Download Cdiff_expression_supmat_BiolInv.

Electronic Supplementary Material 1
for
Gene expression and drought response in an invasive thistle
Kathryn G. Turner1,2, Kristin A. Nurkowski3, Loren H. Rieseberg3,4
1
Department of Bioagricultural Sciences and Pest Management, Colorado State University, 1177
Campus Delivery, Fort Collins, CO 80523-1177 USA
2
Corresponding author; [email protected], voice 970-491-5261, fax 970-491-3862
3
Department of Botany and Biodiversity Research Centre, University of British Columbia, Room
3529-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada
4
Department of Biology, Indiana University, Bloomington, IN 47405 USA;
[email protected]
Figure S1. Observed niche overlap between native and invaded ranges of Centaurea
diffusa.
Putative climatic niche expansion as determined by principal components analysis of WorldClim
bioclimatic data from 662 occurrence locations in the native and invasive ranges of C. diffusa.
Shaded area represents 99% confidence ellipse for each range. The centroid of each niche is
marked by a large point. The first two principal components explained 32% and 27% of variance
among occurrence locations respectively. PC1 is most strongly correlated with precipitation in
driest month and quarter. PC2 is most strongly correlated with precipitation of coldest and
wettest quarters. Modified from Turner et al. (2015).
Figure S2: Heat map of genes with drought-induced expression differences between native
and invasive Centaurea diffusa for the drought treatment from time point 2.
A heat map of the 227 induced differently expressed genes for drought samples only from the
final time point. All genes had a significant range-by-treatment interaction, determined by mixed
model analysis. Normalized, scaled, expression values are displayed. Both the genes (rows) and
samples (columns) were clustered using dendrograms constructed using Euclidean distances and
hierarchical clustering. Range is displayed in the colored bar above the heat map (red for native
populations, and black for invasive). In the drought treatment only dendrogram, two samples of
invasive population US001 cluster within the native range samples, close to samples from
populations in Turkey and Bulgaria.
Figure S3: Heat map of genes with drought induced expression differences between native
and invasive Centaurea diffusa for the control treatment from time point 2.
A heat map of the 227 induced differently expressed genes for control samples only from the
final time point. All genes had a significant range-by-treatment interaction, determined by mixed
model analysis. Normalized, scaled, expression values are displayed. Both the genes (rows) and
samples (columns) were clustered using dendrograms constructed using Euclidean distances and
hierarchical clustering. Range is displayed in the colored bar above the heat map (red for native
populations, and black for invasive). In the control treatment only dendrogram, all invasive
populations cluster within a branch that contains samples from all native populations (Bulgaria,
Turkey, and Russia).
Table S1: Centaurea diffusa experimental population information.
Population
ID
BG001
RU008
TR001
CA001
Range
Latitude
Native
Native
Native
Invasive
Collection
year
2008
2006
2008
2008
43.38194
44.05
41.75111
49.01494
US001
Invasive
2008
US003
Invasive
2008
Longitude
28.4575
43.06
27.24778
-122.882
Environment
(PC1 value)
-0.4691047
2.5006967
0.1627519
-5.6572239
Shoot mass (g)
(mean ± SE)
3.437 (±0.215)
4.417 (±0.327)
2.468 (±0.188)
4.016 (±0.106)
45.61523
-120.788
2.4523743
3.547 (±0.116)
46.60415
-116.642
1.0105056
3.516 (±0.292)
Voucher
Accession
V236763
V232687
V236765
V232677V232679,
V232704 V232706
V232694 V232697
Vouchers are located in the University of British Columbia Herbarium. Environment term was
determined by principal components analysis described in text, and was used in all mixed model
analyses. Population mean shoot mass was assessed from non-experimental plants grown at the
same time under the control treatment conditions as experimental plants, from dry-weight
aboveground biomass after approximately 19 weeks of growth, and were first described in
Turner et al. (2014).
Table S2: Abiotic environmental data variables used in principal component analysis.
Bioclim variable
Annual mean temperature
Mean diurnal temperature range (mean of monthly (max temp – min temp))
Isothermality (BIO2/BIO7)*100
Temperature seasonality (standard deviation*100)
Max temperature of warmest month
Min temperature of coldest month
Temperature annual range (BIO5-BIO6)
Mean temperature of wettest quarter
Mean temperature of driest quarter
Mean temperature of warmest quarter
Mean temperature of coldest quarter
Annual precipitation
Precipitation of wettest month
Precipitation of driest month
Precipitation seasonality (coefficient of variation)
Precipitation of wettest quarter
Precipitation of driest quarter
Precipitation of warmest quarter
Precipitation of coldest quarter
Altitude
Latitude
Code
BIO1
BIO2
BIO3
BIO4
BIO5
BIO6
BIO7
BIO8
BIO9
BIO10
BIO11
BIO12
BIO13
BIO14
BIO15
BIO16
BIO17
BIO18
BIO19
ALT
LAT
Data taken from WorldClim dataset, current conditions (interpolations of observed data,
representative of years 1950-2000) from ~1km tiles numbers 6, 7, 11,12,13,15,16,17,18
(Hijmans et al. 2005).
Table S3: Results from likelihood ratio tests for genes with significant model terms.
[Selection only.]
Contig
Name
TAIR
Accessions
Range-byTreatment
Range
Treatment
Contig100
AT1G51470,
AT1G21065
0.579277
1
0.001302
1
Contig10001
AT5G39820,
AT3G59140
0.356843
1
0.007906
0.64572
PC1
GO Terms
GO:0008150, GO:0009507,
GO:0004553, GO:0008422,
GO:0009651, GO:0009651,
GO:0012505, GO:0019137
GO:0003700, GO:0005575,
GO:0006355, GO:0006355,
GO:0007275, GO:0005774,
GO:0005774, GO:0005774,
GO:0006810, GO:0042626,
GO:0042626, GO:0055085,
GO:0055085
Results from likelihood ratio tests (LRTs) are reported for each fixed effect term in mixed effect
models of gene expression, for all 11,047 genes with at least one significant fixed effect
(α=0.05). Random effect of population was significant for 9988 genes (not shown). Q values
corrected for multiple comparisons are reported for each fixed effect. TAIR 10 accessions (The
Arabidopsis Information Resource; arabidopsis.org) and GO term mappings are included where
possible. [Selection only, full table available at http://dx.doi.org/10.6084/m9.figshare.1372537
(Turner et al. 2015), or in associated Dryad repository.]
Table S4: Gene Ontology terms for genes with a significant effect of seed collection
environment (PC1).
GO.ID
Term
P-value
GO:0006506
GPI anchor biosynthetic process
1.70E-05
GO:0009247
glycolipid biosynthetic process
7.10E-05
GO:0010260
organ senescence
GO:0030091
protein repair
0.00055
GO:0007568
aging
0.00111
GO:0042780
tRNA 3'-end processing
0.00185
GO:0007154
cell communication
0.00188
GO:0000255
allantoin metabolic process
0.00239
GO:0006664
glycolipid metabolic process
0.00388
GO:0010467
gene expression
0.00407
GO:0060560
developmental growth involved in morphog...
0.00415
GO:0006661
phosphatidylinositol biosynthetic process
0.00424
GO:0016070
RNA metabolic process
0.00495
GO:0006629
lipid metabolic process
0.00525
GO:0010275
NAD(P)H dehydrogenase complex assembly
0.00539
GO:0006505
GPI anchor metabolic process
0.0062
GO:0007165
signal transduction
0.0065
GO:0050665
hydrogen peroxide biosynthetic process
0.00691
GO:0044700
single organism signaling
0.00695
GO:0006354
DNA-templated transcription, elongation
0.00727
GO:1903409
reactive oxygen species biosynthetic pro...
0.00765
GO:0055114
oxidation-reduction process
0.00819
0.0001
Results of Fisher’s exact tests examining the number of gene associations with GO terms. Genes
of interest were determined in mixed model analysis to have a significant effect of composite
abiotic environment for seed collection location (PC1). Environment of the collection location
was a significant covariate for 1111 genes. Ontology type is biological process (BP) for all
terms. Analyses of genes with significant environment effect were limited to the type ‘biological
processes’ as the set most likely to have implications for the evolution and ecology of this
system. The analysis was conducted using the Fisher algorithm and parent-child method, and Pvalues for this test are reported. Of the 1111 genes with a significant environmental covariate,
734 had ‘biological processes’ GO annotations. When this set was analyzed for GO term
enrichment, 22 GO terms were significantly overrepresented (Supplementary Material 1: Table
S5). We found that this set included many metabolic processes, and as well as organ senescence,
aging, and protein repair.
Table S5: Gene Ontology terms for genes with a significant effect of drought treatment.
[Selection only.]
GO ID
Term
GO:2000112
regulation of cellular macromolecule bio...
P-value
< 0.0001
GO:0010468
regulation of gene expression
< 0.0001
GO:0031326
regulation of cellular biosynthetic proc...
< 0.0001
GO:0010556
regulation of macromolecule biosynthetic...
< 0.0001
GO:0009889
regulation of biosynthetic process
< 0.0001
GO:0032774
RNA biosynthetic process
< 0.0001
Results of Fisher’s exact tests examining the number of gene associations with GO terms. Genes
of interest were determined in mixed model analysis to have a significant difference between
control and drought treatments. Ontology type is biological process (BP) for all terms. The
analysis was conducted using the Fisher algorithm and parent-child method, and P-values for this
test are reported. [Selection only, full table available at
http://dx.doi.org/10.6084/m9.figshare.1372537 (Turner et al. 2015), or in associated Dryad
repository.]
Table S6: Genes previously identified as part of the drought response gene regulatory
network in domesticated sunflower (Helianthus annuus) and also identified as responding
to drought in Centaurea diffusa.
TAIR
Accession
Name
AT1G10940
SNRK2.4
AT4G35090
AT4G21960
CAT2
PRXR1
AT1G07890
APX1
AT5G62530
AT3G25800
ALDH12
A1
PP2AA2
AT3G45140
LOX2
AT2G44060
LEA14
AT1G15690
AVP1
Description
Encodes a plant protein kinase similar to the calcium/calmodulin-dependent protein
kinase subfamily and the SNF1 kinase subfamily (SnRK2) whose activity is activated
by ionic (salt) and non-ionic (mannitol) osmotic stress. Kinase activity of its homolog
in tobacco is induced by hyperosmotic condition within 1 minute.
Encodes a peroxisomal catalase, highly expressed in bolts and leaves. mRNA
expression patterns show circadian regulation with mRNA levels being high in the
subjective early morning. Loss of function mutations have increased H2O2 levels and
increased H2O2 sensitivity. Mutants accumulate more toxic ions yet show decreased
sensitivity to Li+. This decreased sensitivity is most likely due to an insensitivity to
ethylene. Note that in Queval et al. (2007) Plant Journal, 52(4):640, SALK_057998 is
named as cat2-1, SALK_076998 is named as cat2-2; in Bueso et al. (2007) Plant
Journal, 52(6):1052, SALK_076998 is named as cat2-1. TAIR has adopted the
nomenclature consistent with that in Bueso et al. (2007) after consultation with the
authors: SALK_076998 (cat2-1), SALK_057998 (cat2-2).
Encodes AT4g21960 (AT4g21960/T8O5_170).
Encodes a cytosolic ascorbate peroxidase APX1. Ascorbate peroxidases are enzymes
that scavenge hydrogen peroxide in plant cells. Eight types of APX have been
described for Arabidopsis: three cytosolic (APX1, APX2, APX6), two chloroplastic
types (stromal sAPX, thylakoid tAPX), and three microsomal (APX3, APX4, APX5)
isoforms. At least part of the induction of heat shock proteins during light stress in
Arabidopsis is mediated by H2O2 that is scavenged by APX1. Expression of the gene
is downregulated in the presence of paraquat, an inducer of photoxidative stress.
Encodes mitochondrial Delta-pyrroline-5- carboxylate dehydrogenase. Involved in the
catabolism of proline to glutamate. Involved in protection from proline toxicity.
Induced at pathogen infection sites. P5CDH and SRO5 (an overlapping gene in the
sense orientation) generate 24-nt and 21-nt siRNAs, which together are components of
a regulatory loop controlling reactive oxygen species (ROS) production and stress
response.
one of three genes encoding the protein phosphatase 2A regulatory subunit
Chloroplast lipoxygenase required for wound-induced jasmonic acid accumulation in
Arabidopsis. Mutants are resistant to Staphylococcus aureus and accumulate salicylic
acid upon infection.
Late embryogenesis abundant protein, group 2; FUNCTIONS IN: molecular_function
unknown; INVOLVED IN: response to cadmium ion, response to desiccation, embryo
development ending in seed dormancy; LOCATED IN: plasma membrane, membrane;
EXPRESSED IN: 25 plant structures; EXPRESSED DURING: 14 growth stages;
CONTAINS InterPro DOMAIN/s: Water stress and hypersensitive response domain
(InterPro:IPR013990), Late embryogenesis abundant protein, group 2
(InterPro:IPR004864); BEST Arabidopsis thaliana protein match is: Late
embryogenesis abundant protein (TAIR:AT1G01470.1); Has 294 Blast hits to 286
proteins in 78 species: Archae - 4; Bacteria - 52; Metazoa - 0; Fungi - 0; Plants - 235;
Viruses - 0; Other Eukaryotes - 3 (source: NCBI BLink).
Encodes a H(+)-translocating (pyrophosphate-energized) inorganic pyrophosphatase
(H(+)-PPase; EC 3.6.1.1) located in the vacuolar membrane. Expression is found in all
tissues examined, including meristems and floral organ primordium. Expression is
particularly enhanced in pollen, and is repressed by light. Over expression and loss of
function phenotypes suggest AVP1 is involved in regulation of apoplastic pH and
auxin transport. The effect on auxin transport likely involves effects of extracellular
pH on subcellular localization of auxin efflux carriers such as PIN1.
TAIR
Accession
Name
AT4G09570
CPK4
AT1G45249
ABF2
AT4G33950
OST1
AT4G01370
MPK4
AT1G09700
HYL1
AT1G52340
ABA2
AT3G57240
BG3
AT4G29010
AIM1
AT3G28860
ABCB19
AT1G70940
PIN3
AT4G21670
CPL1
AT5G19330
ARIA
Description
Encodes a member of Calcium Dependent Protein Kinase (CDPK) gene
family.Positive regulator of ABA signaling. Phosphorylates ABA responsive
transcription factors ABF1 and ABF4.
Leucine zipper transcription factor that binds to the abscisic acid (ABA)–responsive
element (ABRE) motif in the promoter region of ABA-inducible genes. Enhances
drought tolerance in vegetative tissues. Required for normal glucose response.
Localized in the nucleus. Expressed constitutively in roots, leaf vascular tissues, and
hydathodes or in all tissues under stress conditions. It's phosphorylated by a ABAactivated 42-KDa kinase. Overexpression of the phosphorylated active form of AREB1
expressed many ABA-inducible genes, such as RD29B, without ABA treatment.
protein_coding ABSCISIC ACID RESPONSIVE ELEMENTS-BINDING FACTOR
2 (ABF2)
ABSCISIC ACID RESPONSIVE ELEMENTS-BINDING FACTOR 2
(ABF2); (AtABF2)
Encodes calcium-independent ABA-activated protein kinase, a member of SNF1related protein kinases (SnRK2) whose activity is activated by ionic (salt) and nonionic (mannitol) osmotic stress. Mutations disrupted ABA induction of stomatal
closure as well as ABA inhibition of light-induced stomatal opening. However,
regulation of stomatal opening/closing by light or CO(2) is not affected in these
mutants. May act in the interval between ABA perception and reactive oxygen species
production in the ABA signalling network.
Encodes a nuclear and cytoplasmically localized MAP kinase involved in mediating
responses to pathogens. Its substrates include MKS1 and probably MAP65-1.The
MAP65-1 interaction is involved in mediating cortical microtuble organization.
Encodes a nuclear dsRNA binding protein. Involved in mRNA cleavage. The mutant is
characterized by shorter stature, delayed flowering, leaf hyponasty, reduced fertility,
decreased rate of root growth, and an altered root gravitropic response. It also exhibits
less sensitivity to auxin and cytokinin.
Encodes a cytosolic short-chain dehydrogenase/reductase involved in the conversion of
xanthoxin to ABA-aldehyde during ABA biosynthesis. Mutants are insensitive to
sucrose and glucose.
encodes a member of glycosyl hydrolase family 17
protein_coding \BETA-1,3GLUCANASE 3\" (BG3) \"BETA-1,3-GLUCANASE 3\" (BG3)"
Functions in beta-oxidation of fatty acids, similar to CuMFP with L-3-hydroxyacylCoA hydrolyase , L-3-hydroxyacyl-dehydrogenase, D-3-hydroxyacyl-CoA epimerase,
and 3, 2-enoyl-CoA isomerase activities
Belongs to the family of ATP-binding cassette (ABC) transporters. Also known as
AtMDR11 and PGP19. Possibly regulates auxin-dependent responses by influencing
basipetal auxin transport in the root. Acts upstream of phyA in regulating hypocotyl
elongation and gravitropic response. Exerts nonredundant, partially overlapping
functions with the ABC transporter encoded by AtPGP1.
A regulator of auxin efflux and involved in differential growth. PIN3 is expressed in
gravity-sensing tissues, with PIN3 protein accumulating predominantly at the lateral
cell surface. PIN3 localizes to the plasma membrane and to vesicles. In roots, PIN3 is
expressed without pronounced polarity in tiers two and three of the columella cells, at
the basal side of vascular cells, and to the lateral side of pericycle cells of the
elongation zone. PIN3 overexpression inhibits root cell growth. Protein
phosphorylation plays a role in PIN3 trafficking to the plasma membrane.
encodes a a novel transcriptional repressor harboring two double-stranded RNAbinding domains and a region homologous to the catalytic domain of RNA polymerase
II C-terminal domain phosphatases found in yeast and in animals that regulate gene
transcription. Protein exhibits innate phosphatase activity in vitro. Mutants exhibit
hyperresponsiveness to ABA, cold, and NaCl.
Encodes an armadillo repeat protein involved in the abscisic acid response. The protein
interacts with a transcription factor, ABF2, which controls ABA-dependent gene
TAIR
Accession
AT3G12120
AT3G48170
AT3G19820
Name
FAD2
ALDH10
A9
AT3G14660
DWF1
HuCL003
92C001,
HaT13l02
4540
CYP72A1
3
AT2G39890
AT3G12580
PROT1
HSP70
AT5G02790
GSTL3
AT1G79620
HuCL212
26C001,
HaT13l02
8104
AT3G04290
AT3G19820
LTL1
DWF1
AT1G07040
Description
expression via the G-box-type ABA-responsive elements.
Major enzyme responsible for the synthesis of 18:2 fatty acids in the endoplasmic
reticulum. Contains His-rich motifs, which contribute to the interaction with the
electron donor cytochrome b5. Mutations in this gene suppress the low temperatureinduced phenotype of Arabidopsis tocopherol-deficient mutant vte2.
protein_coding FATTY ACID DESATURASE 2 (FAD2) FATTY ACID
DESATURASE 2 (FAD2)
aldehyde dehydrogenase 10A9
Involved in the conversion of the early brassinosteroid precursor 24methylenecholesterol to campesterol. Brassinosteroids affect cellular elongation.
Mutants have dwarf phenotype. DWF1 is a Ca2+-dependent calmodulin-binding
protein.
unknown protein
putative cytochrome P450
Encodes a proline transporter with affinity for gly betaine, proline and GABA. Protein
is expressed in the vascular tissue, specifically the phloem. protein_coding
PROLINE TRANSPORTER 1 (PROT1) PROLINE TRANSPORTER 1
(PROT1);PROLINE TRANSPORTER 1 (ATPROT1)
heat shock protein 70
Encodes a member of the lambda family of glutathione transferases. It has thiol
transferase activity and self S-glutathionylation activity in vitro. protein_coding
GLUTATHIONE TRANSFERASE LAMBDA 2 (GSTL2)
GLUTATHIONE
TRANSFERASE LAMBDA 2 (GSTL2)
Leucine-rich repeat protein kinase family protein; FUNCTIONS IN: protein
serine/threonine kinase activity, kinase activity, ATP binding; INVOLVED IN:
transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid
phosphorylation; LOCATED IN: endomembrane system; EXPRESSED IN: 8 plant
structures; EXPRESSED DURING: 4 anthesis, petal differentiation and expansion
stage; CONTAINS InterPro DOMAIN/s: Protein kinase, ATP binding site
(InterPro:IPR017441), Protein kinase, catalytic domain (InterPro:IPR000719),
Leucine-rich repeat-containing N-terminal domain, type 2 (InterPro:IPR013210),
Leucine-rich repeat (InterPro:IPR001611), Serine-threonine/tyrosine-protein kinase
(InterPro:IPR001245), Protein kinase-like domain (InterPro:IPR011009),
Serine/threonine-protein kinase, active site (InterPro:IPR008271); BEST Arabidopsis
thaliana protein match is: Leucine-rich repeat protein kinase family protein
(TAIR:AT5G49760.1); Has 173131 Blast hits to 132948 proteins in 4769 species:
Archae - 163; Bacteria - 18653; Metazoa - 51943; Fungi - 10632; Plants - 70309;
Viruses - 438; Other Eukaryotes - 20993 (source: NCBI BLink).
Li-tolerant lipase 1 (LTL1); FUNCTIONS IN: hydrolase activity, acting on ester
bonds, carboxylesterase activity; INVOLVED IN: lipid metabolic process; LOCATED
IN: endomembrane system; EXPRESSED IN: 19 plant structures; EXPRESSED
DURING: 12 growth stages; CONTAINS InterPro DOMAIN/s: Lipase, GDSL
(InterPro:IPR001087), Esterase, SGNH hydrolase-type (InterPro:IPR013830); BEST
Arabidopsis thaliana protein match is: GDSL-like Lipase/Acylhydrolase superfamily
protein (TAIR:AT5G33370.1); Has 3364 Blast hits to 3325 proteins in 174 species:
Archae - 0; Bacteria - 234; Metazoa - 0; Fungi - 3; Plants - 3111; Viruses - 0; Other
Eukaryotes - 16 (source: NCBI BLink). protein_coding LI-TOLERANT LIPASE 1
(LTL1)
(ATLTL1);LI-TOLERANT LIPASE 1 (LTL1)
Involved in the conversion of the early brassinosteroid precursor 24-
TAIR
Accession
Name
AT1G74670
GASA6
AT2G48020
HuCL017
73C001,
HaT13l00
7466
AT5G40010
AATP1
AT4G34529
HuCD847
422, CIB1
AT5G59320
LTP3
AT5G59320
LTP3
AT5G59320
LTP3
Description
methylenecholesterol to campesterol. Brassinosteroids affect cellular elongation.
Mutants have dwarf phenotype. DWF1 is a Ca2+-dependent calmodulin-binding
protein.
Gibberellin-regulated family prot
Major facilitator superfamily protein; FUNCTIONS IN: carbohydrate transmembrane
transporter activity, sugar:hydrogen symporter activity; INVOLVED IN: transport,
transmembrane transport; LOCATED IN: plasma membrane, chloroplast, vacuole,
membrane; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 14 growth
stages; CONTAINS InterPro DOMAIN/s: Sugar transporter, conserved site
(InterPro:IPR005829), Major facilitator superfamily (InterPro:IPR020846), General
substrate transporter (InterPro:IPR005828), Sugar/inositol transporter
(InterPro:IPR003663), Major facilitator superfamily, general substrate transporter
(InterPro:IPR016196); BEST Arabidopsis thaliana protein match is: Major facilitator
superfamily protein (TAIR:AT5G18840.1); Has 32576 Blast hits to 32035 proteins in
2204 species: Archae - 531; Bacteria - 16009; Metazoa - 5272; Fungi - 6662; Plants 2708; Viruses - 2; Other Eukaryotes - 1392 (source: NCBI BLink).
Encodes a mitochondrial ATPase involved in seed and silique development.
protein_coding AAA-ATPASE 1 (AATP1) AAA-ATPASE 1 (AATP1);ATPASEIN-SEED-DEVELOPMENT (ASD); AAA-ATPase 1 (AATP1); FUNCTIONS IN:
nucleoside-triphosphatase activity, ATPase activity, nucleotide binding, ATP binding;
EXPRESSED IN: stem, inflorescence meristem, root, flower, stamen; EXPRESSED
DURING: 4 anthesis, petal differentiation and expansion stage; CONTAINS InterPro
DOMAIN/s: ATPase, AAA-type, core (InterPro:IPR003959), ATPase, AAA+ type,
core (InterPro:IPR003593), ATPase, AAA-type, conserved site (InterPro:IPR003960);
BEST Arabidopsis thaliana protein match is: P-loop containing nucleoside
triphosphate hydrolases superfamily protein (TAIR:AT3G28580.1); Has 35875 Blast
hits to 26437 proteins in 2942 species: Archae - 1242; Bacteria - 8120; Metazoa 8429; Fungi - 4077; Plants - 2736; Viruses - 205; Other Eukaryotes - 11066 (source:
NCBI BLink).
Encodes a transcription factor CIB1 (cryptochrome-interacting basic-helix-loop-helix).
CIB1 interacts with CRY2 (cryptochrome 2) in a blue light-specific manner in yeast
and Arabidopsis cells, and it acts together with additional CIB1-related proteins to
promote CRY2-dependent floral initiation. CIB1 positively regulates FT expression.
protein_coding CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX
1 (CIB1)
CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1
(CIB1)
Predicted to encode a PR (pathogenesis-related) protein. Belongs to the lipid transfer
protein (PR-14) family with the following members: At2g38540/LTP1,
At2g38530/LTP2, At5g59320/LTP3, At5g59310/LTP4, At3g51600/LTP5,
At3g08770/LTP6, At2g15050/LTP7, At2g18370/LTP8, At2g15325/LTP9,
At5g01870/LTP10, At4g33355/LTP11, At3g51590/LTP12, At5g44265/LTP13,
At5g62065/LTP14, At4g08530/LTP15.
Predicted to encode a PR (pathogenesis-related) protein. Belongs to the lipid transfer
protein (PR-14) family with the following members: At2g38540/LTP1,
At2g38530/LTP2, At5g59320/LTP3, At5g59310/LTP4, At3g51600/LTP5,
At3g08770/LTP6, At2g15050/LTP7, At2g18370/LTP8, At2g15325/LTP9,
At5g01870/LTP10, At4g33355/LTP11, At3g51590/LTP12, At5g44265/LTP13,
At5g62065/LTP14, At4g08530/LTP15.
Predicted to encode a PR (pathogenesis-related) protein. Belongs to the lipid transfer
protein (PR-14) family with the following members: At2g38540/LTP1,
At2g38530/LTP2, At5g59320/LTP3, At5g59310/LTP4, At3g51600/LTP5,
At3g08770/LTP6, At2g15050/LTP7, At2g18370/LTP8, At2g15325/LTP9,
At5g01870/LTP10, At4g33355/LTP11, At3g51590/LTP12, At5g44265/LTP13,
At5g62065/LTP14, At4g08530/LTP15.
TAIR
Accession
AT4G21960
Name
AT5G57655
PRXR1
HuCL001
78C003,
HaT13l00
0974
AT1G26770
EXPA10
AT2G36630
HuCL004
21C002,
HaT13l00
5065
AT3G13050
NiaP
AT1G76490
HMG1
AT3G14310
AT3G55610
AT2G39800
AT1G14540
PME3
P5CS2
P5CS1
HuCL031
43C001,
HaT13l01
2190
AT5G59845
HuCL036
24C001,
HaT13l02
3985
AT2G36880
MAT3
Description
Encodes AT4g21960 (AT4g21960/T8O5_170). protein_coding (PRXR1)
(PRXR1)
xylose isomerase family protein
Encodes an expansin. Naming convention from the Expansin Working Group (Kende
et al, Plant Mol Bio). Involved in the formation of nematode-induced syncytia in roots
of Arabidopsis thaliana.
Sulfite exporter TauE/SafE family protein; INVOLVED IN: N-terminal protein
myristoylation; LOCATED IN: endomembrane system, integral to membrane;
EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 15 growth stages;
CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF81
(InterPro:IPR002781); BEST Arabidopsis thaliana protein match is: Sulfite exporter
TauE/SafE family protein (TAIR:AT2G25737.1); Has 1587 Blast hits to 1517 proteins
in 484 species: Archae - 83; Bacteria - 808; Metazoa - 0; Fungi - 0; Plants - 200;
Viruses - 0; Other Eukaryotes - 496 (source: NCBI BLink).
Encodes a plant nicotinate transporter than can also transport trigonelline (Nmethylnicotinate).
Encodes a 3-hydroxy-3-methylglutaryl coenzyme A reductase, which is involved in
melavonate biosynthesis and performs the first committed step in isoprenoid
biosynthesis. Expression is activated in dark in leaf tissue but not controlled by light in
the root (confine
protein_coding HYDROXY METHYLGLUTARYL COA
REDUCTASE 1 (HMG1) HYDROXY METHYLGLUTARYL COA REDUCTASE
1 (HMG1);3-HYDROXY-3-METHYLGLUTARYL COA REDUCTASE 1
(HMGR1); (AtHMGR1)
encodes a pectin methylesterase, targeted by a cellulose binding protein (CBP) from
the parasitic nematode Heterodera schachtii during parasitism.
delta 1-pyrroline-5-carboxylate synthase 2
delta1-pyrroline-5-carboxylate synthase 1
Peroxidase superfamily protein
Gibberellin-regulated family protein; FUNCTIONS IN: molecular_function unknown;
INVOLVED IN: response to gibberellin stimulus; LOCATED IN: endomembrane
system; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth
stages; CONTAINS InterPro DOMAIN/s: Gibberellin regulated protein
(InterPro:IPR003854); BEST Arabidopsis thaliana protein match is: Gibberellinregulated family protein (TAIR:AT2G39540.1); Has 30201 Blast hits to 17322
proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422;
Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink).
methionine adenosyltransferase 3 (MAT3); FUNCTIONS IN: methionine
adenosyltransferase activity; INVOLVED IN: one-carbon metabolic process, Sadenosylmethionine biosynthetic process; LOCATED IN: plasma membrane;
EXPRESSED IN: 25 plant structures; EXPRESSED DURING: 16 growth stages;
CONTAINS InterPro DOMAIN/s: S-adenosylmethionine synthetase
(InterPro:IPR002133), S-adenosylmethionine synthetase superfamily
(InterPro:IPR022636), S-adenosylmethionine synthetase, N-terminal
(InterPro:IPR022628), S-adenosylmethionine synthetase, C-terminal
(InterPro:IPR022630), S-adenosylmethionine synthetase, conserved site
(InterPro:IPR022631), S-adenosylmethionine synthetase, central domain
(InterPro:IPR022629); BEST Arabidopsis thaliana protein match is: Sadenosylmethionine synthetase family protein (TAIR:AT3G17390.1); Has 30201 Blast
TAIR
Accession
Name
AT1G13680
HuCL133
63C001,
HaT13l00
9831
AT2G28630
KCS12
AT5G39000
AT4G11649
AT1G78000
HuCL181
65C001,
HaT13l00
6316
OSM34,
HuDY909
416
SULTR1
Description
hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338;
Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI
BLink).
protein_coding METHIONINE ADENOSYLTRANSFERASE 3 (MAT3)
METHIONINE ADENOSYLTRANSFERASE 3 (MAT3)
PLC-like phosphodiesterases superfamily protein; FUNCTIONS IN: phospholipase C
activity, phosphoric diester hydrolase activity; INVOLVED IN: intracellular signaling
pathway, lipid metabolic process; LOCATED IN: endomembrane system;
EXPRESSED IN: embryo, flower, seed; EXPRESSED DURING: F mature embryo
stage, petal differentiation and expansion stage, E expanded cotyledon stage, D
bilateral stage; CONTAINS InterPro DOMAIN/s: Phospholipase C,
phosphatidylinositol-specific , X domain (InterPro:IPR000909), PLC-like
phosphodiesterase, TIM beta/alpha-barrel domain (InterPro:IPR017946); BEST
Arabidopsis thaliana protein match is: PLC-like phosphodiesterases superfamily
protein (TAIR:AT1G49740.1); Has 30201 Blast hits to 17322 proteins in 780 species:
Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses 0; Other Eukaryotes - 2996 (source: NCBI BLink).
Encodes KCS12, a member of the 3-ketoacyl-CoA synthase family involved in the
biosynthesis of VLCFA (very long chain fatty acids).
protein_coding 3KETOACYL-COA SYNTHASE 12 (KCS12)
3-KETOACYL-COA SYNTHASE
12 (KCS12)
Malectin/receptor-like protein kinase family protein; FUNCTIONS IN: kinase activity;
INVOLVED IN: protein amino acid phosphorylation; LOCATED IN: endomembrane
system; CONTAINS InterPro DOMAIN/s: Protein kinase, ATP binding site
(InterPro:IPR017441), Malectin/receptor-like protein kinase (InterPro:IPR021720),
Protein kinase, catalytic domain (InterPro:IPR000719), Serine-threonine/tyrosineprotein kinase (InterPro:IPR001245), Protein kinase-like domain
(InterPro:IPR011009), Serine/threonine-protein kinase, active site
(InterPro:IPR008271); BEST Arabidopsis thaliana protein match is: Malectin/receptorlike protein kinase family protein (TAIR:AT5G38990.1); Has 116422 Blast hits to
114937 proteins in 4415 species: Archae - 91; Bacteria - 12945; Metazoa - 43415;
Fungi - 9851; Plants - 32921; Viruses - 374; Other Eukaryotes - 16825 (source: NCBI
BLink).
osmotin-like protein
sulfate transporter 1;2
Genes identified by Marchand et al. (2014) as part of the sunflower drought response gene
network and also identified by this study has having a significant drought treatment or range-bytreatment response in Centaurea diffusa. Modifed from Marchand et al. (2014).