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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).