber) and biomass (dry weight/unit area). Thus, rubber yield
may be improved by increasing either biomass and/or rubber content.
The altered guayule described herein produce more rubber and have
higher rubber content than non-altered guayule, thereby increasing
the processing efficiency of the altered guayule shrub.
[0070] Because changes in PaAos functionality changes the amount of
rubber produced by guayule, this invention also involves increasing
a guayule's rubber production by reducing the amount of functional
PaAos present in the genetically altered guayule (compared to the
amount of functional PaAos present in non-altered guayule). In one
embodiment, the genetically altered guayule has a mutation in
PaAos, such as, a null mutation which results in (i) no protein is
produced, (ii) a truncated protein is produced which has no
functionality, or (iii) a full-length protein is produced which has
no functionality. Other mutations simply reduce the functionality
(activity) of PaAos. Non-limiting examples of mutations that reduce
or eliminate PaAos functionality include (i) changing a codon
encoding an amino acid to a stop codon (see Table 1 supra for the
sequence of stop codons), (ii) changing the translation initiation
codon (ATG) to any other codon to disrupt protein translation,
(iii) changing a ribosome binding site's sequence to disrupt
protein translation, (iv) changing one or more splice site codons
to alter protein sequence, (v) deleting some or all of the gene's
DNA sequence, (vi) inserting DNA into the gene, and (vii) changing
one or more DNA codon sequences to encode non-conservative amino
acids. Within SEQ ID NO: 9, nucleotides 34-36 encode ATG, the
translation initiation codon for G7-11 guayule. Similarly,
nucleotides 1-3 of SEQ ID NOs: 12 and 14 encode ATG, the
translation initiation codon for cultivars PI 478652 and W6549,
respectfully. Thus, a change in the nucleotide sequence of the
equivalent codon in any other guayule would have the same result.
Within PaAos, non-conservative amino acid substitutions at D318,
5332, E336, R339, 5359, 1408, 5411, and/or L459 (to name a few)
result in PaAos with reduced functionality. One alters guayule DNA
using the methods described herein and assesses changes in PaAos
functionality via the methods described herein (e.g., assessing the
amount of rubber produced by the altered guayule) or using methods
known to one of ordinary skill in the art. One can utilize SNPs,
antibodies, and other methods to identify the guayule that encode
the altered amino acids.
[0071] Various methods exist to create a mutation. These methods
are well-known to one of ordinary skill in the art. One method is
by transforming the plant with a plasmid containing 5' sequence and
3' sequence of the gene and allowing a cross-over event to occur,
thereby excising the DNA from the plant's genome that is between
the plasmid's 5' sequence and 3' sequence. Also, one can use
transposon-mediated mutation to delete or add DNA to PaAos which
would result in the encoded protein having a reduced functionality
compared to a non-altered PaAos. Two other methods involve using a
chemical mutagen (such as ethyl methanesulfonate (EMS)) or physical
agents (radiation, UV, or proton, for example) to generate genetic
mutations in plant cells and/or germplasm. Also, one may use TALEN
or CRISPR-Cas9 to mutate the sequence of the target gene (PaAos)
such that a desired mutation is generated. One of ordinary skill in
the art can also use targeted cleavage events to induce targeted
mutagenesis, induce targeted deletions of cellular DNA sequences,
and facilitate targeted recombination and integration at
predetermined chromosomal locations to generate one or more of the
null mutations discussed above or to reduce the mutated protein's
functionality. Nucleotide editing techniques are well-known and
described in Urnov, et al., Nature 435(7042):646-51 (2010); U.S.
Patent Publications 2003/0232410, 2005/0208489, 2005/0026157,
2005/0064474, 2006/0188987, 2009/0263900, 2009/0117617,
2010/0047805, 2011/0207221, 2011/0301073, 2011/089775,
2011/0239315, and 2011/0145940; and International Publication WO
2007/014275, the disclosures of which are incorporated by reference
in their entireties for all purposes. Cleavage occurs by using
specific nucleases such as engineered zinc finger nucleases (ZFN),
transcription-activator like effector nucleases (TALENs), or using
the CRISPR/Cas9 system with an engineered crRNA/tracr RNA ('single
guide RNA') to guide specific cleavage. U.S. Patent Publication
2008/0182332 describes the use of non-canonical zinc finger
nucleases (ZFNs) for targeted modification of plant genomes; U.S.
Patent Publication 2009/0205083 describes ZFN-mediated targeted
modification of a plant EPSPS locus; U.S. Patent Publication
2010/0199389 describes targeted modification of a plant Zp15 locus
and U.S. Patent Publication No. 20110167521 describes targeted
modification of plant genes involved in fatty acid biosynthesis. In
addition, Moehle, et al., Proc. Natl. Acad. Sci. USA
104(9):3055-3060 (2007) describes using designed ZFNs for targeted
gene addition at a specified locus. U.S. Patent Publication
2011/0041195 describes methods of making homozygous diploid
organisms. Information on CRISPR/Cas9 system is found, e.g., at
en.wikipedia.org/wiki/CRISPR;
neb.com/tools-and-resources/feature-articles/crispr-cas9-and-targeted-gen-
ome-editing-a-new-era-in-molecular-biology; and Cong, et al.,
Science, 339:819-823 (2013). Sigma-Aldrich (St. Louis, Mo.) and
Origene Technologies, Inc. (Rockville, Md.) are among the companies
that sell CRISPR/Cas9 kits.
[0072] After using any of these various methods to induce genetic
alterations in a cell's genome, one induces the treated cells to
grow into plants and then screen the plants using the methods
described herein for PaAos having reduced or no functionality,
and/or for reduced amounts of PaAos or no PaAos (via reduction in
gene expression and/or mRNA translation and/or other mechanism),
and/or for elevated production of rubber (compared to amounts
present in non-altered plants). Thus, another embodiment of this
invention is the generation of altered guayule having a genetic
alteration in PaAos such that the altered guayule produces more
rubber than produced by non-altered guayule.
[0073] Another embodiment of this invention is that one increases
rubber production in guayule by increasing the amount of SA in
altered guayule compared to the amount of SA present in untreated
or non-altered guayule. One administers SA to guayule by spraying
SA onto the guayule, drenching the soil around guayule with SA,
adding SA to irrigation water which is then used to irrigate
guayule. Another embodiment is to generate genetically altered
guayule that produce an increased amount of SA than is produced by
non-altered guayule by reducing the amount of functional PaAos in
the genetically altered guayule. Such a reduction can be caused by
a mutation in PaAos. The quantity (effective amount) of SA
administered to the altered guayule being grown in tissue culture
is the amount sufficient to generate a concentration in the tissue
culture media ranging from approximately 0.1 nM to approximately
100 nM in one embodiment, from approximately 1 nM to approximately
100 nM solution in another embodiment, from approximately 5 nM to
approximately 100 nM solution in another embodiment, and from
approximately 10 nM to approximately 50 nM solution in another
embodiment. For guayule plants in soil, from approximately 1 nM to
approximately 100 nM SA solution in one embodiment, from
approximately 5 nM to approximately 50 nM SA solution in another
embodiment, or approximately 10 nM SA solution may be administered
once, twice, or more per week. One can apply approximately 1 mL,
approximately 10 mL, approximately 100 mL of the SA solution,
depending on the SA concentration and the frequency of application.
In one embodiment, 50 mL of 10 nM SA solution is applied twice
weekly. To produce 10 nM SA solution, 0.0013812 mg SA is dissolved
in 1 liter of 0.0000065% ethanol. To produce 100 nM SA solution,
0.013812 mg SA is dissolved in 1 liter of 0.0000065% ethanol. SA
may be administered in a controlled release formulation, similar to
children's liquid aspirin formulations or as a powder. SA can be
administered early in a guayule plant's life (post-seedling stage
which is approximately one month after germination of the seed),
later in a guayule plant's life (several months prior to cut
harvest), on a seasonal basis (during heat season, cold season, or
both), or on a daily, weekly or monthly basis throughout the
lifespan of the guayule plant. Administering SA to a guayule plant
when exposed to cold temperatures (between approximately 7.degree.
C. and approximately 15.degree. C. or between approximately
10.degree. C. and approximately 15.degree. C.; for approximately 8
hours per day), as occurs during the cold season, results in
synergistically increase in rubber production. The term
"administering SA to a guayule" and similar phrases means that
exogenous SA is applied to the soil or plant or plant part.
[0074] Many techniques involving molecular biology discussed herein
are well-known to one of ordinary skill in the art and are
described in, e.g., Green and Sambrook, Molecular Cloning, A
Laboratory Manual 4th ed. 2012, Cold Spring Harbor Laboratory;
Ausubel et al. (eds.), Current Protocols in Molecular Biology,
1994--current, John Wiley & Sons; and Kriegler, Gene Transfer
and Expression: A Laboratory Manual (1993). Unless otherwise noted,
technical terms are used according to conventional usage.
Definitions of common terms in molecular biology maybe found in
e.g., Benjamin Lewin, Genes IX, Oxford University Press, 2007 (ISBN
0763740632); Krebs, et al. (eds.), The Encyclopedia of Molecular
Biology, Blackwell Science Ltd., 1994 (ISBN 0-632-02182-9); and
Robert A. Meyers (ed.), Molecular Biology and Biotechnology: a
Comprehensive Desk Reference, VCH Publishers, Inc., 1995 (ISBN
1-56081-569-8).
[0075] The terms "approximately" and "about" refer to a quantity,
level, value or amount that varies by as much as 30% in one
embodiment, or in another embodiment by as much as 20%, and in a
third embodiment by as much as 10% to a reference quantity, level,
value or amount. As used herein, the singular form "a", "an", and
"the" include plural references unless the context clearly dictates
otherwise. For example, the term "a bacterium" includes both a
single bacterium and a plurality of bacteria.
[0076] The term "nucleic acid consisting essentially of",
"polynucleotide consisting essentially of", and "RNA consisting
essentially of", and grammatical variations thereof, means a
polynucleotide that differs from a reference nucleic acid sequence
by 20 or fewer nucleotides and also perform the function of the
reference polynucleotide sequence. Such variants include sequences
which are shorter or longer than the reference nucleic acid
sequence, have different residues at particular positions, or a
combination thereof.
[0077] Having now generally described this invention, the same will
be better understood by reference to certain specific examples and
the accompanying drawings, which are included herein only to
further illustrate the invention and are not intended to limit the
scope of the invention as defined by the claims. The examples and
drawings describe at least one, but not all embodiments, of the
inventions claimed. Indeed, these inventions may be embodied in
many different forms and should not be construed as limited to the
embodiments set forth herein; rather, these embodiments are
provided so that this disclosure will satisfy applicable legal
requirements.
EXAMPLE 1
Construction of Genetically Altered Guayule
[0078] To better understand the role of PaAos in rubber synthesis,
genetically altered P. argentatum plants are generated in which
either PaAos is over-expressed or PaAos is silenced by RNAi. The
various plasmids used to achieve the overexpression or silencing of
PaAos in guayule are shown in FIG. 1. To generate these plasmids,
the guayule Aos (PaAos) is amplified by PCR using genomic DNA as a
template. The primers used to amplify PaAos are designed from the
cDNA PaAos sequence published in NCBI database (GeneBank accession
no. X78166.2) and have the following sequences: forward primer
5'-cttaagaggtggtATGGACCCATCGTCTAAACCC-3' (SEQ ID NO: 1) and reverse
primer 5'-ggatccTCATATACTAGCTCTCTTCAGGG-3' (SEQ ID NO: 2). The
nucleotides in lower case and underlined in the forward primer are
the recognition nucleotides for restriction enzyme AflII; the
nucleotides in lower case and underlined in the reverse primer are
the recognition nucleotides for restriction enzyme BamHI. The PCR
cycle program is the following: 94.degree. C. for 2 minutes
(initial heating step) and PaAos is amplified at 40 cycles of
94.degree. C. for 30 seconds (denaturation), 71.degree. C. for 30
seconds (annealing) and 68.degree. C. for 1 minute (extension) and
an additional 5 minutes extension at 68.degree. C. The resulting
amplicon is purified and subcloned into pGEM T Easy vector
(Promega, Madison, Wis.) using manufacturer's recommended protocol
and sequenced to confirm the sequence of the plasmids. The cDNA
sequence is in SEQ ID NO: 9 and the amino acid sequence is in SEQ
ID NO: 10. Subsequently, the PaAos amplicon is cut using AflII and
BamHI (Promega, Madison, Wis.). Plasmid pND6 has a Nos promoter
driving the NPTII gene for conferring kanamycin resistance and a
potato ubiquitin promoter (Garbarino and Belknap, Plant Mol. Biol.
24:119-127 (1994)) controlling the GUSplus gene (CambiaLabs,
Canberra, Australia). See FIG. 1. Plasmid pND6-Aos (FIG. 1) is
generated by replacing the GUSplus gene in pND6 with cDNA PaAos
sequence (SEQ ID NO: 9). Plasmid pND6-AosiL (FIG. 1) is generated
by replacing the GUSplus gene in pND6 with an inverted repeat of a
partial cDNA PaAos sequence (SEQ ID NO: 11) containing a loop
sequence of the Bar gene between the inverted repeat of the partial
cDNA PaAos sequence; the complete sequence replacing GUSplus is SEQ
ID NO: 45. The plasmids pND6, pND6-AosiL, and pND6-Aos are used to
transform Agrobacterium EHA101 competent cells using the protocol
described in Hood, et al., J. Bacteriol. 168:1291-1301 (1986).
[0079] The transformed Agrobacterium EHA101 either harboring pND6,
pND6-AosiL, or pND6-Aos are used to transform guayule G7-11 using
the protocols set forth below. See also Dong, et al. (2006) and
Dong, et al., Industrial Crops and Products 46:15-24 (2013). For
Agrobacterium transformation, the overnight Agrobacterium culture
are prepared by inoculating 50 .mu.L glycerol stock into a 50 mL
Falcon tube containing 5 mL LB medium plus 40 mg/L rifampcin and
200 mg/L spectinomycin, and shaking at 200 rpm at 28.degree. C. The
suspension then is centrifuged for 15 minutes at 1600 .times. g at
room temperature. The supernatant is discarded, and the pellet is
re-suspended in 25 mL of inoculation solution (1/10 MS salts plus
BA (2 mg/L), NAA (0.5 mg/L), glucose (10 g), acetosyringone (200
.mu.M), pluronic F68 (0.05%), pH=5.2 (PhytoTechnology Labs, Shawnee
Mission, Kans.)). For leaf transformation, leaf sections are cut
from the plants in the Magenta boxes (Caisson Labs, Smithfield,
Utah). The adaxial side of each leaf is placed facing up in a Petri
dish containing 5 ml Agrobacterium suspension. The leaf is cut into
.about.10 mm strips and immediately placed in an empty Petri dish
in non-overlapping manner When this Petri dish is full, all leaf
strips are blotted with the filter paper and placed into another
empty Petri dish. The Petri dish is sealed by parafilm and left in
the dark at room temperature. The co-cultivation is replaced by
this co-desiccation according to Cheng, et al., In Vitro Cell Dev.
Biol. Plant, 39, 595-604 (2003). After three days, leaf strips are
transferred to MSB1T (MS medium with BA (1 mg/L), sucrose (30 g/L),
phytagel (3 g/L), and timentin (400 mg/L)) (Cheng, et al., Plant
Cell Rep., 17(8):646-649 (1998)) for recovery at low light for 5
days. The leaf strips are then transferred to MSB1TK30 (MS medium
containing BA (1 mg/L), sucrose (30 g/L), phytagel (3 g/L),
timentin (250 mg/L), and kanamycin (30 mg/L)) for selection under
low light for two weeks. The leaf strips are then subcultured every
2 weeks under high light till green shoots emerged. Green shoots 10
mm and longer are transferred to 1/2MS10.1TK10 for rooting (same as
1/2MSI0 but with timentin (250 mg/L) and kanamycin (10 mg/L)).
After 2-4 weeks, the rooted plantlets are micropropogated and
subsequently transplanted into soil.
[0080] While the genetically altered guayule are still growing in
tissue culture under selection, the genetically altered plants are
screened for integration of the expression vectors, pND6-Aos (PaAos
in forward orientation; SEQ ID NO: 9), pND6-AosiL (SEQ ID NO: 45
which contains a portion of reverse complement of PaAos (SEQ ID NO:
11)), and pND6 (negative control). DNA is extracted from
genetically altered plants using Sigma Kit (Sigma-Aldrich, St.
Louis, Mo.). Approximately 150 mg leaf tissue (3 leaf tissues) are
cut from the plants grown in tissue-cultured, placed into 2 mL
tubes and snapped-frozen in liquid nitrogen. A bead is added to
pulverize the tissue into a fine powder at a frequency of 30/s for
1 minute using the mixer mill MM 400 tissue lyser (Verder
Scientific, Inc., Newtown, Pa.).
[0081] PCR is carried out in 50 tit mixture containing Taq 2X
Master Mix (New England Biolabs, Ipswich, MA), 200 ng guayule
genomic DNA or 20 pg plasmid DNA, and 100 ng of PaAos specific
primers; namely SEQ ID NOs: 1 and 2 for guayule transformed with
pND6-Aos; and SEQ ID NOs: 3 and 4 for guayule transformed with
pND6-AosiL. See FIG. 2. After heating the samples to 94.degree. C.
for 2 minutes, the reaction proceeds with 35 cycles of 94.degree.
C. for 30 seconds, 71.degree. C. to amplify the PaAos in the
overexpression lines (pND6-Aos) for 30 seconds or 56.degree. C. for
the PaAos in the RNAi lines (pND6-AosiL) for 30 seconds, and
68.degree. C. for 1 minute. A final elongation step is carried out
at 68.degree. C. for 5 minutes. PCR products are separated by
electrophoresis on a 1% (w/v) agarose gel. The band for the
overexpression lines is at .about.1.4 kbp, as expected; the band
for the RNAi lines is at -0.5 kbp as expected. The genetically
altered guayule plants harboring the empty plasmid (pND6 (negative
control)) are confirmed by GUS staining (Karcher, S., ABLE 23:29-42
(2002)). Briefly, plant tissues are placed in a 50 mL tube
containing GUS assay solution (1 mM X-Gluc
(5-bromo-4-chloro-3-indolyl) B-D-glucuronic acid in 50 mM
Na.sub.2HPO.sub.4, pH 7.0 and 0.1% Triton X-100). The reaction is
incubated at 37.degree. C. for 1 hour followed by washing for 30
minutes with 70% ethanol to extract the chlorophyll.
Example 2
Determination of RNA Expression Levels in Genetically Altered
Plants
[0082] Guayule containing intact PaAos (non-altered; G7-11) and
genetically altered guayule containing one of the plasmids (pND6,
pND6-Aos, or pND6-AosiL) are further screened to determine the RNA
level (see Table 3). Leaves from the various genetically altered
plants (which are grown in tissue culture) are collected and
snap-frozen in liquid nitrogen for RNA extraction. RNA is extracted
using TRIzol.RTM. according to manufacturer's recommended protocol
(Ambion, Pittsburg, Pa.). RNA concentration is quantified with the
NanoDrop ND1000 (ThermoScientific, Wilminton, Del.). RNA cleanup is
performed using the RNeasy MinElute Cleanup kit according to
manufacturer's recommended protocol (Qiagen Inc., Valencia,
Calif.). The RNA is eluted with 30-50 tit of RNase-free water along
with on-column DNase 1 treatment.
[0083] Using the RNA isolated from the leaves of the genetically
altered plants, cDNA is generated using iScript cDNA synthesis kit
(Bio-Rad, Hercules, CA) according to the manufacturer's recommended
protocol for semi-quantitative PCR and real-time quantitative PCR
(qRT-PCR). An amount of 1 .mu.g of RNA is used in the 20 mL
reaction mixture. For qRT-PCR, 2 .mu.L of the diluted cDNA (1:20)
is used in a 15 .mu.L reaction mixture. In the qRT-PCR volume, 7.5
mL of iQ SYBR.RTM. Green Supermix is used (Bio-Rad, Hercules,
Calif.). The qRT-PCR is run using the 7500 Fast Real-Time PCR
system (Applied Biosystem, Waltham, Mass.) with the following
thermal cycle: 95.degree. C. pre-incubation for 3 minutes;
amplification is performed for 40 cycles at 95.degree. C. for 15
seconds and at 60.degree. C. for 30 seconds; the dissociation stage
is set for 95.degree. C. for 15 seconds, at 60.degree. C. for 1
minute, and at 95.degree. C. for 15 seconds. Each qRT-PCR run is
performed with three independent tissue samples, each sample having
two technical replicates. The 18S gene (-200 bp) is used as an
internal control. The primers used for each sequence, PCR reaction
conditions, and the expected amplicon size are contained in FIG. 2.
Crossing point value, which is the point at which the fluorescence
crosses the threshold, and melting curve analyses are noted. The
melting curve data are collected for all genes to ensure a single
peak, indicating amplification of a specific region by a pair of
primers. The relative expression values are calculated using the
2(-Delta C(T)) method (Livak and Schmittgen, Methods, 25:402-408
(2001)). See Table 3 below.
TABLE-US-00003 TABLE 3 P. argentatum Average Relative Genotypes
Expression of Aos G7-11 1.02 .+-. 0.2 pND6-10 1.14 .+-. 0.2 pND6-12
1.02 .+-. 0.3 pND6-29 1.04 .+-. 0.2 pND6-32 1.00 .+-. 0.3 pND6-33
1.11 .+-. 0.3 pND6-35 0.90 .+-. 0.2 pND6-41 0.91 .+-. 0.2
pND6-AosiL.sub.5-1 0.39 .+-. 0.1* pND6-AosiL.sub.7-2 0.49 .+-. 0.1*
pND6-AosiL.sub.8-1 0.53 .+-. 0.1* pND6-AosiL.sub.9-15 0.44 .+-.
0.1* pND6-AosiL.sub.9-16 0.37 .+-. 0.04* pND6-AosiL.sub.12-1 0.55
.+-. 0.1* pND6-AosiL.sub.12-3 0.48 .+-. 0.1* pND6-AosiL.sub.13-2
0.55 .+-. 0.05* pND6-AosiL.sub.15-3 0.36 .+-. 0.1*
pND6-AosiL.sub.15-4 0.48 .+-. 0.2* pND6-Aos.sub.4-1 2.15 .+-. 0.1**
pND6-Aos.sub.4-2 2.11 .+-. 0.3** pND6-Aos.sub.5-1 2.29 .+-. 0.4**
pND6-Aos.sub.7-1 2.40 .+-. 0.6** pND6-Aos.sub.7-3 2.11 .+-. 0.2**
pND6-Aos.sub.8-2 2.15 .+-. 0.2** pND6-Aos.sub.10-1 2.44 .+-. 0.7**
pND6-Aos.sub.10-2 2.12 .+-. 0.4** pND6-Aos.sub.11-5 2.30 .+-. 0.3**
pND6-Aos.sub.14-2 2.23 .+-. 0.1** G7-11 = wild-type control; pND6 =
empty vector (pND6 without Aos); pND6-AosiL = PaAos is
knocked-down/silenced; pND6-Aos = PaAos is over-expressed Results
are average of three independent plants, each plant having three
technical replicates. * and ** indicate significant difference in
comparison to G7-11 guayule and/or pND6 (controls) at p > 0.05
and 0.005, respectively.
[0084] Next, to gain more insight as to where the PaAos is
spatially located, the expression pattern of PaAos in various
guayule tissues is analyzed using qRT-PCR. Total RNA is extracted
from leaves, petiole, stem, root, young flower, mature flower,
peduncle, stembark of 8-week-old tissue-cultured genetically
altered plants as well as 2-month-old greenhouse grown genetically
altered plants using the protocol described above. qRT-PCR is
performed as described above on these samples of total RNA. Primers
(SEQ ID NOs: 7 and 8 in FIG. 2) are designed to amplify .about.200
bp PCR product in PaAos coding sequence. The expression level for
each tissue are compared to the tissue cultured and greenhouse leaf
tissues, respectively. The 18S gene (-200 bp) (forward primer is
SEQ ID NO: 5 and reverse primer is SEQ ID NO: 6, described supra
and in FIG. 2) is used as an internal control. As shown in Table 4,
infra, the largest level of PaAos expression is present in the
stem, root and stembark tissues, suggesting that these tissues are
sites in which PaAos is functioning.
TABLE-US-00004 TABLE 4 Growth Conditions: MS Medium Greenhouse
Tissue Source Relative Expression Leaf 0.98 .+-. 0.1 1.04 .+-. 0.2
Petiole 0.31 .+-. 0.06 0.41 .+-. 0.1 Stem 2.27 .+-. 0.2 3.37 .+-.
0.4 Root 2.47 .+-. 0.2 3.74 .+-. 0.3 Young Flower no data 1.23 .+-.
0.4 Mature Flower no data 0.69 .+-. 0.2 Peduncle no data 0.25 .+-.
0.1 Bark no data 4.49 .+-. 1.2 The error bars represent tissues
collected from 3 individual plants.
Example 3
Rubber Quantification in Tissue
[0085] Rooted plantlets (genetically altered, empty vector
transformed (pND6 without PaAos), and wild-type control) from
transferred shoot tips are grown on half-strength MS medium
(PhytoTechnology Laboratories, Overland Park, Kans.) in Magenta
boxes (Caisson Labs, Smithfield, Utah) for 6 weeks. The top part of
the plantlets are separated from the medium and lyophilized for 48
hours. The dried tissues are placed in a 50 mL stainless steel
grinding jar containing grinding ball, frozen in liquid nitrogen
for 5 minutes and finely ground using the Retsch mixer mill MM 400
at a frequency of 30/second for 1 minute (Verder Scientific Inc.,
Newtown, Pa.). Three hundred milligrams (0.3 g) of pulverized
tissues are partitioned with Ottawa sand (Fisher Scientific, Fair
Lawn, New Jersey) and loaded into 11 mL stainless steel extraction
cells (Dionex, Sunnyvale, Calif.). Three sequential extractions are
performed using the Accelerated Solvent Extractor (ASE 2000;
Dionex, Sunnyvale, Calif.): 1. Acetone: to remove resinous material
and the low molecular weight organic solubles; 2. Methanol: to
remove chlorophyll and other alcohol-soluble materials; 3.
Cyclohexane: to remove rubber. Natural rubber is quantified
gravimetrically. The percent (%) rubber is the amount (% dw) of
cyclohexane extract from 0.3 g dried tissue. The pND6-AosiL plants
have 1.5 to 2 times more rubber than G7-11, pND6 and pND6-Aos in
tissue-cultured environment (Table 5). In Table 5, the rubber
content is quantified from leaf and stems of the indicated guayule
genotypes grown in MS media.
TABLE-US-00005 TABLE 5 Rubber content of guayule plant shoots
determined by Accelerated Solvent Extraction P. argentatum Average
Rubber Genotypes Content (%) G7-11.1 1.01 .+-. .01 G7-11.2 1.11
.+-. .02 pND6-12 1.13 .+-. 0.2 pND6-33 1.10 .+-. 0.1 pND6-35 1.04
.+-. 0.2 pND6-AosiL.sub.5-1 1.8 .+-. 0.1* pND6-AosiL.sub.7-2 2.0
.+-. 0.3** pND6-AosiL.sub.8-1 2.1 .+-. 0.04*** pND6-AosiL.sub.8-2
1.7 .+-. 0.1** pND6-AosiL.sub.9-15 1.7 .+-. 0.02**
pND6-AosiL.sub.9-16 2.3 .+-. 0.4* pND6-AosiL.sub.12-1 2.46 .+-.
0.3* pND6-AosiL.sub.12-3 1.62 .+-. 0.002*** pND6-Aos.sub.4-1 0.96
.+-. 0.2 pND6-Aos.sub.4-2 0.85 .+-. 0.1 pND6-Aos.sub.5-1 1.09 .+-.
0.1 pND6-Aos.sub.5-2 1.23 .+-. 0.1 pND6-Aos.sub.7-1 0.96 .+-. .02
pND6-Aos.sub.8-2 1.23 .+-. 0.1 pND6-Aos.sub.11-5 1.23 .+-. 0.1
Note: The rubber content is quantified from shoots (leaves + stems)
of guayule genotypes grown in MS media. Error bars represent three
biological plants with three technical replicates each. *, ** and
*** indicate significant difference in comparison to G7-11 guayule
and/or pND6 (controls) at p > 0.05, 0.005 and 0.0005,
respectively.
[0086] Next, the genetically altered guayule plants are
transplanted into soil and grown for 2 months under 27.degree. C.
(16 h)/25.degree. C. (8 h) and 27.degree. C. (16 h)/10.degree. C.
(8 h) in growth chamber conditions, representing a microcosm of
what guayule plants experience in the field during winter. Under
these conditions, pND6-AosiL plants also exhibited elevated rubber
content, having up to 31% times more rubber in comparison with
G7-11, pND6 and pND6-Aos plants (Table 6). In Table 6, the rubber
content is quantified from shoots and roots of the indicated
guayule genotypes grown in soil. These plants are approximately 4
months old when rubber content is analyzed (tissue culture (approx.
1.5 months), greenhouse (approx. 1 month), and growth chamber
(approx. 2 months)).
TABLE-US-00006 TABLE 6 Rubber content of guayule plant tissue
determined by Accelerated Solvent Extraction Average Rubber Content
(%) Shoot Root P. argentatum 27.degree. C. (16 h)/ 27.degree. C.
(16h)/ 27.degree. C. (16h)/ 27.degree. C. (16h)/ Genotypes
25.degree. C. (8 h) 10.degree. C. (8h) 25.degree. C. (8h)
10.degree. C. (8h) G7-11.1 1.22 .+-. 0.09 1.13 .+-. 0.11 1.10 .+-.
0.04 0.95 .+-. 0.10 G7-11.2 1.06 .+-. 0.12 1.37 .+-. 0.09 0.63 .+-.
0.12 0.71 .+-. 0.09 pND6-12 1.04 .+-. 0.18 1.31 .+-. 0.06 0.65 .+-.
0.07 0.72 .+-. 0.16 pND6-33 0.90 .+-. 0.06 1.14 .+-. 0.12 0.62 .+-.
0.08 0.82 .+-. 0.10 pND6-35 1.18 .+-. 0.08 1.27 .+-. 0.10 1.09 .+-.
0.06 0.94 .+-. 0.03 pND6-AosiL.sub.7-2 1.49 .+-. 0.07*** 1.86 .+-.
0.11*** 0.56 .+-. 0.03 1.26 .+-. 0.09** pND6-AosiL.sub.8-1 1.48
.+-. 0.05 1.91 .+-. 0.07*** 0.78 .+-. 0.14 1.19 .+-. 0.04**
pND6-AosiL.sub.9-16 1.46 .+-. 0.04*** 2.01 .+-. 0.08*** 0.66 .+-.
0.12 1.16 .+-. 0.02** pND6-AosiL.sub.12-1 1.55 .+-. 0.07* 1.80 .+-.
0.05*** 1.26 .+-. 0.04*** 1.52 .+-. 0.07** pND6-Aos.sub.4-1 0.97
.+-. 0.26 1.13 .+-. 0.2 0.57 .+-. 0.05 0.79 .+-. 0.09
pND6-Aos.sub.4-2 1.21 .+-. 0.10 1.30 .+-. 0.08 1.05 .+-. 0.10 0.94
.+-. 0.11 pND6-Aos.sub.5-1 0.98 .+-. 0.30 1.04 .+-. 0.12 0.54 .+-.
0.11 0.62 .+-. 0.10 pND6-Aos.sub.7-1 0.96 .+-. 0.30 1.15 .+-. 0.14
0.57 .+-. 0.06 0.55 .+-. 0.08 Note: The rubber content is
quantified from shoots and roots of guayule genotypes grown in
soil. Plants are transferred to soil from tissue culture and are
grown in a growth chamber environment. Error bars represent three
biological plants with three technical replicates each. *, ** and
*** indicate significant difference in comparison to G7-11 and/or
pND6 (controls) at p > 0.05, 0.005 and 0.0005, respectively.
[0087] Because rubber is also accumulated in root tissue, the
rubber content in the root tissues is also quantified. For the root
rubber content, the consistent, significant difference is only
under 27.degree. C. (16 h)/10.degree. C. (8 h) in which pND6-AosiL
guayule have an increased in rubber content compared with the
controls and pND6-Aos (Table 6). The data in Table 6 demonstrate
that the combination of cold temperature and silencing PaAos is
synergistic, causing guayule to produce a greater amount of rubber
than guayule exposed to just cold temperature or to just PaAos
silencing. For example, cold treatment alone increased shoot rubber
content in the control (pND6-12) by 19%--from an average of 1.04%
to 1.24%. But cold treatment of the Aos-downregulated plants
(pND6-AosiL) increased rubber by 27%--from average 1.50% to 1.90%.
In root tissues, cold treatment increased the rubber content for
the control (pND6-12) by 5.1% (from 0.79 to 0.83% rubber), but cold
treatment of the Aos-downregulated plants (pND6-AosiL) increased
rubber by 57%--from average 0.82% to 1.28%. See Table 7, infra.
From the ASE results, the increased in rubber content is very
apparent in the pND6-AosiL genotypes.
TABLE-US-00007 TABLE 7 Average Rubber Content (%) Shoot Root P.
argentatum 27.degree. C. (16 h)/ 27.degree. C. (16 h)/ 27.degree.
C. (16 h)/ 27.degree. C. (16 h)/ Genotypes 25.degree. C. (8 h)
10.degree. C. (8 h) 25.degree. C. (8 h) 10.degree. C. (8 h) pND6-12
1.04 1.24 0.79 0.83 pND6-AosiL.sub.7-2 1.50 1.90 0.82 1.28
pND6-Aos.sub.4-1 1.03 1.16 0.68 0.73
Example 4
Protein Detection in Rubber Particles
[0088] Guayule washed rubber particles (WRPs) are isolated from
genetically altered guayule lines (pND6-AosiLand pND6-Aos) and
non-altered guayule using the protocol set forth in Cornish and
Backhaus, Phytochemistry, 29: 3809-3813 (1990). Rubber particles
are extracted from non-altered and genetically altered 1 year old
greenhouse plants. First, .about.60 g to .about.70 g of stembark
tissues are peeled off from the plant, grounded with a blender
containing cold-extraction buffer, and further purified with
cold-washed buffer three times by centrifugation. The protein
extracts (1 mg) are run on an SDS-PAGE and detected with silver
staining. On the SDS-PAGE gel, endogenous Aos protein runs as
.about.53 kDa in the non-altered and overexpressed plants but not
in the RNAi lines. To determine the dry weight of the WRPs, 50 tit
of the protein extracts are aliquoted 3.times. on a weighing paper,
oven-dried over-night in a 60.degree. C. incubator and weighed the
next day. Generally, approximately 0.5 mg/tit to approximately 1.5
mg/.sub.tit WRPs are extracted.
Example 5
Hormone Production
[0089] PaAos is an enzyme in the biosynthetic pathway that produces
several different plant hormones, including jasmonic acid, SA,
abscisic acid, gibberellin A20, gibberellin A.sub.1, and
gibberellin A3. As such, the amount of these hormones is quantified
in genetically altered (pND6-AosiL and pND6-Aos), empty vector
transformed (pND6 without PaAos; control), and wild-type (G7-11,
control) tissue-cultured guayule plants using the protocol
described in Pan et al., Nature Protocols 5:986-992 (2010). See
Table 8, infra. Briefly, leaves and stems are snap-frozen and
ground to powder with mortar and pestle. Solvent extraction
solution containing 2-propanol/H.sub.2O/concentrated HCl
(2:1:0.002; vol/vol/vol) and internal standards are added to
.about.50 mg of pre-weighed tissues. After solvent extraction,
sample concentration and re-dissolution, 50 .mu.L of the sample
solution is placed into the liquid chromatography-tandem
spectrometry (Agilent GC-MS 5977A; Agilent Technologies, Santa
Clara, Calif.) for hormone analysis. Three biological plants, with
three technical replicates of each plant, are used.
TABLE-US-00008 TABLE 8 Concentration (ng/gfw) P. argentatum
Jasmonic Salicylic Abscisic Gibberellin Gibberellin Gibberellin
Genotypes Acid Acid Acid A.sub.20 A.sub.1 A.sub.3 G7-11 5.36 .+-.
1.2 5.50 .+-. 0.8 11.01 .+-. 1.9 15.95 .+-. 0.7 9.95 .+-. 0.07 3.52
.+-. 0.2 pND6-12 1.57 .+-. 0.1 4.89 .+-. 0.6 7.05 .+-. 0.8 14.11
.+-. 1.2 12.39 .+-. 2.2 2.19 .+-. 0.01 pND6-33 4.76 .+-. 1.0 5.04
.+-. 0.1 7.24 .+-. 0.3 13.86 .+-. 2.6 12.70 .+-. 2.3 1.79 .+-. 0.09
pND6-35 1.96 .+-. 0.4 5.6 .+-. 0.5 7.10 .+-. 0.6 14.41 .+-. 1.2
14.65 .+-. 0.2 2.16 .+-. 0.3 pND6-AosiL.sub.7-2 0.57 .+-. 0.1**
9.51 .+-. 0.5* 4.71 .+-. 0.6* 9.63 .+-. 1.2* 5.13 .+-. 0.8* 0.86
.+-. 0.3* pND6-AosiL.sub.9-16 0.57 .+-. 0.01** 7.65 .+-. 0.2* 2.96
.+-. 0.3* 8.85 .+-. 2.1* 7.81 .+-. 0.2** 0.80 .+-. 0.3*
pND6-AosiL.sub.12-1 0.68 .+-. 0.05** 9.65 .+-. 1.1* 3.64 .+-. 0.5*
10.59 .+-. 0.2* 6.75 .+-. 1.1* 1.32 .+-. 0.07* pND6-Aos.sub.4-1
1.48 .+-. 0.2 4.03 .+-. 0.7 9.13 .+-. 1.71 15.49 .+-. 0.6 10.78
.+-. 0.1 1.93 .+-. 0.06 pND6-Aos.sub.4-2 3.25 .+-. 0.2 4.76 .+-.
0.6 13.9 .+-. 1.3 no data 14.63 .+-. 2.7 1.80 .+-. 0.1
pND6-Aos.sub.7-1 1.41 .+-. 0.3 5.50 .+-. 0.02 8.84 .+-. 0.3 13.64
.+-. 1.2 13.96 .+-. 0.01 1.84 .+-. 0.1 .+-.represent three
biological plants with three technical replicates each plant. * and
**indicate significant difference in comparison to G7-11 and/or
pND6 (controls) at p > 0.05 and 0.005, respectively.
[0090] As evident in Table 8, the amount of jasmonic acid, abscisic
acid and gibberellic acids are reduced in the pND6-AosiL guayule
compared to the amount in the controls (wild-type (G7-11) and empty
vector transformed plants) and pND6-Aos guayule. Conversely, the SA
content is elevated in pND6-AosiL compared to the controls and
pND6-Aos lines. These results suggest that knocking down PaAos
expression not only reduces production of jasmonic acid but also
affects the level of other hormones as well.
Example 6
Plant Architecture and Photosynthetic Rates
[0091] Three independent events from each of the overexpression
(pND6-Aos) and of the silenced (pND6-AosiL) lines; as well as two
pND6 and one wild-type (G7-11) controls are selected for further
studies. pND6-AosiL plants grown in greenhouse (data not shown) and
growth chamber conditions are bigger (see FIG. 3)), have darker
green leaves (data not shown), and increased chlorophyll
measurement than the wild type and other genetically altered plants
(see FIG. 4). As demonstrated in FIG. 3, under 27.degree. C. (16
h)/25.degree. C. (8 h) and 27.degree. C. (16 h) /10.degree. C. (8
h) environments, pND6-AosiL plants are significantly taller and
wider in both conditions. These plant architectural traits reflect
the fact that pND6-AosiL plants are larger and have more shoot and
root biomass.
[0092] pND6-AosiL genotypes have also a greater number of stems
than the wild-type and empty vector controls. Well-branched guayule
plants are an indicator of having increased rubber yield because of
the presence of more sink tissue available to store rubber.
Additionally, the mature stembark tissues in pND6-AosiL have
thicker diameter (ranging from approximately 35% to approximately
54%) under both 27.degree. C. (16 h)/25.degree. C. (8 h) and
27.degree. C. (16 h)/10.degree. C. (8 h) in comparison to the
controls and pND6-Aos. See FIG. 5.
[0093] Based on this observation, the photosynthetic rate of the
plants is measured using LI-COR 6400.times.t (LI-COR Biosciences,
Lincoln, Neb.) to measure the photosynthetic rate. Measurements are
taken between 0900 to 1200h. Fully expanded middle leaf are clamped
on the Li-Cor head. After the measured and set parameters are
stabilized, the reading is taken. The middle leaf position is
chosen because this position shows significant differences based on
chlorophyll meter measurements, FIG. 4. (SPAD-502; Minolta Camera
Ltd., Japan). The pND6-AosiL plants exhibit higher photosynthetic
rate (23-31%) in comparison to G7-11, pND6 and pND6-Aos plants
(Table 9, infra). Additional physiological measurements reveal that
pND6-AosiL stomatal limitation is one of the factors involved in
the higher photosynthetic rate as pND6-AosiL plants show higher
stomatal conductance and transpiration rate when compared to G7-11,
pND6 and pND6-Aos plants (Table 9, infra). Furthermore, chlorophyll
fluorescence measurements clearly show PSII and ETR parameters used
for elucidating the efficiency of PSII are significantly higher
than G7-11, pND6 and pND6-Aos plants (Table 9, infra) in both
27.degree. C. (16 h)/25.degree. C. (8 h) and 27.degree. C. (16
h)/10.degree. C. (8 h) treatment conditions. Having higher PSII and
ETR indicate that amount of light energy absorbed and carbon
assimilated is available more in pND6-AosiL plants to convert into
energy for the plant to use (i.e., growth and development as well
as rubber production) compared to the controls and pND6-Aos plants.
Meanwhile, the NPQ measurements for the pND6-AosiL plants are lower
under the 27.degree. C. (16 h) /25.degree. C. (8 h) condition and
higher under the 27.degree. C. (16 h)/10.degree. C. (8 h) treatment
in comparison with the controls and pND6-Aos plants. Having higher
NPQ suggests that pND6-AosiL have improved heat dissipation ability
compared to G7-11, pND6 and pND6-Aos plants which could help
prevent lipid or other cell membrane damage under environmental
stress.
TABLE-US-00009 TABLE 9 P. argentatum Genotypes Pn g .PHI.PSII ETR
NPQ 27.degree. C. (16 h)/25.degree. C. (8 h) G7-11 5.75 .+-. 0.8
0.093 .+-. 0.03 2.33 .+-. 0.6 0.146 .+-. 115.73 .+-. 1.97 .+-.
0.015 11.3 0.2 pND6-10 6.29 .+-. 0.7 0.110 .+-. 0.03 2.74 .+-. 0.6
0.141 .+-. 111.1 .+-. 1.74 .+-. 0.015 11.6 0.1 pND6-12 6.20 .+-.
0.8 0.109 .+-. 0.02 2.66 .+-. 0.5 0.145 .+-. 114.4 .+-. 1.90 .+-.
0.015 12.1 0.2 pND6-AosiL.sub.7-1 8.56 .+-. 0.147 .+-. 3.41 .+-.
0.196 .+-. 165.2 .+-. 1.33 .+-. 0.6*** 0.01*** 0.3*** 0.027*
10.7*** 0.2*** pND6-AosiL.sub.8-1 8.40 .+-. 0.155 .+-. 3.67 .+-.
0.180 .+-. 141.4 .+-. 1.27 .+-. 0.6*** 0.02*** 0.4*** 0.008* 6.2**
0.2*** pND6-AosiL.sub.9-16 7.96 .+-. 0.162 .+-. 3.57 .+-. 0.186
.+-. 134.4 .+-. 1.19 .+-. 0.5*** 0.03*** 0.5*** 0.018* 3.3** 0.3***
pND6-Aos.sub.4-1 5.62 .+-. 0.9 0.110 .+-. 0.04 2.59 .+-. 0.7 0.133
.+-. 104.7 .+-. 6.7 1.92 .+-. 0.008 0.3 pND6-Aos.sub.5-1 5.70 .+-.
0.8 0.110 .+-. 0.04 2.60 .+-. 0.7 0.133 .+-. 104.7 .+-. 6.7 1.95
.+-. 0.008 0.3 pND6-Aos.sub.7-1 5.87 .+-. 0.9 0.113 .+-. 0.04 2.65
.+-. 0.7 0.137 .+-. 107.7 .+-. 6.3 2.07 .+-. 0.008 0.4 27.degree.
C. (16 h)/10.degree. C. (8 h) G7-11 2.23 .+-. 0.5 0.054 .+-. 0.02
1.31 .+-. 0.4 0.070 .+-. 55.4 .+-. 5.4 1.58 .+-. 0.007 0.2 pND6-10
2.04 .+-. 0.4 0.057 .+-. 0.02 1.55 .+-. 0.3 0.064 .+-. 50.7 .+-.
4.9 1.56 .+-. 0.006 0.2 pND6-12 2.28 .+-. 0.4 0.065 .+-. 0.03 1.67
.+-. 0.7 0.066 .+-. 51.6 .+-. 2.7 1.51 .+-. 0.003 0.3
pND6-AosiL.sub.7-1 4.14 .+-. 0.104 .+-. 2.54 .+-. 0.104 .+-. 81.0
.+-. 2.29 .+-. 0.4*** 0.02*** 0.4*** 0.011*** 8.2*** 0.3*
pND6-AosiL.sub.8-1 4.15 .+-. 0.112 .+-. 2.71 .+-. 0.102 .+-. 77.0
.+-. 2.33 .+-. 0.4*** 0.05*** 0.8*** 0.013*** 4.5*** 0.2**
pND6-AosiL.sub.9-16 4.14 .+-. 0.101 .+-. 2.60 .+-. 0.101 .+-. 79.4
.+-. 1.95 .+-. 0.6*** 0.03*** 0.5*** 0.009*** 6.9*** 0.1**
pND6-Aos.sub.4-1 2.27 .+-. 0.5 0.059 .+-. 0.02 1.51 .+-. 0.3 0.065
.+-. 60.4 .+-. 5.5 1.35 .+-. 0.011 0.3 pND6-Aos.sub.5-1 2.97 .+-.
0.3 0.069 .+-. 0.01 1.81 .+-. 0.2 0.077 .+-. 58.5 .+-. 6.3 1.25
.+-. 0.007 0.2 pND6-Aos.sub.7-1 2.45 .+-. 0.6 0.063 .+-. 0.01 1.93
.+-. 0.3 0.065 .+-. 50.1 .+-. 5.8 1.44 .+-. 0.010 0.2 Pn = net
photosynthetic rate; g = stomatal conductance; E = Transpiration
rate; .PHI.PSII = Efficiency of Photosystem II; ETR = Electron
Transport Rate; NPQ = Non-photochemical quenching *, ** and
***indicate significant difference in comparison to G7-11 and/or
pND6 (controls) at p > 0.05, 0.005 and 0.0005, respectively.
Example 7
Quality of Natural Rubber from pND6-AOSiL Plants
[0094] The length of the polymer chain, a.k.a. rubber molecular
weight, is the primary determinant of quality in natural rubber.
Gel permeation chromatography (GPC) is used to measure the
molecular weight of rubber from guayule tissue culture plants'
extracts. Cyclohexane extractables collected from ASE (see Example
3 and Table 5 supra) are re-suspended in approximately 3 mL of
tetrahydrofuran (THF) overnight with gentle shaking (Multi-Purpose
Rotator, Thermo Scientific, Waltham, Mass.). The solution is
syringe-filtered through a 1.6 .mu.m glass microfiber GF/A filter
(Whatman GE Healthcare, Piscataway, N.J.), then injected into a
Hewlett Packard 1100 series HPLC (1.0 mL/min flow rate, 50 .mu.L
injection volume, THF continuous phase) and size exclusion
separated by two Agilent PL gel 10 .mu.m Mixed-B columns in series
(35.degree. C.) (Santa Clara, Calif.). The resulting chromatograms
are used to calculate the rubber molecular weight shown in FIG. 6
(using Astra software (Wyatt Technology Corp., Santa Barbara,
Calif.)). The molecular weight of natural rubber from three
pND6-AosiL transformed guayule plants (silenced) is greater than
from wild-type guayule line G7-11, two negative control pND6
transformed guayule plants and three pND6-Aos transformed guayule
plants (overexpressed) indicating better quality rubber in the
PaAos silenced guayule plants. In FIG. 6, the asterisks (*) and
(**) above the three pND6-AosiL transformed guayule plant lines
indicate significant difference in comparison to the negative
control pND6 transformed guayule plant lines at p >0.05 and p
>0.005, respectively.
Example 8
Exogenous Salicylic Acid (SA) Addition Reduces PaAos Gene
Expression
[0095] The effect of SA on guayule PaAos gene expression is tested
in wild-type guayule G7-11 plants. SA is added to the growth medium
(K0) in tissue culture at different concentrations, 0 nM, 10 nM and
100 nM. Shoot tips are transferred to the growth media, and plants
are grown for 8 weeks. The rubber content of the plant tissues is
determined by standard procedures (ASE, see Example 3 supra). In
comparison to 0 nM of SA, the addition of 10 nM and 100 nM of SA
increases the amount of rubber produced in a significant manner See
FIG. 7. The effect of exogenous 10 nM SA on one month old guayule
plants grown in the soil under greenhouse conditions is also
examined 50 ml of 10 nM SA solution of water and 0.0005% ethanol is
administered to the soil twice weekly for two months and results in
significant differences in the height and primary stem diameter
relative to mock or water treated G7-11 plants (FIG. 8). The
qRT-PCR results of PaAOS from the SA treated plants also show low
expression pattern. The rubber content in the SA treated plants
slightly increases and significantly differs compared to the mock
treated G7-11 plants (FIG. 8). These data demonstrate that
guayule's rubber content is increased by exogenous addition of SA
to the plant.
Example 9
Transcription Factor Overexpression Results in More Rubber
Production
[0096] PaAos promoter sequence is obtained (SEQ ID NO: 18) and is
analyzed for transcription factors' binding sites using PlantPAN2.0
software (plantpan2.itps.ncku.edu.tw). The binding sites of a
number of transcription factors, including WRKY3, WRKY71, MYBS3,
CBF, and FLC, are identified. See FIG. 11A-11C, and Chen, et al.,
BMC Genomics 12:85-97 (2012). The Hevea nucleotide sequences of
WRKY3, WRKY71, and MYBS3 are used to identify the DNA sequence of
these three transcription factor genes in P. argentatum by
searching for high percent identical sequences in a P. argentatum
EST database in NCBI (using a computer algorithm, "BLAST") and also
in a newly assembled guayule genome (unpublished).
[0097] Based on the sequence information obtained from the sequence
comparisons, RT-PCR forward primers and reverse primers are
designed to amplify partial coding sequence of guayule's WRKY3-like
(SEQ ID NOs: 19 and 20), WRKY71-like (SEQ ID NOs: 21 and 22), and
MYBS3-like (SEQ ID NOs: 23 and 24). FIG. 12 contains these
sequences as well as the annealing temperature and amplicon's size.
These primers are used in the following protocol to isolate the
coding sequences of the indicated transcription factors.
[0098] Approximately 150 mg stem tissue (4 stem tissues) are cut
from guayule plants grown in tissue-cultured, placed into 2 mL
tubes, and snapped-frozen in liquid nitrogen. Mortar and pestle are
used to pulverize the tissues into a fine powder. RNA is extracted,
quantified, and cleaned up using the protocols describe above in
Example 2. Using the RNA isolated from the stem of wild-type
guayule (line G7-11) and genetically altered guayule (i.e., pND6,
pND6-AOSiL and pND6-AOS lines described above) cDNA is generated
using iScript cDNA synthesis kit (Bio-Rad, Hercules, Calif.) using
manufacturer's recommended protocol for semi-quantitative PCR and
real-time quantitative PCR (qRT-PCR). An amount of 1 .mu.g of RNA
is used in the 20 mL reaction mixture. For PCR and qRT-PCR, 2 .mu.L
of the diluted cDNA (1:20) is used in a 25 .mu.L and 15 .mu.L
reaction mixture, respectively. PCR is carried out in 25 tit of a
mixture containing Taq 2.times. Master Mix (New England Biolabs,
Ipswich, Mass.). After heating the samples to 94.degree. C. for 2
minutes, the reaction proceeded with 40 cycles of 94.degree. C. for
30 seconds, 58.degree. C. to amplify the PaWRKY3-like,
PaWRKY71-like, and PaMYBS3-like in the above mentioned guayule
lines for 30 seconds, and 68.degree. C. for 1 minute. A final
elongation step is carried out at 68.degree. C. for 5 minutes. PCR
products are separated by electrophoresis on a 1% (w/v) agarose
gel; the expected PCR fragment is excised from the gel and purified
with QIAquick.RTM. Gel Extraction Kit (Qiagen, Germantown, Md.) and
sent to Elim Biopharmceuticals (Hayward, Calif.) for sequencing. In
the qRT-PCR volume, 7.5 mL of iQ SYBR.RTM. Green Supermix is used
(Bio-Rad, Hercules, Calif.). The qRT-PCR is run using the 7500 Fast
Real-Time PCR system (Applied Biosystem, Waltham, Mass.) with the
following thermal cycle: 95.degree. C. pre-incubation for 3
minutes; amplification is performed for 40 cycles at 95.degree. C.
for 15 seconds and at 60.degree. C. for 30 seconds; the
dissociation stage is set for 95.degree. C. for 15 seconds, at
60.degree. C. for 1 minute, and at 95.degree. C. for 15 seconds.
Each qRT-PCR run is performed with three independent tissue
samples, each sample having two technical replicates. The PaAos and
18S genes are used as internal controls. The primers used for each
sequence, PCR annealing temperature, and the expected amplicon size
are listed in FIG. 12. Crossing point value, which is the point at
which the fluorescence crosses the threshold, and melting curve
analyses are noted. The melting curve data are collected for all
genes to ensure a single peak, indicating amplification of a
specific region by a pair of primers. The relative expression
values are calculated using the 2(-Delta C(T)) method (see Livak
and Schmittgen (2001) supra). As seen in FIG. 13A-13C, the
transcriptional expression of each of the three transcription
factors (PaWRKY3-like, PaWRKY71-like, and PaMYBS3-like) increases
by a factor of 2- to 10-fold, compared to empty vector (pND6) or
non-altered controls (18S gene and PaAos). The expression of the
PaAos and the content of AOS protein on rubber particles, are
reduced for lines overexpressing these transcription factors.
Rubber content in guayule overexpressing these three transcription
factors is increased by a factor of 2- to 10-fold compared to empty
vector or wild type controls.
[0099] Plasmids are prepared to overexpress PaWRKY3-like,
PaWRKY71-like, and PaMYBS3-like in guayule. The cDNA sequence of
each transcription factor is cloned into plasmid pND6 shown in FIG.
1 and replaces GUS. The primers used to generate and amplify
PaWRKY3-like, PaWRKY71-like and PaMYBS3-like cDNAs are designed
from the cDNA sequence obtained from guayule genome database
assembly. The restriction enzymes AflII and B amHI are used for
insertion of the the cDNAs into pND6 as described above in Example
1; thus primer pairs SEQ ID NOs: 27 and 28; 29 and 30; and 31 and
32, respectively are used to generate the cDNAs with the desired
restrictions sequences. The PCR cycle program is 94.degree. C. for
2 minutes (initial heating step) and PaWRKY3-like, PaWRKY71-like,
and PaMYBS3-like are independently amplified at 40 cycles of
94.degree. C. for 30 seconds (denaturation), 58.degree. C. for 1
minute (annealing) and 68.degree. C. for 1 minute (extension) and
an additional 5 minutes extension at 68.degree. C. The resulting
amplicons are purified and subcloned into pGEM T Easy vector
(Promega, Madison, Wis.) using the manufacturer's recommended
protocol and sequenced to confirm the sequence of the plasmids.
PaWRKY3-like genomic sequence is SEQ ID NO: 39 and coding sequence
is SEQ ID NO: 40. PaWRKY71-like genomic sequence is SEQ ID NO: 41
and coding sequence is SEQ ID NO: 42. PaMYBS3-like genomic sequence
is SEQ ID NO: 43 and coding sequence is SEQ ID NO: 44. The
PaWRKY3-like, PaWRKY71-like, and PaMYBS3-like amplicons are
digested with AflII and B amHI (Promega, Madison, Wis.) using the
manufacturer's recommended protocol and are inserted into pPZP200
(Hajdukiewicz, et al. (1994)). As described above in Example 1, the
PaWRKY3-like, PaWRKY71-like, and PaMYBS3-like amplicons replace GUS
in pND6 to generate pND6-PaWRKY3-like, pND6-PaWRKY71-like, and
pND6-PaMYBS3-like. Agrobacterium EHA101 competent cells are
transformed with one of each of these plasmids using the protocol
described above in Example 1.
[0100] The transformed Agrobacterium EHA101 harboring either pND6,
pND6-PaWRKY3-like, pND6-PaWRKY71-like or pND6-PaMYBS3-like are used
to transform guayule G7-11 using the protocols set forth above in
Example 1. See, also, Dong, et al. (2006) and Dong, et al. (2013).
The transformed cells in the leaf strips are induced to grow using
the protocols set forth above in Example 1. The shoot tips of the
rooted plantlets are maintained or planted, as described above in
Example 1. While the genetically altered guayule are growing in
tissue culture under selection, the genetically altered plants are
screened for integration of the expression vectors,
pND6-PaWRKY3-like, pND6-PaWRKY71-like and pND6-PaMYBS3-like using
the protocol described above in Example 1.
[0101] PCR is performed in 50 tit mixture containing Taq 2.times.
Master Mix (New England Biolabs, Ipswich, Mass.), 200 ng guayule
genomic DNA or 20 pg plasmid DNA, and 100 ng of pND6-WRKY3-like,
pND6-WRKY71-like and pND6-MYBS3-like specific primers; namely SEQ
ID NOs: 33 and 34; 35 and 36; and 37 and 38; respectively, (see
also FIG. 12) for guayule transformed with pND6-WRKY3-like,
pND6-WRKY71-like and pND6-MYBS3-like. After heating the samples to
94.degree. C. for 2 minutes, the reaction proceeds with 35 cycles
of 94.degree. C. for 30 seconds, 71.degree. C. to amplify the DNA
for 30 seconds, and 68.degree. C. for 1 minute. A final elongation
step is carried out at 68.degree. C. for 5 minutes. PCR products
are separated by electrophoresis on a 1% (w/v) agarose gel. The
band for the overexpression lines are about 800 bp, about 550 bp
and about 400 bp for pND6-WRKY3-like, pND6-WRKY71-like, and
pND6-MYBS3-like, respectively. The genetically altered guayule
plants harboring the empty plasmid (pND6 (negative control)) are
confirmed by GUS staining using the protocol described above in
Example 1.
[0102] Genetically altered guayule containing intact PaWRKY3-like,
PaWRKY71-like, PaMYBS3-like, and genetically altered guayule
containing the control plasmid (pND6) are further screened to
determine the RNA level using the protocols described above in
Example 2 and FIG. 12. Collection of tissues, extraction, clean-up
and quantification of RNA and cDNA synthesis are performed using
the protocols described above in Example 2. Genetically altered
guayule lines that overexpress PaWRKY3-like, PaWRKY71-like, and
PaMYBS3-like genes significantly more than controls are then
selected for further analyses, as described below.
[0103] Genetically altered guayule lines that overexpress
PaWRKY3-like, PaWRKY71-like, or PaMYBS3-like and non-altered
guayule are grown as described in Example 3, above, and rubber
content is assessed using the protocols described in Example 3,
above. The average rubber content of the shoots of the genetically
altered guayule lines for PaWRKY3-like, PaWRKY71-like, and
PaMYBS3-like are determined as described above. The genetically
altered guayule lines containing PaWRKY3-like, PaWRKY71-like, or
PaMYBS3-like are transplanted into soil and grown in the conditions
described above in Example 3. The average rubber content of the
shoots and roots of the genetically altered guayule lines
PaWRKY3-like, PaWRKY71-like, and PaMYBS3-like are determined as
describe above. Next, the quality of the rubber produced by the
genetically altered guayule lines containing PaWRKY3-like,
PaWRKY71-like, or PaMYBS3-like are assess using the protocols
described above in Example 7. For these experiments, the plant
biomass, rubber content, and quality are similar to or higher than
the PaAosiL genetically altered guayule described above.
[0104] The foregoing detailed description and certain
representative embodiments and details of the invention have been
presented for purposes of illustration and description of the
invention. It is not intended to be exhaustive or to limit the
invention to the precise forms disclosed. It will be apparent to
practitioners skilled in the art that modifications and variations
may be made therein without departing from the scope of the
invention. All references cited herein are incorporated by
reference.
Sequence CWU 1
1
45134DNAArtificial Sequenceprimer, chemical synthesis 1cttaagaggt
ggtatggacc catcgtctaa accc 34229DNAArtificial Sequenceprimer,
chemical synthesis 2ggatcctcat atactagctc tcttcaggg
29324DNAArtificial Sequenceprimer, chemical synthesis 3atgagcccag
aacgacgccc ggcc 24424DNAArtificial Sequenceprimer, chemical
synthesis 4gatctcggtg acgggcagga ccgg 24520DNAArtificial
Sequenceprimer, chemical synthesis 5caacaaaccc cgacttctgg
20620DNAArtificial Sequenceprimer, chemical synthesis 6cacccgtcac
caccatagta 20720DNAArtificial Sequenceprimer, chemical synthesis
7aacccggaag aaaccaaact 20820DNAArtificial Sequenceprimer, chemical
synthesis 8cgcaaccgac tggaaataat 2091422DNAParthenium argentatum
9atggacccat cgtctaaacc cctccgtgaa atccccggct cttatggcat tcctttcttt
60caaccgataa aagaccggtt ggagtatttt tacgggaccg gaggtcgaga cgagtacttc
120cggtcccgca tgcaaaaata ccaatccacg gtatttcgag ccaacatgcc
accgggccct 180ttcgtaagca gcaacccgaa ggtaatcgtc ctactcgacg
ccaaaagctt tccgatactc 240tttgatgtat ccaaagtcga gaagaaagat
ttgttcaccg gaacttacat gccgtcaacc 300aaactcactg gcggctatcg
cgtactctcg tacctcgacc catccgaacc tagacatgct 360caacttaaga
acctcttgtt cttcatgctt aaaaattcaa gcaaccgagt cattcctcag
420ttcgaaacca cttacaccga actctttgaa ggtcttgaag ccgagctagc
caaaaacggg 480aaagccgcgt tcaacgatgt tggtgaacaa gcggctttcc
ggtttttggg cagggcttat 540tttaactcga acccggaaga aaccaaacta
ggaactagtg cgcctacgtt aattagctcg 600tgggtgttat ttaatcttgc
ccccacgctc gacctcggac ttccgtggtt cttgcaggaa 660cctcttctac
acactttccg actgccggcg ttcctgatta agagtactta caacaaactt
720tacgattatt tccagtcggt tgcgactccg gttatggaac aagcagaaaa
attaggggtt 780ccgaaggatg aagctgtgca caatatctta ttcgcggttt
gcttcaatac ttttggtggt 840gttaagatcc tcttcccgaa tacactcaaa
tggatcggac ttgctggtga gaatttgcat 900acccaattgg cggaagagat
tagaggtgct ataaaatcat acggggacgg taacgtgacg 960ctggaagcaa
tcgagcagat gccgttgacg aagtcagtgg tgtacgagtc cctcaggatt
1020gaaccaccag tgcctccgca atatggaaaa gccaaaagca actttaccat
agagtcacac 1080gacgccactt tcgaagtcaa aaaaggagaa atgttattcg
ggtaccaacc gtttgcaacc 1140aaggacccaa aagtatttga ccgacctgag
gaatatgtcc ctgatcggtt cgttggggat 1200ggcgaggcat tgttgaagta
cgtatggtgg tctaatgggc cggagacaga gagtccgaca 1260gttgaaaata
aacaatgtgc cggaaaagac tttgtcgtgc ttataacgag gttgtttgtc
1320attgaacttt tccggcgata tgactctttt gaaatcgaat taggcgagtc
tcctttgggt 1380gcagctgtca cacttacgtt cctgaagaga gctagtatat ga
142210473PRTParthenium argentatum 10Met Asp Pro Ser Ser Lys Pro Leu
Arg Glu Ile Pro Gly Ser Tyr Gly1 5 10 15Ile Pro Phe Phe Gln Pro Ile
Lys Asp Arg Leu Glu Tyr Phe Tyr Gly 20 25 30Thr Gly Gly Arg Asp Glu
Tyr Phe Arg Ser Arg Met Gln Lys Tyr Gln 35 40 45Ser Thr Val Phe Arg
Ala Asn Met Pro Pro Gly Pro Phe Val Ser Ser 50 55 60Asn Pro Lys Val
Ile Val Leu Leu Asp Ala Lys Ser Phe Pro Ile Leu65 70 75 80Phe Asp
Val Ser Lys Val Glu Lys Lys Asp Leu Phe Thr Gly Thr Tyr 85 90 95Met
Pro Ser Thr Lys Leu Thr Gly Gly Tyr Arg Val Leu Ser Tyr Leu 100 105
110Asp Pro Ser Glu Pro Arg His Ala Gln Leu Lys Asn Leu Leu Phe Phe
115 120 125Met Leu Lys Asn Ser Ser Asn Arg Val Ile Pro Gln Phe Glu
Thr Thr 130 135 140Tyr Thr Glu Leu Phe Glu Gly Leu Glu Ala Glu Leu
Ala Lys Asn Gly145 150 155 160Lys Ala Ala Phe Asn Asp Val Gly Glu
Gln Ala Ala Phe Arg Phe Leu 165 170 175Gly Arg Ala Tyr Phe Asn Ser
Asn Pro Glu Glu Thr Lys Leu Gly Thr 180 185 190Ser Ala Pro Thr Leu
Ile Ser Ser Trp Val Leu Phe Asn Leu Ala Pro 195 200 205Thr Leu Asp
Leu Gly Leu Pro Trp Phe Leu Gln Glu Pro Leu Leu His 210 215 220Thr
Phe Arg Leu Pro Ala Phe Leu Ile Lys Ser Thr Tyr Asn Lys Leu225 230
235 240Tyr Asp Tyr Phe Gln Ser Val Ala Thr Pro Val Met Glu Gln Ala
Glu 245 250 255Lys Leu Gly Val Pro Lys Asp Glu Ala Val His Asn Ile
Leu Phe Ala 260 265 270Val Cys Phe Asn Thr Phe Gly Gly Val Lys Ile
Leu Phe Pro Asn Thr 275 280 285Leu Lys Trp Ile Gly Leu Ala Gly Glu
Asn Leu His Thr Gln Leu Ala 290 295 300Glu Glu Ile Arg Gly Ala Ile
Lys Ser Tyr Gly Asp Gly Asn Val Thr305 310 315 320Leu Glu Ala Ile
Glu Gln Met Pro Leu Thr Lys Ser Val Val Tyr Glu 325 330 335Ser Leu
Arg Ile Glu Pro Pro Val Pro Pro Gln Tyr Gly Lys Ala Lys 340 345
350Ser Asn Phe Thr Ile Glu Ser His Asp Ala Thr Phe Glu Val Lys Lys
355 360 365Gly Glu Met Leu Phe Gly Tyr Gln Pro Phe Ala Thr Lys Asp
Pro Lys 370 375 380Val Phe Asp Arg Pro Glu Glu Tyr Val Pro Asp Arg
Phe Val Gly Asp385 390 395 400Gly Glu Ala Leu Leu Lys Tyr Val Trp
Trp Ser Asn Gly Pro Glu Thr 405 410 415Glu Ser Pro Thr Val Glu Asn
Lys Gln Cys Ala Gly Lys Asp Phe Val 420 425 430Val Leu Ile Thr Arg
Leu Phe Val Ile Glu Leu Phe Arg Arg Tyr Asp 435 440 445Ser Phe Glu
Ile Glu Leu Gly Glu Ser Pro Leu Gly Ala Ala Val Thr 450 455 460Leu
Thr Phe Leu Lys Arg Ala Ser Ile465 47011313DNAParthenium argentatum
11cgccggaaaa gttcaatcac aaacaacctc gttataagca cggcaaagtc ttttccggca
60cattgtttat tttcaactga tcggactctc tgtctccggc ccattagacc accatacgta
120cttcaacaat gcctcgccat ccccaacgag ccgatcaggg acatattcct
caggtcggtc 180aaatactttt gggtccttgg ttgcaaacgg ttggtacccg
aataacattt ctcctttttt 240gacttcgaaa gtggcgtcgt gtgactctat
ggtaaagttg cttttggctt ttccatattg 300cggaggcact ggt
313121422DNAParthenium argentatum 12atggacccat cgtctaaacc
cctccgtgaa atccccggct cttatggcat tcctttcttt 60caaccgataa aagaccgatt
ggagtatttt tacgggaccg gaggtcgaga cgagtacttc 120cggtcccgca
tgcaaaaata ccaatccacg gtatttcgag ccaacatgcc accgggccct
180ttcgtaagca gcaacccgaa ggtcatcgtc ctactcgacg ccaagagctt
tccgatactc 240tttgatgtat ccaaagtcga gaagaaagat ttgttcaccg
gaacttacat gccgtcaacc 300aaactcactg gcggctaccg cgtactctcg
tacctcgacc catccgaacc tagacatgct 360cagctgaaga acctcttgtt
cttcatgctt aaaaattcaa gcaaccgagt cattcctcag 420ttcgaaacca
cttacaccga actctttgaa ggtcttgaag ccgagctagc caaaaacggg
480aaagccgcgt tcaacgatgt tggtgaacaa gcggctttcc ggtttttggg
cagggcttat 540tttaactcga acccggaaga aaccaaacta ggaactagtg
cgcctacgtt aattagctcg 600tgggtgttat ttaatcttgc ccccacgctc
gacctcggac ttccgtggtt cttgcaggaa 660cctcttctac acactttccg
actgccggcg ttcctgatta agagtactta caacaaactt 720tacgattatt
tccagtcggt tgcgactccg gttatggaac aagcagaaaa attaggggtt
780ccgaaggatg aagctgtgca caatatctta ttcgcggttt gcttcaatac
ttttggtggt 840gtaaagatcc tcttcccgaa tacactcaaa tggatcggac
ttgctggtga gaatttgcat 900acccaattgg cggaagagat tagaggtgct
ataaaatcat acggggacgg tgacgtgacg 960ctggaagcaa tcgagcagat
gccgttgacg aagtcagtgg tgtacgagtc cctcaggatt 1020gaaccaccag
tgcctccgca atatggaaaa gccaaaagca actttaccat agagtcacac
1080gacgccactt tcgaagtcaa aaaaggagaa atgttattcg ggtaccaacc
gtttgcaacc 1140aaggacccaa aagtatttga ccgacccgag gaatatgtcc
ctgatcggtt cgttggggat 1200ggcgaggcat tgttgaagta catatggtgg
tctaatgggc cggagacaga gagtccgaca 1260gttgaaaata aacaatgtgc
cggaaaagac tttgttgtgc ttataacgag gttgtttgtc 1320attgaacttt
tccggcgata tgactccttt gaaatcgaat taggcgagtc tcctttgggt
1380gcagctgtca cacttacgtc cctgaagaga gctagtatat ga
142213473PRTParthenium argentatum 13Met Asp Pro Ser Ser Lys Pro Leu
Arg Glu Ile Pro Gly Ser Tyr Gly1 5 10 15Ile Pro Phe Phe Gln Pro Ile
Lys Asp Arg Leu Glu Tyr Phe Tyr Gly 20 25 30Thr Gly Gly Arg Asp Glu
Tyr Phe Arg Ser Arg Met Gln Lys Tyr Gln 35 40 45Ser Thr Val Phe Arg
Ala Asn Met Pro Pro Gly Pro Phe Val Ser Ser 50 55 60Asn Pro Lys Val
Ile Val Leu Leu Asp Ala Lys Ser Phe Pro Ile Leu65 70 75 80Phe Asp
Val Ser Lys Val Glu Lys Lys Asp Leu Phe Thr Gly Thr Tyr 85 90 95Met
Pro Ser Thr Lys Leu Thr Gly Gly Tyr Arg Val Leu Ser Tyr Leu 100 105
110Asp Pro Ser Glu Pro Arg His Ala Gln Leu Lys Asn Leu Leu Phe Phe
115 120 125Met Leu Lys Asn Ser Ser Asn Arg Val Ile Pro Gln Phe Glu
Thr Thr 130 135 140Tyr Thr Glu Leu Phe Glu Gly Leu Glu Ala Glu Leu
Ala Lys Asn Gly145 150 155 160Lys Ala Ala Phe Asn Asp Val Gly Glu
Gln Ala Ala Phe Arg Phe Leu 165 170 175Gly Arg Ala Tyr Phe Asn Ser
Asn Pro Glu Glu Thr Lys Leu Gly Thr 180 185 190Ser Ala Pro Thr Leu
Ile Ser Ser Trp Val Leu Phe Asn Leu Ala Pro 195 200 205Thr Leu Asp
Leu Gly Leu Pro Trp Phe Leu Gln Glu Pro Leu Leu His 210 215 220Thr
Phe Arg Leu Pro Ala Phe Leu Ile Lys Ser Thr Tyr Asn Lys Leu225 230
235 240Tyr Asp Tyr Phe Gln Ser Val Ala Thr Pro Val Met Glu Gln Ala
Glu 245 250 255Lys Leu Gly Val Pro Lys Asp Glu Ala Val His Asn Ile
Leu Phe Ala 260 265 270Val Cys Phe Asn Thr Phe Gly Gly Val Lys Ile
Leu Phe Pro Asn Thr 275 280 285Leu Lys Trp Ile Gly Leu Ala Gly Glu
Asn Leu His Thr Gln Leu Ala 290 295 300Glu Glu Ile Arg Gly Ala Ile
Lys Ser Tyr Gly Asp Gly Asp Val Thr305 310 315 320Leu Glu Ala Ile
Glu Gln Met Pro Leu Thr Lys Ser Val Val Tyr Glu 325 330 335Ser Leu
Arg Ile Glu Pro Pro Val Pro Pro Gln Tyr Gly Lys Ala Lys 340 345
350Ser Asn Phe Thr Ile Glu Ser His Asp Ala Thr Phe Glu Val Lys Lys
355 360 365Gly Glu Met Leu Phe Gly Tyr Gln Pro Phe Ala Thr Lys Asp
Pro Lys 370 375 380Val Phe Asp Arg Pro Glu Glu Tyr Val Pro Asp Arg
Phe Val Gly Asp385 390 395 400Gly Glu Ala Leu Leu Lys Tyr Ile Trp
Trp Ser Asn Gly Pro Glu Thr 405 410 415Glu Ser Pro Thr Val Glu Asn
Lys Gln Cys Ala Gly Lys Asp Phe Val 420 425 430Val Leu Ile Thr Arg
Leu Phe Val Ile Glu Leu Phe Arg Arg Tyr Asp 435 440 445Ser Phe Glu
Ile Glu Leu Gly Glu Ser Pro Leu Gly Ala Ala Val Thr 450 455 460Leu
Thr Ser Leu Lys Arg Ala Ser Ile465 470141422DNAParthenium
argentatum 14atggacccat cgtctaaacc cctccgtgaa atccccggct cttatggcat
tcctttcttt 60caaccgataa aagaccgatt ggagtatttt tacgggaccg gaggtcgaga
cgagtacttc 120cggtcccgca tgcaaaaata ccaatccacg gtatttcgag
ccaacatgcc accgggccct 180ttcgtaagca gcaacccgaa ggtcatcgtc
ctactcgacg ccaaaagctt tccgatactc 240tttgatgtat ccaaagtcga
gaagaaagat ttgttcaccg gaacttacat gccgtcaacc 300aaactcactg
gcggctaccg cgtactctcg tacctcgacc catccgaacc tagacatgct
360caacttaaga acctcttgtt cttcatgctt aaaaattcaa gcaaccgagt
cattcctcag 420ttcgaaacca cttacaccga actctttgaa ggtcttgaag
ccgagctagc caaaaacggg 480aaagccgcgt tcaacgatgt tggtgaacaa
gcggctttcc ggtttttggg cagggcttat 540tttaactcga acccggaaga
aaccaaacta ggaactagtg cgcctacgtt aattagctcg 600tgggtgttat
ttaatcttgc ccccacgctc gacctcggac ttccgtggtt cttgcaggaa
660cctcttctac acactttccg actgccggcg ttcctgatta agagtactta
caacaaactt 720tacgattatt tccagtcggt tgcgactccg gttatggaac
aagcagaaaa attaggggtt 780ccgaaggatg aagctgtgca caatatctta
ttcgcggttt gcttcaatac ttttggtggt 840gttaagatcc tcttcccgaa
tacactcaaa tggatcggac ttgctggtga gaatttgcat 900acccaattgg
cggaagagat tagaggtgct ataaaatcat acggggacgg taacgtgacg
960ctggaagcaa tcgagcagat gccgttgacg aagtcagtgg tgtacgagtc
cctcaggatt 1020gaaccaccag tgcctccgca atatggaaaa gccaaaagca
actttaccat agagtcacac 1080gacgccactt tcgaagtcaa aaaaggagaa
atgttattcg ggtaccaacc gtttgcaacc 1140aaggacccaa aagtatttga
ccgacctgag gaatatgtcc ctgatcggtt cgttggggat 1200ggcgaggcat
tgttgaagta cgtatggtgg tctaatgggc cggagacaga gagtccgaca
1260gttgaaaata aacaatgtgc cggaaaagac tttgtcgtgc ttataacgag
gttgtttgtc 1320attgaacttt tccggcgata tgactctttt gaaatcgaat
taggcgagtc tccttggggt 1380gcagctgtca cacttacgtc cctgaagaga
gctagtatat ga 142215473PRTParthenium argentatum 15Met Asp Pro Ser
Ser Lys Pro Leu Arg Glu Ile Pro Gly Ser Tyr Gly1 5 10 15Ile Pro Phe
Phe Gln Pro Ile Lys Asp Arg Leu Glu Tyr Phe Tyr Gly 20 25 30Thr Gly
Gly Arg Asp Glu Tyr Phe Arg Ser Arg Met Gln Lys Tyr Gln 35 40 45Ser
Thr Val Phe Arg Ala Asn Met Pro Pro Gly Pro Phe Val Ser Ser 50 55
60Asn Pro Lys Val Ile Val Leu Leu Asp Ala Lys Ser Phe Pro Ile Leu65
70 75 80Phe Asp Val Ser Lys Val Glu Lys Lys Asp Leu Phe Thr Gly Thr
Tyr 85 90 95Met Pro Ser Thr Lys Leu Thr Gly Gly Tyr Arg Val Leu Ser
Tyr Leu 100 105 110Asp Pro Ser Glu Pro Arg His Ala Gln Leu Lys Asn
Leu Leu Phe Phe 115 120 125Met Leu Lys Asn Ser Ser Asn Arg Val Ile
Pro Gln Phe Glu Thr Thr 130 135 140Tyr Thr Glu Leu Phe Glu Gly Leu
Glu Ala Glu Leu Ala Lys Asn Gly145 150 155 160Lys Ala Ala Phe Asn
Asp Val Gly Glu Gln Ala Ala Phe Arg Phe Leu 165 170 175Gly Arg Ala
Tyr Phe Asn Ser Asn Pro Glu Glu Thr Lys Leu Gly Thr 180 185 190Ser
Ala Pro Thr Leu Ile Ser Ser Trp Val Leu Phe Asn Leu Ala Pro 195 200
205Thr Leu Asp Leu Gly Leu Pro Trp Phe Leu Gln Glu Pro Leu Leu His
210 215 220Thr Phe Arg Leu Pro Ala Phe Leu Ile Lys Ser Thr Tyr Asn
Lys Leu225 230 235 240Tyr Asp Tyr Phe Gln Ser Val Ala Thr Pro Val
Met Glu Gln Ala Glu 245 250 255Lys Leu Gly Val Pro Lys Asp Glu Ala
Val His Asn Ile Leu Phe Ala 260 265 270Val Cys Phe Asn Thr Phe Gly
Gly Val Lys Ile Leu Phe Pro Asn Thr 275 280 285Leu Lys Trp Ile Gly
Leu Ala Gly Glu Asn Leu His Thr Gln Leu Ala 290 295 300Glu Glu Ile
Arg Gly Ala Ile Lys Ser Tyr Gly Asp Gly Asn Val Thr305 310 315
320Leu Glu Ala Ile Glu Gln Met Pro Leu Thr Lys Ser Val Val Tyr Glu
325 330 335Ser Leu Arg Ile Glu Pro Pro Val Pro Pro Gln Tyr Gly Lys
Ala Lys 340 345 350Ser Asn Phe Thr Ile Glu Ser His Asp Ala Thr Phe
Glu Val Lys Lys 355 360 365Gly Glu Met Leu Phe Gly Tyr Gln Pro Phe
Ala Thr Lys Asp Pro Lys 370 375 380Val Phe Asp Arg Pro Glu Glu Tyr
Val Pro Asp Arg Phe Val Gly Asp385 390 395 400Gly Glu Ala Leu Leu
Lys Tyr Val Trp Trp Ser Asn Gly Pro Glu Thr 405 410 415Glu Ser Pro
Thr Val Glu Asn Lys Gln Cys Ala Gly Lys Asp Phe Val 420 425 430Val
Leu Ile Thr Arg Leu Phe Val Ile Glu Leu Phe Arg Arg Tyr Asp 435 440
445Ser Phe Glu Ile Glu Leu Gly Glu Ser Pro Trp Gly Ala Ala Val Thr
450 455 460Leu Thr Ser Leu Lys Arg Ala Ser Ile465
4701621DNAParthenium argentatum 16atggacccat cgtctaaacc c
211722DNAParthenium argentatum 17tcatatacta gctctcttca gg
22182564DNAParthenium argentatum 18aatccagcta agtctaactt gttaatattc
aactaaggta aattagttta tgtttgtagg 60aaagtaacat aaatttgccg ggtgtcacat
cttatgtccg attaacccct tactcaaccc 120aatactatag ccattgataa
ccttatctaa tctccttcct gtaattgtca ttcattgaac 180atgaaacacg
gatctatttt cattctcatg ttgttcaatt attcttttct cgttatatga
240ttcaaagagg tcaaacttct ctaagtttga gtgtggccac gcatttacac
cagtttggat 300caacgagggt cccagaatac acaacttttt tataataaag
aagaacagaa ttcctttgac 360aacatacaac tcccacttaa ccttaggtat
gctcccaacc aaataccctt attgttgtct
420tttcacgata cagtgttagg aaagattaaa gaacaaactt taggcaaatg
ttagttccaa 480tatgtctctc agttcaaagg acatttagat catatcaatt
tcaaaatatc acatgacttt 540gatctttaga gatcatttag aaacgagtta
cgtcaaatat cattctctaa tgtatatcag 600tgaacttggc cctcaacacc
tttagatttc atctcatgaa caaacaatca ctcacaatag 660tcataattcg
aattgattcc cttgaattcg attgactacg gacattttga atacttttat
720tcatgtatac ttaaacgtac aaaaattgaa catagcaaca caatttataa
tgcattcaac 780ctttaaatta aaataaagaa atgtagctat caattgttca
aagcaccaaa tactaataga 840tcaaaccact ctctagcatt ccttaaccct
atacgaggcg tataggtaca aaccaatgca 900cttattatgc agacatggga
aattgtgaac gtaacacgac ttgtataggg caatacgaga 960tgtatctggg
gcgtgtaaat aacgattgag ggtgtggaaa tattatggcc cttaaattta
1020agggatattc attgcctata aattatcgca aagcgggtat atattaaata
cttttctata 1080ttgtacccat cactatatat atatatatat atatatatat
atatatatat atatatatat 1140ataacctaca tgaaaatata taagcaggtt
atcttttaaa ttttataaaa ctgcttcaaa 1200attcaggcat acgagcataa
cgaaacttta taagatttat gtatgatttc ataacgaatc 1260tctatcaaaa
acatattcaa tcaagacaat gtgtagcata tgggttaatt acatgcacat
1320acacttcttc ataacattaa aaatttaaat ttaatattat tttataatgc
gtgtacaaat 1380caaacattgt tttaagttct tttatagcaa ctgtcacgtt
taaaatttgc tcaccgtaat 1440cagtaggaaa atattaaaag attataaaaa
cgaagtaaac aatgtataaa aaaataaaaa 1500gactagaacc taagggccgt
cagctcgtct ttatatacag tagttcattc atccaaatac 1560gcacaccatt
ttctcacact caacattttc tcacacaaac atggatccat catctgaagc
1620ccctcctcgt gaaatccctg gttcatacgg cattcctttt atccaaccga
tcaaagaccg 1680gttggagtat ttttacggga ccggaggccc agatgggttc
ttccagtccc gcgttcaaaa 1740ataccaatcc actgtgttcc gaaccaatat
gccacccggc ccttttataa gcagcaaccc 1800aaaagtcatt gtcctcttag
acgccaaaag ctttcccgta ttgtttgatg tttctaaagt 1860cgagaagaaa
gatttattta ccggaactta tatgccgtca actaacctca ctggcggcta
1920ccgcgtactc tcgtacatcg acccatccga acctagacat gctcaactta
agaacctctt 1980gttcttcatg cttaaaaatt caagcaaccg agtcattcct
cagttccaaa caacttacac 2040cgaactcttt gaaggtcttg aaaccgaatt
ggccaaaaat gggaaagccg cgttcaacga 2100cgttggtgaa caagcggctt
tccggttttt gggccgggct tatttcaact ctaacccgga 2160agaaaccaaa
ctaggaacta gtgcgccgaa gttaattacc acgtgggtgt tgttcaatct
2220tagcccgata ggcactgctg gacttccgtg gttcttggag gaccctctta
tccacacttt 2280ccgactgccg tcgtttctgg taaagagtaa ctacaacaag
ctttacgatt attttgagtc 2340ggctgcgact caggttgtgg agcaagcaga
aatattaggg gttccgaaag atgaagcttt 2400gcacaatatc ttattcgcgg
tttgcttcaa tacttttgaa aatacgcaaa caaagtaaaa 2460aataaaaata
aaagaaccta aggtacatcc tcgtctatat atacacttgt ttttattcat
2520ccaaaataaa cacaccatct tctcacactc aaaacagtca aaac
25641920DNAArtificial Sequencechemical synthesized 19aaccgcagtc
tacacgaaga 202020DNAArtificial Sequencechemical synthesized
20tcgaagaatt atccggcgtg 202120DNAArtificial Sequencechemical
synthesized 21tgtggcttgt ggagtgaaga 202220DNAArtificial
Sequencechemical synthesized 22accaccactg aaaccaccat
202320DNAArtificial Sequencechemical synthesized 23cttggtccga
agacgaacat 202420DNAArtificial Sequencechemical synthesized
24ggcttgaacg acgtttcttc 202520DNAArtificial Sequencechemical
synthesized 25ccgtcccaag cagttacaat 202620DNAArtificial
Sequencechemical synthesized 26tacgtgttca gtggttccca
202729DNAArtificial Sequencechemical synthesized 27cttaagatgt
ctgcacaatc ttttcagag 292832DNAArtificial Sequencechemical
synthesized 28ggatccttaa caaaaagcac aaaaagaaaa ac
322933DNAArtificial Sequencechemical synthesized 29cttaagatgt
taaagattga accaattttt gtt 333028DNAArtificial Sequencechemical
synthesized 30ggatccttag ttctgttctt ctttgggc 283128DNAArtificial
Sequencechemical synthesized 31cttaagatgg taacatatag gaggggtt
283231DNAArtificial Sequencechemical synthesized 32ggatccttat
gggttgtacc ttgctttaaa a 313321DNAArtificial Sequencechemical
synthesized 33cttaagaggt ggtatgtctg c 213426DNAArtificial
Sequencechemical synthesized 34ttaacaaaaa gcacaaaaag aaaaac
263523DNAArtificial Sequencechemical synthesized 35cttaagaggt
ggtatgttaa aga 233622DNAArtificial Sequencechemical synthesized
36ttagttctgt tcttctttgg gc 223721DNAArtificial Sequencechemical
synthesized 37cttaagaggt ggtatggtaa c 213825DNAArtificial
Sequencechemical synthesized 38ttatgggttg taccttgctt taaaa
25394884DNAParthenium argentatum 39gggttcttgt tgttttgatg tgtagttact
aataagccct ttatttttgc tgttagaatt 60cagatctttt tttttttttt taggaatccc
atttggttgg attgttttta ggtttagatt 120ttgatataca aaaaaaaaat
aatgtaaata taattttatg ttttgaataa atgtggtctg 180ctcatttcat
ttgagtgatt ggtttaatga ttttttgttg attgtttgcc aaaagtggaa
240atctttaggt ttattttttg ttattctgta aacattgttt ttgtgcatag
aatctttttg 300ttttgcctaa aatgaccaaa tgtttatgat atcataactg
cattcttagt ttttactata 360tttattactg aaaagatata tttttttttg
tagttgaagt ggctgatatt caagaattaa 420gagagaagca ctggcatttg
atgggtggtt ttacttttaa tgagcatggt gggataattg 480gagattggat
gccacctagc ccaagcccac gttctttatt cgcagctgtg ttgggtgatg
540aaatggggtc acggtcgggg tgtgggtccg agtctgaaaa gtttgagacc
ggtaatgatg 600gtgtgttcac ctttcctggg ccagataggc tcattgggtc
ggaacacggt gagggtactc 660aaaggggaga tatagttgat ccagtggcgg
aaccgggtga atttagagac cagaaagcgg 720gcccgcgggc tggtcttgtt
gaaaggatgg cagctagaac tggtcataat gctcctcggt 780tggatactga
ttttattaag cctgtgtatg gttcccaaaa ccaacaaact cagtcaccgt
840acttgactgt gtcacctggt ctcagcccgg gttcttttct ggaatcacct
gtttttctgt 900caaactcact ggtaagcgcg atagaacttt ttttttttat
aacatttaga gttatatata 960tgacgtgcag ttgtttggat gtgtgttttg
aagtgatttt gtgatattga gttgttggaa 1020tatcacgttt aggtatatta
ataattactt ttgaaggtgt cttgagggtt tggcaaattc 1080tgattgttta
gtaacaaatt aactaagagt gtgctagtca ttttactcta atatctattg
1140ataatcagtt atattttcga ctagtatcaa actgataatt taatcacttt
cagtatgcac 1200atgcaaacac ccccttaatg ccatgtttat gcaatccttt
ttgttcgtgt tttcgggttc 1260tcaattatat ttggaaatgt ttgataatga
atagttgttt ggaggttttt gtgtgttata 1320ataatgccaa atggtctcga
ttggttctta tgtaggttca accttctcca acaactggga 1380aattgcaatt
tgctccaaat ggcaacagta ttgataacat gagtaaagat aacttctttg
1440aggattctaa taacatttcc tttgccttta aacctttcct agattcggct
cctatatcct 1500ctgaccatgt aagcaaagta acatacattt ataattttta
tcttatattt tgtgtaaggg 1560tggtgagttc aacacatttg cttgtacatg
tgtccatttg ggctgtgttt tatctcaaac 1620gggtcaaata aaaaaaaaac
taaaaaggta agggtgaagt aggctgaaag tcaacctact 1680tttatttgaa
ggtatatgtt agtattttaa tacatgttgc tttccattca taattaacac
1740actatttttt cgtgaaaacg gacaaaaagg gtttgtgggt caaaccggtc
tgttttgatc 1800cgtattaaga tgacctgctt ttacccgaag tcatttgact
tgttaactat attttatgta 1860ttaagtttct tagatacatt atcctcttta
tagtcttcaa ctgctgatgc tgtttcctct 1920ccgattattt aggtcaatgt
caatccacct tttatgtctg cacaatcttt tcagagtaat 1980gaagctttta
cccaacctga ggaacaattt cagcctcaaa agagtgaacc ggcccaaatt
2040tactcagact ttactgaaag gaagaacttt tcgctacaaa tggctccatt
tgaagctcgt 2100aatggcaatt ctgatctgac tcaacagcat catgataaac
atcacgatga gattgacgca 2160gatcagagta taaatggaga tattactaat
gctagcagtg catcatctga tgatgggtat 2220aattggagaa aatatggaca
gaaacaagta aaaggaagtg agtatcctag aagctattat 2280aaatgcactc
acccaaattg tactgttaaa aagaaagtcg agcgttcttt tgaaggtcat
2340attactgaga ttatctacaa aggggcccac aatcacccta aagttgctcc
tacccgcaga 2400tcggcgattg ggtcctcaag tgtgctgagt gatataagtg
aactaactgg gaatggagtt 2460gagggtggtt ctgtttgggg gacaaatatg
caacagaagg gtggaggtaa ttgggggcaa 2520gaaagtaatt ttgaggtgac
atcatcggcg atggttatgc agggtcagaa tggtcaatat 2580gaatctagtg
atgctgttga tgggtcatcc actttttcta atgatgaaga agatgaccgt
2640gcaacacatg gcagtgtatc acttggttat gatggtgaag gagatgaatc
tgagtctaaa 2700agaaggttcg actgtttttc tttttgtgct ttttgttaag
tgattataac cgtcatcgat 2760ttttgctgtt ttagtaacct atttctgcgt
atgattatct aattatatca ggatgagatg 2820actggataca gtttttgctc
aaagtatgta atcttaatta atatataatt aatttatcaa 2880atgtatcatt
acaaaatcta tactatttta aaaatgatat attttttaat taaacgtttg
2940aggaggttag tgtgttaaaa ttacagtttg ggcaactttt gacccatgtt
tgttttagct 3000ttttttattc tacctatttg accgttggtg agggaaaaaa
aaaacaccca acacctccct 3060tgtaaatttt aattatttgt ttcaacttta
agacacattc aaacactatt tcttgtaacg 3120atttttgtta aagcttatga
tttgcttgtg attattatat ttcatacacg tcactttcaa 3180gatgcatatc
caaacactcc ctaatcctta actgtatgat gttttagaaa agttgaagca
3240tatgcagcag atgtaagtgg cgcaaccaga gcaatcaggg aaccaagagt
tgttgttcaa 3300actaccagtg acgtggacat tttggatgat gggtatcgct
ggcgcaagta tggacagaag 3360gtcgtgaaag gaaaccctaa cccaaggtca
tcattttgtg ctgttatgta tctgttatct 3420aacttagctg tgaattggtt
agacgtagca aaatgggcgg gtcaattgtg tttgggtcaa 3480ataaggagtt
cctaaacgcc aggtaaattg ggtcaggtcg gtcttctgga caaagcttct
3540gccctataaa gcgaaatttt ctaataaaag gatgtaggat gttataagcc
tccggagtat 3600atgttggcaa cttaggcccg cctcccttca aattgtgtct
gaatttttcc cattttttgg 3660tttataaatt gtgatgtcaa ttgtttagat
gtggcaaaat ttgtgggttt agatcgaaac 3720gagtttcttt tggtaccagt
cagggtcagc ccatatctgc tatttttcct ttttcttact 3780ttttcgatat
ggattaaata tgactacaaa gttaaacatt aaaatggtaa tttaatttat
3840taataatatc atttatagtt tcatcaaaat gagcaacttt tggtaccaag
ttcttgaaag 3900tgcccgtttg acccattgac ttaattatag atatatattt
tttttgtttt tttttttttt 3960ttttgaaata aattgttttt tatggcacag
gagttactac aagtgcacaa gcacaggctg 4020cacagtgaga aaacatgtcg
aaagggcatc acatgaccta agatcagtga taacaacata 4080cgaagggaag
cacaaccatg atgtcccagc tgcccgtaac agcagccata acaacaacac
4140cattcagcct caagttcaaa tgcccgggct atctcgtggt caaaacacca
tgcctcggct 4200cgaaaggcct ccctatggtt tacccaatgg tcagcacctg
ggttctgctc caacccatgg 4260ctatggttac caaatgaacc aacaaggacc
aggagggcta gcccatatgg ccatggccaa 4320ccaagggaga atgcctgttc
ttcctcttca tcactatttg aatcaaccac aacaaatcaa 4380tgaaatggga
ctgatggtgt caaaaggtga gccgaaggtg gagaccatgt ctgatcctgg
4440cctgaaccta gccagtggtg cagcgattta ccatcagatg atgaaccggt
taccgcttgg 4500acatcagatg taaagtttga tagaagtatg cattcttttt
ggcaaagagt agaatattta 4560aacttgatat cacattatct tttttgttac
aactttaggg gttttcttgt tttttaagta 4620tttatttcaa gaatttgaag
ctatattggt agaaggttat tatcatttat acaacagttt 4680aattttaata
gaaattttat gtcagattta acatgagtct gtctgatagt ggcactccat
4740ttatccttca cagaaatgtg tgggccctcg atgagcaaaa ctgaattgca
ccacttttaa 4800attgcactac gtgaaaataa cgttaaaagc ggcggacggt
taatcatgca tcatgtggtg 4860gcgttagtag ccaaaagaca atgg
488440786DNAParthenium argentatum 40atgtctgcac aatcttttca
gagtaatgaa gcttttaccc aacctgagga acaatttcag 60cctcaaaaga gtgaaccggc
ccaaatttac tcagacttta ctgaaaggaa gaacttttcg 120ctacaaatgg
ctccatttga agctcgtaat ggcaattctg atctgactca acagcatcat
180gataaacatc acgatgagat tgacgcagat cagagtataa atggagatat
tactaatgct 240agcagtgcat catctgatga tgggtataat tggagaaaat
atggacagaa acaagtaaaa 300ggaagtgagt atcctagaag ctattataaa
tgcactcacc caaattgtac tgttaaaaag 360aaagtcgagc gttcttttga
aggtcatatt actgagatta tctacaaagg ggcccacaat 420caccctaaag
ttgctcctac ccgcagatcg gcgattgggt cctcaagtgt gctgagtgat
480ataagtgaac taactgggaa tggagttgag ggtggttctg tttgggggac
aaatatgcaa 540cagaagggtg gaggtaattg ggggcaagaa agtaattttg
aggtgacatc atcggcgatg 600gttatgcagg gtcagaatgg tcaatatgaa
tctagtgatg ctgttgatgg gtcatccact 660ttttctaatg atgaagaaga
tgaccgtgca acacatggca gtgtatcact tggttatgat 720ggtgaaggag
atgaatctga gtctaaaaga aggttcgact gtttttcttt ttgtgctttt 780tgttaa
786413124DNAParthenium argentatum 41cgaaaaccca tccgagggga
ttccgcaccc tcgcgactga aaaccgcggt aatccggacc 60cgtaaggcgc gtccgaaacg
gtcctacata ttatatttct atgtttaaac gacatgttta 120atactcggtt
gtcgtgctta tctttatata cgttttgctc taaatttgtt cgaaaaattt
180ggtttttgta tacaataact taacttttcc atgattttct aatacaccat
cgcgacgtaa 240ttttttatca tcacgtggag cgcgacgata acttactagt
tataagttaa taaccaaaaa 300aaaaaaatgg ttatgaataa caattattta
tgaaaagaaa aaaataggca tcatatacca 360ataagcataa atcaatacaa
cgtttgtttt atcagggatg aatcaacttt ataattttat 420atattgagtg
attgaattga agactcataa gaggatcaaa tgcaatttat tgttagttag
480ggaagcaagg tgttattgac ccctaaattc ccaaacggta acacacccca
ccccaccccc 540aacatctctc tctctctctc tctctctctc tctctctctc
tctctctctc tccacttttt 600atataccaat tatccaaaaa ggcaaaaacc
ctcttcacac tatactcaaa aataacctct 660ctttctctcc atctctctct
atatatctcc atctatccct aaaataaaga atccatgcct 720ttgatcagtc
catggaaaac aactcagagt caaacaacaa ctcaaacaat tcaaacataa
780tgacaagcac agcattttcc gatcatattc cggcaaccta tggtggtaac
ttttttgata 840tgttaactta tcaggacgac ggtagctcat gtctctttga
tctgcttcaa caacctgctc 900ctcctttgaa cttggtaccg gaaaataata
ataataataa taataataat aataataata 960ataataataa taataatctt
ctaccaccag tggaaatggt gaatacaccg acacaaaact 1020cttcttccgt
atcatgttct tcaaatgatg ttgatcagga gaataaaagc agatctgttc
1080atgaagaaga tgatgttcat gatggtgatg atgatcaaga aaagagtgct
actaataaac 1140agtaagaaca ctagttttgt ttagttttga acacacacta
tcgggtgtgt ttttatgtac 1200tttgctaact gtgtgttttt cacacactgt
ttggtgtttc ttgtgtgtgt tttttacact 1260taaatgagtt tttatgagtt
tgtgtgtgct gtttatcgca tccattattg ctagatttat 1320attaagaaaa
tatcattcta taaaattagc acacacttat ggtggtgtgt gtgtgtgtgt
1380atttggtgtt tttgtttgtg tttttaacac acatgagttt ttatgagttt
gtatgtgttc 1440ttcatcaaat caatcatgct taatggatat caagaaaata
tttttcttca aaactagcac 1500acacttatgg tgtgttatta tttttttatt
tttatttttt tgtgtgtgta tatggtgttt 1560cttgtgtgag tttttcacac
acacatgagc ttttatgtgt ttgtatgtgt tcttctttaa 1620atctatcttg
ctaaatgaat attaagaaaa tatctttcta caaaactagc acacactttg
1680gtgtttgtgt gtttgtgtat tgatgattaa tctttcattt ttctattatt
gttggttgtt 1740cacatacaca tgaactttta tgagttcttc attccttctt
cattgccagt aaatgaaatc 1800aagaatttaa gaaaagttat attccactaa
ataagtgtaa ttcctgtgta tttttcaggt 1860attaaatcag tggtttctgg
ccaaaaaaaa aaaaaaaaaa aaagaaaaat cattaatttc 1920ttgtttcaca
cttacacgtt ttcttcaagg tctttaattt gaccaagaat agttaggtcc
1980ttttcacaca catatacaca cccaaaacta gatttgatga ccaggtcttt
agtggtgcac 2040cagttttcta gatttaataa gtctttattc ttctttctcc
ttatcgtttt atttcttaca 2100aaatatttta tcttattctt cttttatata
tatatatata tatatattat gtcgtttatt 2160cttgaactaa aatgtggctg
tttcactgtg ttgcgtaggt taaaacccaa aaagaagaat 2220ccaaagaagc
aaaggggacc aagatttgca ttcatgacta agactgatat tgatcacttg
2280gatgatggtt atagatggag aaagtacggt cagaaagctg tgaaaaacag
cccttttcct 2340aggtgtatac tctctctttc tctctagatt ccatctcttt
ctctctctac acccttgttt 2400gagttgccct aacatatgac tatatctata
tcctttggag tttgatccat tcataccatg 2460taattaaaga tagttcatac
ttcttttatg gttattttca attaaacgag tcgcgttcat 2520atagatattg
atatggtatc gacataaaca cacatcgtgt tgtattagat tgacatggta
2580taaatttgaa aacacatata tacacaatca tccatcatat atgttaaaga
ttgaaccaat 2640ttttgttgta caaaatagga gttaccatag gtgcacaagt
gtggcttgtg gagtgaagaa 2700gcgagttgaa agatcgtctg atgatccatc
gatcgtgatc acaacttacg aaggtaccca 2760cactcatctg catccgatta
tgcctcgagg aaacattgag atcttgtcgg agcccaccgg 2820tcatggtggt
ttcagtggtg gtggtagtaa tagtggtgtt acttcttttc tttttacaca
2880gcttcacaac caacaccaac aaccacaact actaccctat gtccatcacc
aaaccacacc 2940atcatcttct ctaggcttta acaccactat tgatagtgca
catcaatcat catactccca 3000tttacttcac gaaagacgat ttttcccttc
atcttcttct acattgctta gagaccatgg 3060actactagag gatgtcatcc
aattccagtt tcagaaagat aagcccaaag aagaacagaa 3120ctaa
312442504DNAParthenium argentatum 42atgttaaaga ttgaaccaat
ttttgttgta caaaatagga gttaccatag gtgcacaagt 60gtggcttgtg gagtgaagaa
gcgagttgaa agatcgtctg atgatccatc gatcgtgatc 120acaacttacg
aaggtaccca cactcatctg catccgatta tgcctcgagg aaacattgag
180atcttgtcgg agcccaccgg tcatggtggt ttcagtggtg gtggtagtaa
tagtggtgtt 240acttcttttc tttttacaca gcttcacaac caacaccaac
aaccacaact actaccctat 300gtccatcacc aaaccacacc atcatcttct
ctaggcttta acaccactat tgatagtgca 360catcaatcat catactccca
tttacttcac gaaagacgat ttttcccttc atcttcttct 420acattgctta
gagaccatgg actactagag gatgtcatcc aattccagtt tcagaaagat
480aagcccaaag aagaacagaa ctaa 504435769DNAParthenium argentatum
43gtaaaaagaa attttgtatt tttatgtttt tttttcgagt ttttgcgttt ttttttcttt
60tgttctcacg gttctcacga tatttagtgt tctcaaagta accctccctt ttatatatat
120atatatatat atatatatag acacacacac tctgaagata ggtgattcta
gtcatataaa 180tgttatcctt tttattgtag gtatgcaaat tgtaaaaaag
aatatccatc caatcattta 240ttcttaggtt tatatccaat tttgttcaaa
accccacctc ccaccacaca tatatcatca 300tcattatttc ccttggtgcc
aaacctaaga cttctctatc tttctctctt tatgtgtgct 360ttttaggtgt
tgaatgattg tgggtcattc ttacttcttt gttttagtaa tacaactttg
420agcgaaaatg gggagaaagt gctcacactg tggaaacata ggccacaatt
caagaacttg 480cactagttac aatagaagca atgtcaatag cacaattttg
gtaggtggtg ctggaggagg 540attaaggcta tttggagttc aacttgactc
accacactct atggtcatga agaaatgtct 600tagcatggat tgtttgccat
ctagctcacc attaccggct tcggtttcat cttcttcttc 660ttctttatct
tcatcgcggg tctccatcaa tgacctaacc gaaaagaata tgtcggttgg
720ttatctctca gacggtctca ttgcccgcgc tcaagaaaga aaaaaaggta
tgcaaactta 780ttatatatct actattagtt acttaaatca tgaatgacta
ctaaattggc tatgaaatat 840atctttatgt tatgttatgc tatattatgt
tatgtcacgt acattgtgat tgacatgcat 900gtgtttcatt tcaagattca
catgtagaga taaaagaatg tagatttcaa tggtaacata 960taggaggggt
tgttttatag gtctcccttg gtccgaagac gaacatcgta gatttctagc
1020cggacttgag aagcttggaa aaggtgattg gagaggaatt tcaagaaact
ttgtgaccac 1080aaggacacct acacaagttg caagtcatgc tcaaaagtac
ttcctccgcc aagcgagtct 1140tgtcaagaag aaacgtcgtt
caagcctctt tgacttggta cgtatttttg cattgcaatt 1200gtactttgca
attaaaggct tgtacatacc accctcaaac attagtctat tgaaggcctt
1260tcaccataca atgtttccat ttggccatga ggcttttaaa gcaaggtaca
acccataatg 1320caataggtaa caaccctata atgcaaaaaa gccgtaaatc
caaattacgg aaattactaa 1380accatgtgcg tctttttata tataaagaaa
tgtaaagtgt gcctaaatta tagttgcatc 1440ttggtggtca caggtgaggg
acaagaatgg gcaacagaat caaataaaga attgcaatat 1500gagtcgaaca
agctcattcg aggatgaata tgaagaggat cataacaata atctttcttt
1560gattgatttc ggttctctaa aacaagagaa gggccacttc aatccgatga
tcaaatccta 1620tgaaacatca ttatcatcaa cgtgttatgc gcctccaagt
ggtacgcttg atttagaact 1680tacccttgct gctcccaacc cgatgaatca
gaacaaatcg tctaccacct ccctccaact 1740cggtccgatt attagtgtta
tttagggata cgtttgatct gacacttttc atatgttaat 1800tcatgttgaa
caatctaatt atgatcaaat gttgtagata ttttcttgaa ttttgagacc
1860tttgacacgg gtcttgtact ccggttagat aatatttttg taactacaaa
tttatatgta 1920tgtactctat taaattagga taaaatcaag agaataatct
tttttttaag ctacaaattt 1980cacatatcta ttttattttc atatatcatc
ataacactca gttttcaaga aaaatatatt 2040agctagatgt gccaaaataa
aataaatata tgaatagtag acatacgaat gaaaaagtga 2100aaatttactt
tggtgataag aaaaatatac ttctttcttt tataatgata tccatatcat
2160ggacccatta ttttatttta ttgtaaaaaa aaggacccca atatcaatgt
caatacctaa 2220ttactctcaa gccatgaaac acgaagttta ctttaaaatt
ctcggtgttt aattatttat 2280atatgtttta gaaactaatg ataaaatagt
aataaaacta ctcccaaatt ctaagaagct 2340taataagaat ttggtgaccg
gaaattggtt atctaagggt tatgttttta accaaatgtt 2400atgtgtgtat
tgggggtcct ctataaatta gtaacatatt tatctaaaaa gactatgcaa
2460aaagatgcaa cctagaacaa gtgtgttatg catataatct tccaagtcga
acgctaatta 2520gcctcgtctt tggtcctgat taacccggaa acagcactaa
agtggaattt tatgcaagaa 2580ttgaaactaa aaggttgttg gaaaaacaag
tgtatgaaaa gatgatacaa tgtaacaaag 2640gtacctaaac cttggattta
gacaagaatt gggtgcagaa atggaccact ttaacaaaga 2700gttgtaccct
ttgtatcaga atttgttcag tatcctgcaa caggaagctg ttaagattaa
2760gacctaagaa ttgatgtgtg gaccttctta gaggatgaag acaagatgga
aagatacaat 2820caatctgaga aaagatttta gatgggtcta gctttataat
gcaagcatct gtctcattat 2880agttcaatcc aacatgatga acaagaatca
aagaaagata tttttagggt ttgaaaatga 2940tagatacgtt taacttggac
aaatttatta attttgatta tctaaaatct aataccccgt 3000taatcaataa
ataaagatct ctttatcaat ctaccatata gtctttgata gatagccagt
3060gaaagtcagg tatgctagca gttttttgtg cttatttggt cacctttgga
aagttggttt 3120cttgtttata accataggac caccaatacc ccgttaatca
ataaataaag taaagtaaaa 3180agcagcttgc gctagacagc tgatctttga
gagagttaag acaacgccgg tggaaactga 3240attcggatat gagacggcct
ccgctgaata cacttaaacg tttactatta agacaccact 3300taataatttt
catatttcca ttcaccccta aaattaaatt attcctcaaa tcaagtcttt
3360ttgttcaata aagccaaact tccataagaa ttaacaatat cgtgtcttca
aagttcaaac 3420cacaaacact aaccccattt gatattttcc catatgtgaa
gtaccaactt ggctcatcag 3480aagttaacca ctctcattaa gtctcttgtt
ttattatcat attcttgaat gtgcgctttt 3540atgaaacagt gacatataaa
aaaacaaaaa cctctgtctg ctttactaac cgattctagg 3600atgtctttta
ttatttttat ttttttattt tcatttgtgt ttgttttcat cttatgtatc
3660atcatttgta ttcacatgtt tttgtgtgga ggatacacct ttgtcctaac
catcaaagta 3720acggtgtaaa tgaatccaac tcctaagagt tcctcaagat
taacatgttt taaggttgaa 3780tcgattaaac aacttcaagt cgagataatc
ataagtaaag ggtactaggg acatcataag 3840taaagggtac tagggacact
acccttaccc taatggctcc gattaataag ggataaccac 3900ctcattttta
atcaaatcca acgtagcact agccaaagca tcctattttt atttattttt
3960ttcaatttta aagattaaaa ctaatatata cttaaaaaca caaatattaa
taaatttctt 4020aactaaaaca agcataacaa agtataaaac attaaaacat
aaaaacatct aaaaataaaa 4080attacaaaaa tgtttaatta atcgccgatg
tgcatttttg tatcgttgtg aaactctttt 4140atcatcatca cgtctagacc
tcttgcaacc attccgtttt taaagataac tcttcgacat 4200aagaaacttg
aacgaaaagt agcttcatcg tattttggcg ggcgaaataa tcttccatta
4260gatcctctag agcttttgca tgatcacgtg gcacattttt ttatgttgcc
gttgtctact 4320actttggctt gagcggcaac atccgtgaga atatggaggc
tactagatac gcctccgttc 4380aagtcaaacg catccgatga atcaaatgga
agtcataact taagattaat tttgtgatgc 4440aaagtttgaa tgcaaaatta
tttgtagata tgagagtatg aaatcggtat tttgggtgta 4500caaaagtaaa
tggagatgag tttattttag gtgtggtaaa gttggtattt atcaactcat
4560gagtgaatct tggactttag acagagtttg aaacaaattg cgctcgaatt
tcaaaagcca 4620aaccccctta agttaaagga gcggacgcaa cctacacatg
ctgacatgct cacttgaaca 4680aagattcata aattaagttt tattacttat
gttgttcttt cctttttata cattacatgt 4740gttggttcac cagatgtttt
acaaggttgt ttttgatgtt ttacccaaca ttgttgtctc 4800ccacctcttt
catttcacct cttctttttt acgtttatct tatttcacat tttcgtttta
4860taattccgac atcttcatac taattatttt aaaataaatt attcaattca
tgtaatacat 4920cattatacat gggcatctaa cctcgtgtgt gtgcgcacgc
acccgctcat gtgtgtatat 4980atatttagag agagagagag agagagagag
agagagagag agagagagag agaagggcgt 5040tggacggtgg tgccaggtgg
cccggggtcc tcctcagtcc tcaccatgag attgtgcggg 5100atgggaccag
ggaggggaca caatgttccc acaagccctg caaggacgtg gaaccttctt
5160gcgcctttcc ttgaaaccat aacacatggc ctaagttata cctatatctt
aaattaattt 5220aagagactcg ttaatcaatc acaattctca aactatcatg
ataattaatt tttgtacgac 5280atgaaggcgt ttgatatttt tatgaagatt
gaattatctg ctaagagagc taagagatac 5340tgataacact attgtataag
tttattccat ataatctata ctatattata atagatttga 5400ggaaaatgca
attgtctttt tttttacatt aatttttaag agtttaagga gttaattttt
5460ttttttttat atatataaaa tatcatcata aaaatgctcg acccacatta
ccattactta 5520acgaggtaaa atgctatcat caacatatct caagattatt
tgcaaacaca atgttgtaga 5580cttaataaac acacgatcgt acatcatatt
cacatttctt ttatccgaga tcatcacaga 5640gtataattgt ttcattttca
tttcgtattg tagaaactta tacatacttt attgagagat 5700cataatcacc
atatgcttat tccttcatag aaatttacat ccccaaaatg tatgctttta
5760agcactaaa 576944369DNAParthenium argentatum 44atggtaacat
ataggagggg ttgttttata ggtctccctt ggtccgaaga cgaacatcgt 60agatttctag
ccggacttga gaagcttgga aaaggtgatt ggagaggaat ttcaagaaac
120tttgtgacca caaggacacc tacacaagtt gcaagtcatg ctcaaaagta
cttcctccgc 180caagcgagtc ttgtcaagaa gaaacgtcgt tcaagcctct
ttgacttggt acgtattttt 240gcattgcaat tgtactttgc aattaaaggc
ttgtacatac caccctcaaa cattagtcta 300ttgaaggcct ttcaccatac
aatgtttcca tttggccatg aggcttttaa agcaaggtac 360aacccataa
369451257DNAArtificial Sequenceanti-sense
RNAmisc_feature(1161)..(1161)n is a, c, g, or t 45ccatggccgc
gggattcgcc ggaaaagttc aatcacaaac aacctcgtta taagcacggc 60aaagtctttt
ccggcacatt gtttattttc aactgatcgg actctctgtc tccggcccat
120tagaccacca tacgtacttc aacaatgcct cgccatcccc aacgagccga
tcagggacat 180attcctcagg tcggtcaaat acttttgggt ccttggttgc
aaacggttgg tacccgaata 240acatttctcc ttttttgact tcgaaagtgg
cgtcgtgtga ctctatggta aagttgcttt 300tggcttttcc atattgcgga
ggcactggtg gatcccccgg gttaagagga gtccaccatg 360agcccagaac
gacgcccggc cgacatccgc cgtgccaccg aggcggacat gccggcggtc
420tgcaccatcg tcaaccacta catcgagaca agcacggtca acttccgtac
ggagccgcaa 480gaaccgcaag agtggacgga cgacctcgtc cgtctgcggg
agcgctatcc ctggctcgtc 540gccgaggtgg acggcgaggt cgccggcatc
gcctacgcgg gcccctggaa ggcacgcaac 600gcctacgact ggacggccga
gtcgaccgtg tacgtctccc cccgccacca gcggacggga 660ctgggctcca
cgctctacac ccacctgctg aagtccctcg aggcacaagg cttcaagagc
720gtggtcgctg tcatcgggct gcccaacgac ccgagcgtgc gcatgcacga
ggcgctcgga 780tatgcccccc gcggcatgct gcgggcggcc ggcttcaagc
acgggaactg gcatgacgtg 840ggtttctggc agctggactt cagcctgccg
gtaccgcccc gtccggtcct gcccgtcacc 900gagagatctc tagtgattgg
atccaccagt gcctccgcaa tatggaaaag ccaaaagcaa 960ctttaccata
gagtcacacg acgccacttt cgaagtcaaa aaaggagaaa tgttattcgg
1020gtaccaaccg tttgcaacca aggacccaaa agtatttgac cgacctgagg
aatatgtccc 1080tgatcggctc gttggggatg acgaggcatt gttgaagtac
gtatggtgat ctaatgggcc 1140ggagacacag agtccgatca nttgaaaata
aacaatgtgc cggaaaagac tttgccgtgc 1200ttataacgag gttgtttgtg
attgaacttt tccggcgccg cgggggagct cggatcc 1257
* * * * *