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Acta Agronomica Sinica ›› 2020, Vol. 46 ›› Issue (5): 668-679.doi: 10.3724/SP.J.1006.2020.94124


Identification of co-expressed modules of cotton genes responding to Verticillium dahliae infection by WGCNA

Ming-Chuan FU(),Hao LI,Yi-Zhen CHEN,Zhan-Ji LIU,Ren-Zhong LIU,Li-Guo WANG   

  1. Cotton Research Center of Shandong Academy of Agricultural Sciences / Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture, Jinan 250100, Shandong, China
  • Received:2019-08-23 Accepted:2020-01-15 Online:2020-05-12 Published:2020-02-18
  • Contact: Ming-Chuan FU E-mail:fumingchuan@shandong.cn
  • Supported by:
    This study was supported by the Agricultural Science and Technology Innovation Project of Shandong Academy of Agricultural Sciences.(CXGC2018B01);This study was supported by the Agricultural Science and Technology Innovation Project of Shandong Academy of Agricultural Sciences.(CXGC2018E06)


Weighted gene co-expression network analysis (WGCNA) is a classic systematic biological method, which can be used to identify co-expressed modules, investigate relationships between modules and specific traits, and screen hub genes in the networks. Verticillium wilt, caused by the fungal pathogen Verticillium dahliae, can cause severe fibre quality reduction and yield loss of cotton. Studying on cotton genes and molecular mechanisms related to defense responses against V. dahliae can shed light on cotton breeding. In this study, 21 transcriptome data of Gossypium barbadense seedling roots infected by V. dahliae were used to investigate differentially expressed genes (DEGs). By filtering out the genes with low variation, 35,647 genes were selected for WGCNA. In total, 22,850 DEGs were identified under V. dahliae infection, with 4685 in common at all inoculated time points. Co-expression network analysis identified 18 modules, in which five modules significantly associated with V. dahliae infection (black, mediumpurple3, darkolivegreen, plum3 positively correlated with the 2 h, 6 h, 48 h, and 72 h inoculated time points, respectively; mediumpurple2 negatively correlated with the 2 h inoculated time point). GO and KEGG enrichment analysis were performed on these five specific modules, which could be enriched in GO terms and metabolic pathways, such as cellular response to stimulus, calcium ion binding and flavonoid biosynthesis. The hub genes were screened by calculating gene connectivity in the corresponding networks, and they may play important roles in the resistance against biotic/abiotic stresses. In summary, by WGCNA, a few defense-related co-expressed modules and hub genes were identified. The results of this study would be beneficial for further understanding of the molecular mechanisms of pathogen resistance in cotton, and provide new gene resources for cotton breeding in the future.

Key words: cotton, Verticillium wilt, WGCNA, hub gene

Table 1

Sequences of the primers used in qRT-PCR"

Forward primer (5°-3°)
Reverse primer (5°-3°)

Fig. 1

DEGs in different time points under infection The column with one black point represents the DEGs only in the corresponding set; the column with two or more black points linked by a solid line represents the intersection among the sets. "

Fig. 2

Determination of soft-thresholding power (β) a: scale-free topology fit index as a function of the soft-thresholding power, the red line represents that R2 is equal to 0.8. b: mean connectivity as a function of the soft-thresholding power. "

Fig. 3

Clustering dendrograms of genes and module detecting a: gene clustering on TOM-based dissimilarity. b: module division by dynamic tree cut, different colors represent different modules. c: module division after merging similar modules. "

Fig. 4

Heat map of the correlation between modules and traits Each row corresponds to a module, and each column corresponds to a trait. The correlation coefficient and the corresponding p-value are shown in each cell. The specific modules which significantly associated with V. dahliae infection are colored in red, and the corresponding numbers of genes and transcription factors are shown in the left cells. "

Fig. 5

GO functional and KEGG pathway enrichment analysis in the black module The vertical axis represents the enriched GO term or KEGG pathway, and the horizontal axis represents the ratio of enriched genes in the module. The point size represents the gene number enriched in the pathway, and the color represents the p-value corrected for multiple testing. "

Supplementary table 1

The GO enrichment of the specific modules (Biological process)"

ID 描述
black GO:0071705 nitrogen compound transport 6.27E-39 3.16E-36
GO:0045184 establishment of protein localization 5.02E-38 1.12E-35
GO:0015031 protein transport 6.65E-38 1.12E-35
GO:0008104 protein localization 5.51E-37 5.61E-35
GO:0015833 peptide transport 5.57E-37 5.61E-35
GO:0042886 amide transport 9.91E-37 8.31E-35
GO:0051641 cellular localization 7.31E-33 5.25E-31
GO:0046907 intracellular transport 3.23E-32 2.03E-30
GO:0051649 establishment of localization in cell 1.02E-31 5.69E-30
GO:0006886 intracellular protein transport 1.19E-31 6.00E-30
GO:0071702 organic substance transport 2.57E-31 1.17E-29
GO:0034613 cellular protein localization 9.85E-31 3.81E-29
GO:0070727 cellular macromolecule localization 9.85E-31 3.81E-29
GO:0033036 macromolecule localization 2.30E-30 8.27E-29
GO:0016192 vesicle-mediated transport 4.18E-25 1.40E-23
GO:0048193 Golgi vesicle transport 1.92E-12 6.03E-11
GO:0007264 small GTPase mediated signal transduction 2.38E-09 7.04E-08
GO:0006888 ER to Golgi vesicle-mediated transport 1.75E-08 4.89E-07
GO:0007154 cell communication 2.02E-08 5.36E-07
GO:0007165 signal transduction 5.62E-07 1.35E-05
GO:0023052 signaling 5.62E-07 1.35E-05
GO:0035556 intracellular signal transduction 8.38E-07 1.92E-05
GO:0006605 protein targeting 1.56E-06 3.42E-05
GO:0051716 cellular response to stimulus 4.75E-06 9.96E-05
GO:0006890 retrograde vesicle-mediated transport, Golgi to ER 3.42E-05 6.88E-04
GO:1902531 regulation of intracellular signal transduction 4.55E-05 8.80E-04
GO:0006913 nucleocytoplasmic transport 5.42E-05 9.73E-04
GO:0051169 nuclear transport 5.42E-05 9.73E-04
GO:0009966 regulation of signal transduction 1.00E-04 1.63E-03
GO:0010646 regulation of cell communication 1.00E-04 1.63E-03
GO:0023051 regulation of signaling 1.00E-04 1.63E-03
GO:0009755 hormone-mediated signaling pathway 1.19E-04 1.71E-03
GO:0032870 cellular response to hormone stimulus 1.19E-04 1.71E-03
GO:0071310 cellular response to organic substance 1.19E-04 1.71E-03
GO:0071495 cellular response to endogenous stimulus 1.19E-04 1.71E-03
GO:0072594 establishment of protein localization to organelle 3.40E-04 4.76E-03
GO:0006904 vesicle docking involved in exocytosis 3.96E-04 5.25E-03
GO:0140029 exocytic process 3.96E-04 5.25E-03
GO:0072657 protein localization to membrane 4.49E-04 5.65E-03
GO:0090150 establishment of protein localization to membrane 4.49E-04 5.65E-03
mediumpurple3 GO:0051640 organelle localization 4.71E-04 5.78E-03
GO:0006520 cellular amino acid metabolic process 9.09E-10 2.99E-07
GO:1901605 alpha-amino acid metabolic process 1.50E-07 2.47E-05
GO:0006790 sulfur compound metabolic process 4.22E-07 4.64E-05
GO:0006544 glycine metabolic process 9.95E-06 8.19E-04
GO:0009069 serine family amino acid metabolic process 1.98E-05 9.92E-04
GO:0034660 ncRNA metabolic process 2.05E-05 9.92E-04
GO:0033866 nucleoside bisphosphate biosynthetic process 2.71E-05 9.92E-04
GO:0034030 ribonucleoside bisphosphate biosynthetic process 2.71E-05 9.92E-04
GO:0034033 purine nucleoside bisphosphate biosynthetic process 2.71E-05 9.92E-04
GO:0006418 tRNA aminoacylation for protein translation 4.26E-05 1.17E-03
GO:0043038 amino acid activation 4.26E-05 1.17E-03
GO:0043039 tRNA aminoacylation 4.26E-05 1.17E-03
GO:0006084 acetyl-CoA metabolic process 4.84E-05 1.23E-03
GO:0006732 coenzyme metabolic process 9.25E-05 1.98E-03
GO:0006555 methionine metabolic process 9.25E-05 1.98E-03
GO:0065008 regulation of biological quality 9.63E-05 1.98E-03
GO:0008652 cellular amino acid biosynthetic process 1.20E-04 1.99E-03
GO:0006637 acyl-CoA metabolic process 1.27E-04 1.99E-03
GO:0035383 thioester metabolic process 1.27E-04 1.99E-03
GO:0001505 regulation of neurotransmitter levels 1.32E-04 1.99E-03
GO:0042133 neurotransmitter metabolic process 1.32E-04 1.99E-03
GO:0006399 tRNA metabolic process 1.33E-04 1.99E-03
GO:1901606 alpha-amino acid catabolic process 1.48E-04 2.12E-03
GO:0051188 cofactor biosynthetic process 1.87E-04 2.57E-03
GO:0009108 coenzyme biosynthetic process 2.21E-04 2.71E-03
GO:0009066 aspartate family amino acid metabolic process 2.22E-04 2.71E-03
GO:0072350 tricarboxylic acid metabolic process 2.22E-04 2.71E-03
GO:0000096 sulfur amino acid metabolic process 3.21E-04 3.57E-03
GO:0033865 nucleoside bisphosphate metabolic process 3.40E-04 3.57E-03
GO:0033875 ribonucleoside bisphosphate metabolic process 3.40E-04 3.57E-03
GO:0034032 purine nucleoside bisphosphate metabolic process 3.40E-04 3.57E-03
GO:0044272 sulfur compound biosynthetic process 3.47E-04 3.57E-03
GO:0009063 cellular amino acid catabolic process 4.06E-04 4.05E-03
GO:0051186 cofactor metabolic process 4.87E-04 4.72E-03
GO:0017144 drug metabolic process 5.26E-04 4.95E-03
GO:0044283 small molecule biosynthetic process 6.99E-04 6.40E-03

Supplementary table 2

The GO enrichment of the specific modules (Molecular function)"

ID 描述
black GO:0008565 protein transporter activity 5.96E-10 1.93E-07
GO:0001883 purine nucleoside binding 7.64E-08 3.59E-06
GO:0005525 GTP binding 7.64E-08 3.59E-06
GO:0032550 purine ribonucleoside binding 7.64E-08 3.59E-06
GO:0032561 guanyl ribonucleotide binding 7.64E-08 3.59E-06
GO:0001882 nucleoside binding 7.76E-08 3.59E-06
GO:0032549 ribonucleoside binding 7.76E-08 3.59E-06
GO:0005096 GTPase activator activity 2.09E-07 8.46E-06
GO:0019001 guanyl nucleotide binding 2.68E-07 9.66E-06
GO:0008047 enzyme activator activity 1.84E-06 5.97E-05
GO:0060589 nucleoside-triphosphatase regulator activity 2.32E-06 6.83E-05
GO:0030695 GTPase regulator activity 3.63E-06 9.81E-05
GO:0042887 amide transmembrane transporter activity 4.96E-05 1.24E-03
GO:0016838 carbon-oxygen lyase activity, acting on phosphates 5.61E-05 1.30E-03
GO:0003924 GTPase activity 1.94E-04 4.20E-03
GO:0010333 terpene synthase activity 2.07E-04 4.20E-03
GO:0000287 magnesium ion binding 2.22E-04 4.23E-03
GO:0098772 molecular function regulator 2.67E-04 4.80E-03
GO:0004743 pyruvate kinase activity 4.22E-04 6.52E-03
GO:0030955 potassium ion binding 4.22E-04 6.52E-03
GO:0031420 alkali metal ion binding 4.22E-04 6.52E-03
mediumpurple3 GO:0004812 aminoacyl-tRNA ligase activity 9.02E-06 1.06E-03
GO:0016875 ligase activity, forming carbon-oxygen bonds 9.02E-06 1.06E-03
GO:0140101 catalytic activity, acting on a tRNA 9.53E-05 5.36E-03
GO:0016874 ligase activity 1.00E-04 5.36E-03
GO:0046912 transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer 1.14E-04 5.36E-03
GO:0140098 catalytic activity, acting on RNA 1.41E-04 5.54E-03
GO:0050662 coenzyme binding 2.28E-04 7.69E-03
darkolivegreen GO:0004650 polygalacturonase activity 1.16E-16 1.19E-14
GO:0016798 hydrolase activity, acting on glycosyl bonds 2.98E-07 1.54E-05
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds 8.84E-07 3.04E-05
GO:0004190 aspartic-type endopeptidase activity 7.33E-05 1.51E-03
GO:0070001 aspartic-type peptidase activity 7.33E-05 1.51E-03
GO:0020037 heme binding 1.75E-04 2.58E-03
GO:0046906 tetrapyrrole binding 1.75E-04 2.58E-03
plum3 GO:0005509 calcium ion binding 1.22E-07 1.93E-06
mediumpurple2 GO:0004298 threonine-type endopeptidase activity 0.00 0.01
GO:0070003 threonine-type peptidase activity 0.00 0.01

Supplementary table 3

The GO enrichment of the specific modules (Cellular component)"

ID 描述
black GO:0030117 membrane coat 1.97E-31 9.24E-30
GO:0048475 coated membrane 1.97E-31 9.24E-30
GO:0098796 membrane protein complex 3.12E-22 9.74E-21
GO:0012505 endomembrane system 1.77E-21 4.15E-20
GO:0005798 Golgi-associated vesicle 4.90E-19 4.17E-18
GO:0012506 vesicle membrane 4.90E-19 4.17E-18
GO:0030120 vesicle coat 4.90E-19 4.17E-18
GO:0030659 cytoplasmic vesicle membrane 4.90E-19 4.17E-18
GO:0030660 Golgi-associated vesicle membrane 4.90E-19 4.17E-18
GO:0030662 coated vesicle membrane 4.90E-19 4.17E-18
GO:0044433 cytoplasmic vesicle part 4.90E-19 4.17E-18
GO:0005794 Golgi apparatus 8.11E-19 6.33E-18
GO:0044431 Golgi apparatus part 5.88E-18 4.24E-17
GO:0030135 coated vesicle 2.02E-17 1.12E-16
GO:0031410 cytoplasmic vesicle 2.02E-17 1.12E-16
GO:0031982 vesicle 2.02E-17 1.12E-16
GO:0097708 intracellular vesicle 2.02E-17 1.12E-16
GO:0098588 bounding membrane of organelle 4.47E-17 2.33E-16
GO:0031090 organelle membrane 4.82E-16 2.38E-15
GO:0098805 whole membrane 5.76E-13 2.70E-12
GO:0030126 COPI vesicle coat 2.09E-12 8.52E-12
GO:0030137 COPI-coated vesicle 2.09E-12 8.52E-12
GO:0030663 COPI-coated vesicle membrane 2.09E-12 8.52E-12
GO:0030118 clathrin coat 2.90E-09 1.13E-08
GO:0030133 transport vesicle 7.84E-09 2.82E-08
GO:0030658 transport vesicle membrane 7.84E-09 2.82E-08
GO:0030119 AP-type membrane coat adaptor complex 7.16E-08 2.40E-07
GO:0030131 clathrin adaptor complex 7.16E-08 2.40E-07
GO:0012507 ER to Golgi transport vesicle membrane 6.69E-07 2.02E-06
GO:0030127 COPII vesicle coat 6.69E-07 2.02E-06
GO:0030134 COPII-coated ER to Golgi transport vesicle 6.69E-07 2.02E-06
GO:0000139 Golgi membrane 1.76E-04 5.15E-04
GO:0031984 organelle subcompartment 3.23E-04 9.17E-04
GO:0098791 Golgi subcompartment 5.41E-04 1.49E-03
GO:0005783 endoplasmic reticulum 6.96E-04 1.86E-03
GO:0033177 proton-transporting two-sector ATPase complex, proton-transporting domain 1.77E-03 4.61E-03
GO:0030136 clathrin-coated vesicle 2.02E-03 4.86E-03
GO:0005905 clathrin-coated pit 2.28E-03 4.86E-03
GO:0012510 trans-Golgi network transport vesicle membrane 2.28E-03 4.86E-03
mediumpurple2 GO:0030125 clathrin vesicle coat 2.28E-03 4.86E-03
GO:0030130 clathrin coat of trans-Golgi network vesicle 2.28E-03 4.86E-03
GO:0030132 clathrin coat of coated pit 2.28E-03 4.86E-03
GO:0030140 trans-Golgi network transport vesicle 2.28E-03 4.86E-03
GO:0030665 clathrin-coated vesicle membrane 2.28E-03 4.86E-03
GO:0005839 proteasome core complex 0.00 0.00
GO:0000502 proteasome complex 0.00 0.00
GO:1905369 endopeptidase complex 0.00 0.00
GO:1905368 peptidase complex 0.00 0.00

Supplementary table 4

The KEGG enrichment of the specific modules"

black mRNA surveillance pathway 4.52E-09 4.75E-07
Endocytosis 1.71E-08 8.99E-07
Protein export 3.16E-07 1.11E-05
RNA transport 8.85E-06 1.96E-04
Ribosome biogenesis in eukaryotes 9.32E-06 1.96E-04
Spliceosome 2.04E-05 3.18E-04
Protein processing in endoplasmic reticulum 2.12E-05 3.18E-04
RNA degradation 6.77E-05 8.91E-04
mediumpurple3 Biosynthesis of amino acids 8.38E-09 7.41E-07
Citrate cycle (TCA cycle) 6.09E-06 2.32E-04
Carbon metabolism 7.88E-06 2.32E-04
Proteasome 1.13E-05 2.49E-04
Phenylalanine, tyrosine and tryptophan biosynthesis 4.01E-05 7.09E-04
Phenylalanine metabolism 6.54E-05 8.48E-04
Tyrosine metabolism 6.72E-05 8.48E-04
Isoquinoline alkaloid biosynthesis 1.74E-04 1.93E-03
Selenocompound metabolism 5.32E-04 5.22E-03
Tropane, piperidine and pyridine alkaloid biosynthesis 7.03E-04 6.21E-03
darkolivegreen Flavonoid biosynthesis 8.66E-10 5.20E-08

Fig. 6

Gene co-expression networks of the specific modules which significantly associated with V. dahliae infection The genes with higher connectivity in the corresponding network are shown with larger circle sizes and darker colors. The transcription factors are indicated by triangles, with other genes being indicated by circles. a: Gene co-expression network of the black module. b: Gene co-expression network of the mediumpurple3 module. c: Gene co-expression network of the darkolivegreen module. d: Gene co-expression network of the plum3 module. e: Gene co-expression network of the mediumpurple2 module. "

Table 2

Function annotation of the hub genes in the modules associating with V. dahliae infection"

Gene ID in G. barbadense
Gene ID in Arabidopsis
Gene function
black Gbar_A11G006460 AT3G26680 Involved in a SNM-dependent recombinational repair process of oxidatively induced DNA damage
Gbar_D12G004330 AT2G15910 CSL zinc finger domain-containing protein
Gbar_D11G006810 AT3G26680 Involved in a SNM-dependent recombinational repair process of oxidatively induced DNA damage
Gbar_A12G013260 AT5G26751 Encodes a SHAGGY-related kinase involved in meristem organization
Gbar_A12G027410 AT5G51830 Encodes one of the several Arabidopsis fructokinases
mediumpurple3 Gbar_A04G004150 AT1G53430 Leucine-rich repeat transmembrane protein kinase
Gbar_D10G024280 AT3G55470 Calcium-dependent lipid-binding (CaLB domain) family protein
Gbar_A08G011260 AT1G64300 Protein kinase family protein
Gbar_A03G016830 AT5G50850 Transketolase family protein
Gbar_A10G021450 AT3G52200 Encodes a dihydrolipoamide S-acetyltransferase, a subunit of the mitochondrial pyruvate dehydrogenase complex
darkolivegreen Gbar_A06G022760 AT1G78020 FCS like zinc finger 6 is induced during energy starvation through SnRK1 signaling
Gbar_A13G004330 AT4G34220 Encodes a receptor like kinase involved in ABA-mediated seedling development and drought tolerance
Gbar_A12G027680 AT5G51550 EXORDIUM like 3
Gbar_D01G008860 AT5G56040 Leucine-rich receptor-like protein kinase family protein
Gbar_D12G021770 AT2G45550 Member of CYP76C
plum3 Gbar_A10G024460 AT5G05960 Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein
Gbar_D03G017340 AT5G47230 Encodes a member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family (ATERF-5)
Gbar_A07G022210 AT2G38830 Ubiquitin-conjugating enzyme/RWD-like protein
Gbar_D12G010820 AT3G60220 Encodes a putative RING-H2 zinc finger protein ATL4 (ATL4)
Gbar_D05G028190 AT3G56400 Function as activator of SA-dependent defense genes and a repressor of JA-regulated genes
mediumpurple2 Gbar_A06G004340 AT1G44790 ChaC-like family protein
Gbar_D13G009340 AT1G13580 Encodes a ceramide synthase that together with LOH1 is essential for production of ceramides containing Very Long Chain Fatty acid VLCFA-Ceramides
Gbar_A07G003530 AT2G25080 Encodes glutathione peroxidase
Gbar_A04G014550 AT1G70280 NHL domain-containing protein
Gbar_A11G016340 AT2G30860 Encodes glutathione transferase belonging to the phi class of GSTs

Supplementary table 5

Function annotation of interacting genes of the hub genes"

Gene ID in G. barbadense
Gene ID in Arabidopsis
Gene Function
black Gbar_D03G018910 AT5G36930 Disease resistance protein (TIR-NBS-LRR class) family
black Gbar_D11G029060 AT3G05545 RING/U-box superfamily protein
black Gbar_A11G009020 AT5G23850 O-glucosyltransferase rumi-like protein (DUF821)
black Gbar_D04G003120 AT5G24080 Protein kinase superfamily protein
black Gbar_D01G005060 AT3G47570 Leucine-rich repeat protein kinase family protein
black Gbar_D11G034710 AT2G38920 SPX (SYG1/Pho81/XPR1) domain-containing protein / zinc finger (C3HC4-type RING finger) protein-like protein
black Gbar_D12G025730 AT5G53620 RNA polymerase II degradation factor
black Gbar_A13G017840 AT5G14230 Ankyrin
black Gbar_D01G019380 AT4G24290 MAC/Perforin domain-containing protein
black Gbar_D13G004090 AT2G15220 Plant basic secretory protein (BSP) family protein
black Gbar_D13G022900 AT4G30060 Core-2/I-branching beta-1,6-N-acetylglucosaminyltransferase family protein
black Gbar_Scaffold3330G000020 AT5G54130 Calcium-binding endonuclease/exonuclease/phosphatase family
black Gbar_A12G023730 AT1G12460 Leucine-rich repeat protein kinase family protein
black Gbar_D09G023870 AT1G06620 Encodes a protein whose sequence is similar to a 2-oxoglutarate-dependent dioxygenase
black Gbar_D03G017310 AT5G53110 RING/U-box superfamily protein
black Gbar_D12G004330 AT2G15910 CSL zinc finger domain-containing protein
black Gbar_D06G023370 AT1G75290 Encodes a protein whose sequence is similar to an isoflavone reductase
black Gbar_D13G019590 AT1G02460 Pectin lyase-like superfamily protein
black Gbar_D04G014850 AT1G59650 Encodes CW14
black Gbar_A12G008940 AT4G37790 Encodes homeobox protein HAT22, member of the HD-Zip II family
black Gbar_D01G009090 AT2G04240 Encodes a small protein with an N-terminal trans-membrane domain and a RING-H2 zinc finger motif located at the C-terminus
black Gbar_D01G000450 AT2G16280 Encodes KCS9, a member of the 3-ketoacyl-CoA synthase family involved in the biosynthesis of VLCFA (very long chain fatty acids)
black Gbar_D02G010580 AT5G66070 E3 ubiquitin ligase that functions in negative regulation of ABA signaling.
black Gbar_A13G012150 AT3G05420 Acyl-CoA binding protein with high affinity for oleoyl-CoA
black Gbar_D12G014610 AT1G50200 Alanyl-tRNA synthetase
black Gbar_D12G017990 AT1G69830 Encodes a plastid-localized α-amylase
black Gbar_D13G008370 AT1G26560 Beta glucosidase 40
black Gbar_D05G027970 AT1G35670 Encodes a Ca(2)-dependent, calmodulin-independent protein kinase that is rapidly induced by drought and high-salt stress but not by low-temperature stress or heat stress
black Gbar_D01G006740 AT5G54590 Encodes CRLK1 (440-amino acid in length) calcium/calmodulin-regulated receptor-like kinase crucial for cold tolerance
black Gbar_D12G025650 AT5G24530 Encodes a putative 2OG-Fe(II) oxygenase that is defense-associated but required for susceptibility to downy mildew
black Gbar_D13G021410 AT4G33050 Encodes a calmodulin-binding protein involved in stomatal movement
black Gbar_D10G001060 AT4G05520 Encodes AtEHD2, one of the Arabidopsis Eps15 homology domain proteins involved in endocytosis (AtEHD1, At3g20290)
black Gbar_D12G022540 AT4G17500 Encodes a member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family (ATERF-1)
black Gbar_D06G015340 AT5G46330 Encodes a leucine-rich repeat serine/threonine protein kinase that is expressed ubiquitousl
black Gbar_D12G027320 AT5G51830 Encodes one of the several Arabidopsis fructokinases
black Gbar_D10G003110 AT2G29120 Member of Putative ligand-gated ion channel subunit family
black Gbar_D07G004760 AT3G47420 Encodes a Pi starvation-responsive protein AtPS3
black Gbar_D07G024150 AT5G14760 Encodes for L-aspartate oxidase involved in the early steps of NAD biosynthesis
black Gbar_D12G020770 AT5G23670 Encodes the LCB2 subunit of serine palmitoyltransferase, an enzyme involved in sphingosine biosynthesis
black Gbar_D13G005810 AT5G23450 Encodes a sphingosine kinase that specifically phosphorylates D-erythro-dihydrosphingosine (DHS), but not N-acetyl-DHS or D-threo-DHS
black Gbar_D13G019790 AT4G31080 Encodes one of two LUNAPARK proteins in Arabidopsis
black Gbar_D12G026490 AT5G52870 Encodes a member of the MAKR (MEMBRANE-ASSOCIATED KINASE REGULATOR) gene family
black Gbar_D11G032600 AT5G27450 Encodes a protein with mevalonate kinase activity involved in the mevalonate pathway
black Gbar_D06G007510 AT5G57620 MYB36 is a transcriptional regulator that acts to promote differentiation of the endodermis during root development
black Gbar_A13G005180 AT1G69850 Encodes an inducible component of low-affinity nitrate uptake. mRNA found primarily in root hairs and the epidermis of roots
black Gbar_D03G004100 AT2G22480 Phosphofructokinase 5
black Gbar_D04G003630 AT3G52430 Encodes a lipase-like gene that is important for salicylic acid signaling and function in resistance (R) gene-mediated and basal plant disease resistance
black Gbar_D07G018560 AT1G05000 Encodes an atypical dual-specificity phosphatase
black Gbar_D13G016920 AT3G02800 Encodes an atypical dual-specificity phosphatase
black Gbar_D13G018380 AT5G18480 Encodes an IPC (inositol phosphorylceramide) glucuronosyltransferase
black Gbar_D05G029400 AT5G38280 Putative receptor serine/threonine kinase PR5K (PR5K) mRNA, PR5-like receptor kinase
black Gbar_D06G004430 AT1G77720 Encodes a predicted protein kinase based on sequence similarity
black Gbar_A05G042760 AT3G24560 Novel gene involved in embryogenesis
black Gbar_A09G027280 AT5G01410 Encodes a protein predicted to function in tandem with PDX2 to form glutamine amidotransferase complex with involved in vitamin B6 biosynthesis
black Gbar_D01G003220 AT1G11330 S-locus lectin protein kinase family protein
black Gbar_D13G023280 AT2G42520 P-loop containing nucleoside triphosphate hydrolases superfamily protein
black Gbar_D12G013250 AT5G26751 Encodes a SHAGGY-related kinase involved in meristem organization
black Gbar_D11G007720 AT3G01090 Encodes a SNF1-related protein kinase that physically interacts with SCF subunit SKP1/ASK1 and 20S proteosome subunit PAD1
black Gbar_D03G011160 AT3G19930 Encodes a sucrose hydrogen symporter that is induced by wounding
black Gbar_D13G001830 AT5G13820 Encodes a protein that specifically binds plant telomeric DNA repeats
black Gbar_D05G019900 AT5G42710 Hypothetical protein
black Gbar_D02G004390 AT3G23230 Encodes a member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family
black Gbar_D11G017280 AT3G02320 N2,N2-dimethylguanosine tRNA methyltransferase
black Gbar_D12G022400 AT4G17610 tRNA/rRNA methyltransferase (SpoU) family protein
black Gbar_D13G025510 AT2G30110 Encodes a ubiquitin-activating enzyme (E1), involved in the first step in conjugating multiple ubiquitins to proteins targeted for degradation
darkolivegreen Gbar_A07G025160 AT5G58520 Protein kinase superfamily protein
darkolivegreen Gbar_D03G003590 AT4G39790 bZIP transcription factor, putative (DUF630 and DUF632)
darkolivegreen Gbar_D03G001100 AT4G36180 Leucine-rich receptor-like protein kinase family protein
darkolivegreen Gbar_D01G009920 AT4G26830 O-Glycosyl hydrolases family 17 protein
darkolivegreen Gbar_D01G016760 AT3G26430 Encodes a functioning member of the GDS(L) lipase family with preference for long chain substrates that does not hydrolyze choline esters
darkolivegreen Gbar_D03G001880 AT5G66560 Phototropic-responsive NPH3 family protein
darkolivegreen Gbar_A13G025790 AT1G55690 Sec14p-like phosphatidylinositol transfer family protein
darkolivegreen Gbar_D01G007300 AT5G54855 Pollen Ole e 1 allergen and extensin family protein
darkolivegreen Gbar_A05G043880 AT3G01790 Ribosomal protein L13 family protein
darkolivegreen Gbar_D13G016400 AT1G61600 DUF1262 family protein (DUF1262)
darkolivegreen Gbar_D02G013480 AT1G14190 Glucose-methanol-choline (GMC) oxidoreductase family protein
darkolivegreen Gbar_D13G010360 AT2G37400 Tetratricopeptide repeat (TPR)-like superfamily protein
darkolivegreen Gbar_D01G007390 AT1G50660 Actin cytoskeleton-regulatory complex pan-like protein
darkolivegreen Gbar_D03G014040 AT5G60050 BTB/POZ domain-containing protein
darkolivegreen Gbar_D02G017350 AT1G60590 Pectin lyase-like superfamily protein
darkolivegreen Gbar_D02G014970 AT1G31050 Basic helix-loop-helix (bHLH) DNA-binding superfamily protein
darkolivegreen Gbar_D01G022140 AT3G53190 Pectin lyase-like superfamily protein
darkolivegreen Gbar_D03G008970 AT4G00910 Aluminum activated malate transporter family protein
darkolivegreen Gbar_D12G024850 AT4G24060 Dof-type zinc finger DNA-binding family protein
darkolivegreen Gbar_A13G005740 AT1G11120 CTTNBP 2 amino-terminal-like protein
darkolivegreen Gbar_D02G016040 AT2G23520 Pyridoxal phosphate (PLP)-dependent transferases superfamily protein
darkolivegreen Gbar_D01G005690 AT4G21700 DUF2921 family protein, putative (DUF2921)
darkolivegreen Gbar_D13G019080 AT1G54820 Protein kinase superfamily protein
darkolivegreen Gbar_D03G002350 AT5G67130 PLC-like phosphodiesterases superfamily protein
darkolivegreen Gbar_D03G012130 AT5G24320 Transducin/WD40 repeat-like superfamily protein
darkolivegreen Gbar_A13G006430 AT3G20015 Eukaryotic aspartyl protease family protein
darkolivegreen Gbar_D01G006010 AT5G05520 Outer membrane OMP85 family protein
darkolivegreen Gbar_D11G035890 AT2G38090 Duplicated homeodomain-like superfamily protein
darkolivegreen Gbar_D12G026880 AT5G23760 Copper transport protein family
darkolivegreen Gbar_D02G017340 AT1G23460 Pectin lyase-like superfamily protein
darkolivegreen Gbar_D03G008720 AT3G61920 UvrABC system protein C
darkolivegreen Gbar_D02G019700 AT4G28100 Transmembrane protein
darkolivegreen Gbar_D02G017750 AT1G60010 D-ribose-binding periplasmic protein
darkolivegreen Gbar_D01G003090 AT1G79030 Chaperone DnaJ-domain superfamily protein
darkolivegreen Gbar_D03G014810 AT5G22930 Enabled-like protein (DUF1635)
darkolivegreen Gbar_D13G021850 AT3G14470 NB-ARC domain-containing disease resistance protein
darkolivegreen Gbar_D13G007120 AT1G25530 Transmembrane amino acid transporter family protein
darkolivegreen Gbar_D02G021450 AT1G58120 Hypothetical protein
darkolivegreen Gbar_D01G005820 AT5G17680 Disease resistance protein (TIR-NBS-LRR class)
darkolivegreen Gbar_A13G019670 AT4G31330 Transmembrane protein, putative (Protein of unknown function, DUF599)
darkolivegreen Gbar_D02G014500 AT3G02820 Zinc knuckle (CCHC-type) family protein
darkolivegreen Gbar_A13G023560 AT1G07970 Cytochrome B561, amino-terminal protein
darkolivegreen Gbar_D02G008760 AT1G22030 BPS1-like protein
darkolivegreen Gbar_D01G021510 AT3G10120 Hypothetical protein
darkolivegreen Gbar_D02G019240 AT4G28310 Microtubule-associated protein
darkolivegreen Gbar_A13G023180 AT3G51950 Zinc finger (CCCH-type) family protein / RNA recognition motif (RRM)-containing protein
darkolivegreen Gbar_A13G017430 AT5G17600 RING/U-box superfamily protein
darkolivegreen Gbar_D01G020700 AT4G24380 Dihydrofolate reductase
darkolivegreen Gbar_Scaffold2990G000010 AT3G22142 Encodes a Protease inhibitor/seed storage/LTP family protein
darkolivegreen Gbar_D02G009130 AT1G09750 Eukaryotic aspartyl protease family protein
darkolivegreen Gbar_D03G000630 AT2G27090 bZIP transcription factor (DUF630 and DUF632)
darkolivegreen Gbar_A13G008810 AT2G03350 DUF538 family protein (Protein of unknown function, DUF538)
darkolivegreen Gbar_D02G001120 AT1G05710 Basic helix-loop-helix (bHLH) DNA-binding superfamily protein
darkolivegreen Gbar_D02G025330 AT1G09812 Multidrug resistance protein
darkolivegreen Gbar_D13G015880 AT1G53050 Protein kinase superfamily protein
darkolivegreen Gbar_A13G011970 AT3G05190 D-aminoacid aminotransferase-like PLP-dependent enzymes superfamily protein
darkolivegreen Gbar_D02G020480 AT5G08540 Ribosomal RNA small subunit methyltransferase J
darkolivegreen Gbar_D13G000740 AT5G05180 Myosin heavy chain, striated protein
darkolivegreen Gbar_A13G008440 AT1G10380 Putative membrane lipoprotein
darkolivegreen Gbar_D02G023270 AT4G34480 O-Glycosyl hydrolases family 17 protein
darkolivegreen Gbar_D03G015720 AT4G23500 Pectin lyase-like superfamily protein
darkolivegreen Gbar_D02G001660 AT3G48400 Cysteine/Histidine-rich C1 domain family protein
darkolivegreen Gbar_D02G023930 AT2G21290 30S ribosomal protein S31
darkolivegreen Gbar_D12G024650 AT4G23895 Pleckstrin homology (PH) domain-containing protein
darkolivegreen Gbar_D12G023010 AT4G16510 YbaK/aminoacyl-tRNA synthetase-associated domain-containing protein
darkolivegreen Gbar_D02G004850 AT5G43960 Nuclear transport factor 2 (NTF2) family protein with RNA binding (RRM-RBD-RNP motifs) domain-containing protein
darkolivegreen Gbar_D03G009270 AT1G33120 Ribosomal protein L6 family
darkolivegreen Gbar_D01G015160 AT3G19850 Phototropic-responsive NPH3 family protein
darkolivegreen Gbar_D03G008670 AT4G23930 Late embryogenesis abundant (LEA) hydroxyproline-rich glycoprotein family
darkolivegreen Gbar_D02G023430 AT4G39210 Encodes the large subunit of ADP-Glucose Pyrophosphorylase which catalyzes the first, rate limiting step in starch biosynthesis
darkolivegreen Gbar_A13G019130 AT1G22490 Basic helix-loop-helix (bHLH) DNA-binding superfamily protein
darkolivegreen Gbar_D11G036510 AT1G70000 Encodes a MYB-like Domain transcription factor that plays a positive role in anthocyanin accumulation in response to light and cytokinin via repression of MYBL2
darkolivegreen Gbar_D13G008600 AT1G58520 GDSL-like lipase/acylhydrolase superfamily protein
darkolivegreen Gbar_D12G028470 AT3G48210 kinetochore protein
darkolivegreen Gbar_D03G009120 AT4G10850 Nodulin MtN3 family protein
darkolivegreen Gbar_A13G003860 AT3G19100 Encodes a protein kinase that positively regulates gibberellic acid (GA) signaling by inactivating the E3 ubiquitin ligase GARU
darkolivegreen Gbar_D02G023340 AT2G21660 Encodes a small glycine-rich RNA binding protein that is part of a negative-feedback loop through which AtGRP7 regulates the circadian oscillations of its own transcript
darkolivegreen Gbar_D01G008490 AT4G14540 nuclear factor Y, subunit B3
darkolivegreen Gbar_D01G011180 AT1G47250 Encodes 20S proteasome subunit PAF2 (PAF2).
darkolivegreen Gbar_D03G005030 AT1G65060 Encodes an isoform of 4-coumarate:CoA ligase (4CL), which is involved in the last step of the general phenylpropanoid pathway
darkolivegreen Gbar_D02G024250 AT2G16700 Encodes actin depolymerizing factor 5 (ADF5).
darkolivegreen Gbar_D02G024080 AT4G34860 Plant neutral invertase family protein
darkolivegreen Gbar_D11G036750 AT1G68560 Encodes a bifunctional alpha-l-arabinofuranosidase/beta-d-xylosidase that belongs to family 3 of glycoside hydrolases
darkolivegreen Gbar_D01G012240 AT5G49630 Is a high affinity amino acid transporter capable of transporting aspartate and tryptophan
darkolivegreen Gbar_A13G017880 AT5G12380 Annexin 8
darkolivegreen Gbar_D01G021800 AT3G23620 BRIX domain containing protein, similar to RNA biogenesis factors in yeast. Binds rRNA and likely also functions in RNA biogenesis in Arabidopsis
darkolivegreen Gbar_D03G012140 AT5G24330 Encodes a SET-domain protein, a H3K27 monomethyltransferases required for chromatin structure and gene silencing
darkolivegreen Gbar_D01G012780 AT2G26430 Encodes an ania-6a type arginine-rich cyclin which confers tolerance to LiCl and NaCl when expressed in yeast.
darkolivegreen Gbar_D12G027500 AT4G25320 AT hook motif DNA-binding family protein
darkolivegreen Gbar_D13G014580 AT3G13080 Encodes an ATP-dependent MRP-like ABC transporter able to transport glutathione-conjugates as well as chlorophyll catabolites
darkolivegreen Gbar_D03G001120 AT4G38960 BBX19 is a B-box containing transcriptional regulator involved in photomporphogenesis and flowering.
darkolivegreen Gbar_D02G019950 AT3G21890 B-box type zinc finger family protein
darkolivegreen Gbar_D02G025320 AT5G65700 Encodes a CLAVATA1-related receptor kinase-like protein required for both shoot and flower meristem function
darkolivegreen Gbar_D02G025580 AT4G20270 Encodes a CLAVATA1-related receptor kinase-like protein required for both shoot and flower meristem function. It has a broad expression pattern and is involved in vascular strand development in the leaf, control of leaf shape, size and symmetry, male gametophyte development and ovule specification and function. The mRNA is cell-to-cell mobile.
darkolivegreen Gbar_D02G024640 AT3G12500 Encodes a basic chitinase involved in ethylene/jasmonic acid mediated signalling pathway during systemic acquired resistance based on expression analyses.
darkolivegreen Gbar_D03G003360 AT5G65640 bHLH093/NFL encodes a bHLH transcription factor involved in GA mediated control of flowering time
darkolivegreen Gbar_D02G020910 AT5G64570 Encodes a beta-d-xylosidase that belongs to family 3 of glycoside hydrolases.
darkolivegreen Gbar_D13G020070 AT4G31910 Encodes an acyltransferase that can modify brassinosteroids (BRs) by acylation and may modulate endogenous BR levels.
darkolivegreen Gbar_D03G005940 AT3G16300 Uncharacterized protein family (UPF0497)
darkolivegreen Gbar_D12G022380 AT5G04770 Encodes a member of the cationic amino acid transporter (CAT) subfamily of amino acid polyamine choline transporters
darkolivegreen Gbar_A13G017960 AT1G55850 Encodes a protein similar to cellulose synthase The mRNA is cell-to-cell mobile.
darkolivegreen Gbar_D04G001300 AT5G05270 Chalcone-flavanone isomerase family protein
darkolivegreen Gbar_Scaffold769G000030 AT1G75820 Putative receptor kinase with an extracellular leucine-rich domain
darkolivegreen Gbar_D02G004490 AT5G43330 Predicted to encode a cytosolic malate dehydrogenase
darkolivegreen Gbar_D01G000430 AT2G16370 Encodes a bifunctional dihydrofolate reductase - thymidylate synthase gene
darkolivegreen Gbar_A13G004830 AT5G48490 Encodes a protein with similarity to a lipid transfer protein that may contribute to systemic acquired resistance (SAR).
darkolivegreen Gbar_D05G039960 AT3G13310 Chaperone DnaJ-domain superfamily protein
darkolivegreen Gbar_A13G003970 AT2G15690 Encodes an atypical PPR-DYW protein
darkolivegreen Gbar_D12G028430 AT1G18330 EARLY-PHYTOCHROME-RESPONSIVE1
darkolivegreen Gbar_D01G004350 AT5G20480 Encodes a predicted leucine-rich repeat receptor kinase (LRR-RLK). Functions as the receptor for bacterial PAMP (pathogen associated molecular patterns).
darkolivegreen Gbar_A13G017640 AT5G17710 Chloroplast GrpE protein involved in chloroplastic response to heat stress and the correct oligomerization of the photosynthesis-related LHCII complex.
darkolivegreen Gbar_D03G006920 AT1G21390 Embryo defective 2170
darkolivegreen Gbar_D12G027570 AT5G51550 EXORDIUM like 3
darkolivegreen Gbar_A13G000700 AT2G40610 Member of Alpha-Expansin Gene Family
darkolivegreen Gbar_D02G012070 AT2G43280 Encodes one of four FRS (FAR1-RELATED SEQUENCE) factor-like genes in Arabidopsis
darkolivegreen Gbar_D13G016510 AT1G53520 Encodes a plastid stroma localized fatty acid binding protein involved in fatty acid metabolism.
darkolivegreen Gbar_A06G022760 AT1G78020 FCS like zinc finger 6 is induced during energy starvation through SnRK1 signaling
darkolivegreen Gbar_A13G006340 AT5G23310 Fe superoxide dismutase
darkolivegreen Gbar_D13G024310 AT2G27510 ferredoxin 3
darkolivegreen Gbar_D02G000800 AT2G43800 Localizes to plasmodesmata (PD) through its transmembrane domain and is required for normal intercellular trafficking
darkolivegreen Gbar_D03G001360 AT1G47260 Encodes mitochondrial gamma carbonic anhydrase. Component of the NADH dehydrogenase complex.
darkolivegreen Gbar_A13G019010 AT1G54690 Encodes HTA3, a histone H2A protein. H2AX is a meiosis-specific isoform of histone H2A
darkolivegreen Gbar_D01G022110 AT2G36830 Encodes a tonoplast intrinsic protein, which functions as water channel
darkolivegreen Gbar_D02G018320 AT1G68360 Encodes a nuclear localized member of the C2H2 family of TFIIIA transcription factors
darkolivegreen Gbar_D13G009120 AT1G05200 Encodes a putative glutamate receptor GLR3 with dual localization in plastid and plasma membrane.
darkolivegreen Gbar_D01G015560 AT1G70710 endo-1,4-beta-glucanase. Involved in cell elongation.
darkolivegreen Gbar_D13G002820 AT4G39010 Cellulase involved in cell wall modification during valve dehiscence.
darkolivegreen Gbar_D02G018880 AT1G28130 Encodes an IAA-amido synthase that conjugates Asp and other amino acids to auxin in vitro
darkolivegreen Gbar_D01G005250 AT3G15095 Encodes HCF243 (high chlorophyll fluorescence), a chloroplast-localized protein involved in the D1 protein stability of the photosystem II complex1.
darkolivegreen Gbar_A13G002560 AT5G03260 LAC11 is a putative laccase, a member of laccase family of genes (17 members in Arabidopsis).
darkolivegreen Gbar_D12G028450 AT5G50150 LOTR1 protein has an unknown function. It contains both DUF4409 and DUF239 domains
darkolivegreen Gbar_D01G021830 AT2G36530 Involved in light-dependent cold tolerance and encodes an enolase
darkolivegreen Gbar_D02G011760 AT3G11710 lysyl-tRNA synthetase 1
darkolivegreen Gbar_D03G009750 AT3G47520 Encodes a protein with NAD-dependent malate dehydrogenase activity, located in chloroplasts
darkolivegreen Gbar_D02G004910 AT4G08850 MIK1 encodes a receptor kinase that forms a complex with MDIS1/MIK2 and binds LURE1, the female pollen guidance chemi-attractant
darkolivegreen Gbar_D03G008120 AT1G64080 Encodes a member of the MAKR (MEMBRANE-ASSOCIATED KINASE REGULATOR) gene family
darkolivegreen Gbar_D13G023490 AT5G12970 Calcium-dependent lipid-binding (CaLB domain) plant phosphoribosyltransferase family protein
darkolivegreen Gbar_D03G013750 AT3G46130 Encodes a putative transcription factor (MYB48) that functions to regulate flavonol biosynthesis primarily in cotyledons.
darkolivegreen Gbar_D11G035630 AT5G14750 Encodes a MyB-related protein containing R2 and R3 repeats, involved in root and hypocotyl epidermal cell fate determination
darkolivegreen Gbar_D13G007380 AT2G02820 Encodes a putative transcription factor (MYB88), involved in stomata development, double loss of MYB88 and FLP (MYB124) activity results in a failure of guard mother cells (GMCs) to adopt the guard cell fate, thus they continue to divide resulting in abnormal stomata consisting of clusters of numerous guard cell-like cells
darkolivegreen Gbar_D02G015320 AT1G70750 Myosin-binding protein
darkolivegreen Gbar_D03G017750 AT4G17980 Encodes ANAC071, a transcription factor involved in cell proliferation in incised inflorescence stems.
darkolivegreen Gbar_A11G035350 AT5G16000 NSP-interacting kinase (NIK1), receptor-like kinase, involved in defense response against geminivirus
darkolivegreen Gbar_A13G010550 AT3G25560 NSP-interacting kinase 2
darkolivegreen Gbar_D11G035920 AT3G09070 Encodes a polarly localised membrane-associated protein that regulates phloem differentiation entry.
darkolivegreen Gbar_D12G028320 AT1G73220 Encodes Organic Cation Transporter 1 (OCT1), likely to be involved in polyamine transport.
darkolivegreen Gbar_D03G016160 AT4G11650 osmotin-like protein
darkolivegreen Gbar_D02G000480 AT5G01840 Encodes a member of the plant specific ovate protein family
darkolivegreen Gbar_D12G027290 AT5G51890 encodes peroxidase involved in the lignification of tracheary elements (TE) in roots
darkolivegreen Gbar_D01G021840 AT3G52960 Thioredoxin superfamily protein
darkolivegreen Gbar_A13G018460 AT1G08650 Encodes a phosphoenolpyruvate carboxylase kinase that is expressed at highest levels in leaves
darkolivegreen Gbar_D01G022280 AT2G37170 A member of the plasma membrane intrinsic protein subfamily PIP2
darkolivegreen Gbar_D13G008460 AT1G18650 Encodes a member of the X8-GPI family of proteins
darkolivegreen Gbar_D02G006410 AT1G48100 Pectin lyase-like superfamily protein
darkolivegreen Gbar_D02G018990 AT1G03860 prohibitin 2
darkolivegreen Gbar_A13G004330 AT4G34220 Encodes a receptor like kinase involved in ABA-mediated seedling development and drought tolerance
darkolivegreen Gbar_D13G003440 AT3G18990 Essential for the complete repression of FLC in vernalized plants
darkolivegreen Gbar_D03G016800 AT4G22790 Encodes a plasma membrane localized MATE type transporter that is involved in CO2 signaling during stomatal aperture regulation
darkolivegreen Gbar_D13G013740 AT1G79380 Encodes a ubiquitin ligase that is an essential upstream modulator of JA signaling in response to various stimuli.
darkolivegreen Gbar_D13G009470 AT3G26420 Zinc finger-containing glycine-rich RNA-binding protein
darkolivegreen Gbar_D03G015290 AT2G30280 Encodes RDM4, a transcriptional regulator functioning in RNA-directed DNA methylation and plant development.
darkolivegreen Gbar_D01G017350 AT2G16600 Encodes cytosolic cyclophilin ROC3. The mRNA is cell-to-cell mobile.
darkolivegreen Gbar_D03G003950 AT5G10350 Encodes a nuclear-localized RNA recognition motif-containing protein that forms homodimers
darkolivegreen Gbar_A13G019760 AT4G31580 Encodes a Serine/arginine-rich (SR) protein RSZp22
darkolivegreen Gbar_D03G015520 AT5G38410 Encodes a member of the Rubisco small subunit (RBCS) multigene family
darkolivegreen Gbar_D01G013700 AT1G17020 Encodes a novel member of the Fe(II)/ascorbate oxidase gene family; senescence-related gene.
darkolivegreen Gbar_D01G008320 AT3G13110 Encodes a mitochondrial serine O-acetyltransferase involved in sulfur assimilation and cysteine biosynthesis. Expressed in the vascular system.
darkolivegreen Gbar_D02G010370 AT1G75520 A member of SHI gene family. Arabidopsis thaliana has ten members that encode proteins with a RING finger-like zinc finger motif
darkolivegreen Gbar_D01G014830 AT2G01940 Encodes a transcription factor that, together with IDD14 and IDD16, regulates auxin biosynthesis and transport and thus aerial organ morphogenesis and gravitropic responses
darkolivegreen Gbar_A13G000980 AT3G52490 Encodes a member of an eight-gene family (SMAX1 and SMAX1-like) that has weak similarity to AtHSP101, a ClpB chaperonin required for thermo tolerance.
darkolivegreen Gbar_D01G008860 AT5G56040 Leucine-rich receptor-like protein kinase family protein
darkolivegreen Gbar_D01G019160 AT1G58100 Encodes TCP8, belongs to the TCP transcription factor family known to bind site II elements in promoter regions.
darkolivegreen Gbar_D12G023520 AT2G45680 TCP family transcription factor
darkolivegreen Gbar_D02G008770 AT1G77920 bZIP transcription factor family protein
darkolivegreen Gbar_D05G039710 AT5G55860 WEB1/PMI2 related protein involved in mecahno transduction
darkolivegreen Gbar_A13G002180 AT3G55120 Catalyzes the conversion of chalcones into flavanone
darkolivegreen Gbar_D01G024260 AT2G37025 TRF-like 8
darkolivegreen Gbar_D13G008210 AT1G07250 UDP-glucosyl transferase 71C4
darkolivegreen Gbar_D02G002150 AT1G05530 Encodes a protein with glucosyltransferase activity with high sequence homology to UGT1 (AT1G05560)
darkolivegreen Gbar_D03G008130 AT3G16520 UDP-glucosyl transferase 88A1
darkolivegreen Gbar_D01G020070 AT4G08300 Nodulin MtN21-like transporter family protein
darkolivegreen Gbar_D02G017680 AT1G70260 Encodes an endoplasmic reticulum (ER)-localized nodulin MtN21-like transporter family protein that negatively regulates resistance against biotrophic pathogens but not the necrotrophic pathogen, B. cinerea, possibly by regulating ROS production, cell death and PR1 expression.
darkolivegreen Gbar_A13G002730 AT2G01770 Encodes an iron transporter required for iron sequestration into vacuoles
darkolivegreen Gbar_D03G003330 AT2G22680 Zinc finger (C3HC4-type RING finger) family protein
darkolivegreen Gbar_D13G002720 AT2G01830 Histidine kinase: cytokinin-binding receptor that transduces cytokinin signals across the plasma membrane
darkolivegreen Gbar_D13G017670 AT3G03660 Encodes a WUSCHEL-related homeobox gene family member with 65 amino acids in its homeodomain
darkolivegreen Gbar_D13G014440 AT1G55910 Member of Putative zinc transporter ZIP2 - like family
mediumpurple2 Gbar_D13G017100 AT2G36780 UDP-Glycosyltransferase superfamily protein
mediumpurple2 Gbar_D12G013470 AT4G02010 Protein kinase superfamily protein
mediumpurple2 Gbar_D05G025460 AT1G33810 Zinc finger/BTB domain protein
mediumpurple2 Gbar_A05G035880 AT5G14390 Alpha/beta-Hydrolases superfamily protein
mediumpurple2 Gbar_A10G019000 AT2G40800 Import inner membrane translocase subunit
mediumpurple2 Gbar_A11G026760 AT1G60690 NAD(P)-linked oxidoreductase superfamily protein
mediumpurple2 Gbar_D06G023300 AT5G60710 Zinc finger (C3HC4-type RING finger) family protein
mediumpurple2 Gbar_A08G010720 AT4G25610 C2H2-like zinc finger protein
mediumpurple2 Gbar_D02G025440 AT2G34670 Benzoyl-CoA reductase subunit C, putative (DUF630 and DUF632)
mediumpurple2 Gbar_D05G005440 AT2G24230 Leucine-rich repeat protein kinase family protein
mediumpurple2 Gbar_D09G012540 AT3G57080 Non-catalytic subunit unique to Nuclear DNA-dependent RNA polymerase V; homologous to budding yeast RPB5.
mediumpurple2 Gbar_D13G019810 AT4G31300 Encodes 20S proteasome subunit PBA1 (PBA1). PBA1 acts as a plant caspase-3-like enzyme.
mediumpurple2 Gbar_D13G011390 AT5G28840 Encodes a protein with GDP-D-mannose 3',5'-epimerase activity. The enzyme is involved in ascorbate biosynthesis
mediumpurple2 Gbar_A11G029250 AT1G56450 20S proteasome beta subunit PBG1 (PBG1) mRNA, complete cds
mediumpurple2 Gbar_D10G008010 AT1G80070 Encodes a factor that influences pre-mRNA splicing and is required for embryonic development
mediumpurple2 Gbar_A12G004970 AT4G20070 The gene encoding Arabidopsis thaliana Allantoate Amidohydrolase (AtAAH) which catalyzes the allantoate deiminase reaction
mediumpurple2 Gbar_D05G011510 AT3G21180 Encodes an autoinhibited Ca(2)-ATPase that contains an N-terminal calmodulin binding autoinhibitory domain.
mediumpurple2 Gbar_D08G006200 AT3G63520 Encodes a protein with 9-cis-epoxycarotenoid dioxygenase activity
mediumpurple2 Gbar_D01G010230 AT5G42310 Encodes a member of the Arabidopsis PPR family
mediumpurple2 Gbar_D01G008710 AT5G47750 D6PK family kinase involved in pulse-induced phototropism and continuous light-induced hypocotyl phototropism, minor contribution to time-dependent phototropism.
mediumpurple2 Gbar_D07G010350 AT1G07810 Encodes an ER-type Ca2+pumping ATPase. The mRNA is cell-to-cell mobile.
mediumpurple2 Gbar_D08G017480 AT1G31930 Encodes XLG3 (extra-large G protein 3) that shows significant similarity to the G protein alpha subunit in its C terminal region
mediumpurple2 Gbar_A07G003530 AT2G25080 Encodes glutathione peroxidase. The mRNA is cell-to-cell mobile.
mediumpurple2 Gbar_A11G016340 AT2G30860 Encodes glutathione transferase belonging to the phi class of GSTs
mediumpurple2 Gbar_A09G017200 AT5G02790 Glutathione S-transferase family protein
mediumpurple2 Gbar_D11G012220 AT3G06720 Encodes importin alpha involved in nuclear import
mediumpurple2 Gbar_A13G010590 AT1G13580 Encodes a ceramide synthase that together with LOH1 is essential for production of ceramides containing Very Long Chain Fatty acid VLCFA-Ceramides.
mediumpurple2 Gbar_D02G015200 AT1G23260 MMZ1/UEV1A encodes a protein that may play a role in DNA damage responses and error-free post-replicative DNA repair by participating in lysine-63-based polyubiquitination reactions
mediumpurple2 Gbar_D09G013360 AT3G57880 Required for maintenance of inflorescence and shoot SAMs and normal development of the derived vascular cambium, functions in the SAM to promote continuous organogenesis, affects SAM development through STM, where it affects intracellular localization of STM in SAM cells in the peripheral region and prevents STM localization toward the cell wall of SAM cells in the peripheral region.
mediumpurple2 Gbar_A06G015880 AT4G04880 Adenosine/AMP deaminase family protein
mediumpurple2 Gbar_A06G015500 AT1G53840 Encodes a pectin methylesterase
mediumpurple2 Gbar_A09G009100 AT5G13640 Arabidopsis phospholipid:diacylglycerol acyltransferase (PDAT)
mediumpurple2 Gbar_A12G002960 AT2G14260 Encodes proline iminopeptidase
mediumpurple2 Gbar_A11G032430 AT1G08540 Enodes a subunit of chloroplast RNA polymerase, confers the ability to recognize promoter sequences on the core enzyme. SIG1 is induced by red and blue light.
mediumpurple2 Gbar_D12G004810 AT3G12800 Short-chain dehydrogenase-reductase B
mediumpurple2 Gbar_D13G009630 AT5G16270 Encodes a SCC1/REC8 ortholog that may be involved in mitosis and may represent a mitotic cohesin
mediumpurple2 Gbar_D12G018730 AT1G76160 SKU5 similar 5
mediumpurple2 Gbar_D13G012850 AT1G73720 Encodes SMU1, a protein involved in RNA splicing.
mediumpurple2 Gbar_D11G002190 AT1G63800 ubiquitin-conjugating enzyme 5
mediumpurple2 Gbar_A11G026970 AT3G04870 Involved in the biosynthesis of carotenes and xanthophylls, reduces zeta-carotene to lycopene.
mediumpurple3 Gbar_D13G023330 AT1G58170 Disease resistance-responsive (dirigent-like protein) family protein
mediumpurple3 Gbar_A11G019370 AT2G23450 Protein kinase superfamily protein
mediumpurple3 Gbar_A04G004150 AT1G53440 Leucine-rich repeat transmembrane protein kinase
mediumpurple3 Gbar_A08G011260 AT1G64300 Protein kinase family protein
mediumpurple3 Gbar_A13G015520 AT5G55340 MBOAT (membrane bound O-acyl transferase) family protein
mediumpurple3 Gbar_D10G024280 AT3G55470 Calcium-dependent lipid-binding (CaLB domain) family protein
mediumpurple3 Gbar_D03G018360 AT4G19010 Encodes for a 4-coumarate-CoA ligase involved in the biosynthesis of the benzenoid ring of ubiquinone from phenylalanine.
mediumpurple3 Gbar_D11G004420 AT4G23340 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
mediumpurple3 Gbar_A06G011840 AT1G22750 Transmembrane protein
mediumpurple3 Gbar_D13G003580 AT2G15780 Cupredoxin superfamily protein
mediumpurple3 Gbar_D13G003030 AT2G21520 Sec14p-like phosphatidylinositol transfer family protein
mediumpurple3 Gbar_D05G014810 AT4G19880 Glutathione S-transferase family protein
mediumpurple3 Gbar_D12G011070 AT2G45300 Encodes 3-phosphoshikimate 1-carboxyvinyltransferase / 5-enolpyruvylshikimate-3-phosphate / EPSP synthase involved in chorismate biosynthesis
mediumpurple3 Gbar_A12G016890 AT1G05210 Transmembrane protein 97, Putative
mediumpurple3 Gbar_A07G021160 AT3G07270 GTP cyclohydrolase I
mediumpurple3 Gbar_D13G022570 AT1G52820 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
mediumpurple3 Gbar_A09G027420 AT1G08230 Codes for a H+driven, high affinity gamma-aminobutyric acid (GABA) transporter
mediumpurple3 Gbar_A09G023570 AT1G60680 NAD(P)-linked oxidoreductase superfamily protein
mediumpurple3 Gbar_D12G016630 AT1G14590 Nucleotide-diphospho-sugar transferase family protein
mediumpurple3 Gbar_A11G014520 AT5G48630 Cyclin family protein
mediumpurple3 Gbar_D09G004390 AT4G23030 MATE efflux family protein
mediumpurple3 Gbar_D05G016380 AT2G44350 Encodes a mitochrondrion targeted citrate synthase, the first enzyme of the tricarboxylic acid cycle, catalyzing the condensation of acetyl-CoA and oxaloacetate, finally yielding citrate and CoA.
mediumpurple3 Gbar_D12G014080 AT3G62830 Encodes an isoform of UDP-glucuronic acid decarboxylase, which is predicted to be membrane-bound by PSORT.
mediumpurple3 Gbar_D01G008230 AT5G25180 Putative cytochrome P450
mediumpurple3 Gbar_D05G020260 AT4G31940 The gene encodes a cytochrome P450 enzyme, CYP82C
mediumpurple3 Gbar_D13G011760 AT3G21430 DNA binding protein
mediumpurple3 Gbar_D11G023600 AT2G22250 Encodes a prokaryotic-type plastidic aspartate aminotransferase with glutamate/aspartate-prephenate aminotransferase (PAT) activity
mediumpurple3 Gbar_A12G004610 AT2G34660 Encodes a multidrug resistance-associated protein that is MgATP-energized glutathione S-conjugate pump
mediumpurple3 Gbar_D11G011340 AT2G37280 Encodes an ATP-binding cassette (ABC) transporter
mediumpurple3 Gbar_D10G026940 AT3G57330 Lesion mimic phenotype when mutation in the gene is combined with a mutation in ACA4
mediumpurple3 Gbar_D13G022050 AT5G20230 Encodes a Al-stress-induced gene. Along with TCF, it promotes lignin biosynthesis in response to cold stress
mediumpurple3 Gbar_D11G036850 AT5G06200 Uncharacterized protein family (UPF0497)
mediumpurple3 Gbar_D04G019360 AT2G44050 6,7-dimethyl-8-ribityllumazine synthase / DMRL synthase / lumazine synthase / riboflavin synthase [Arabidopsis thaliana]
mediumpurple3 Gbar_D11G018340 AT1G65930 Encodes a NADP+isocitrate dehydrogenase that is believed to function in the cytosol
mediumpurple3 Gbar_D05G036060 AT3G23550 MATE efflux family protein
mediumpurple3 Gbar_A07G006230 AT5G08170 Porphyromonas-type peptidyl-arginine deiminase family protein
mediumpurple3 Gbar_D10G026400 AT5G05580 Encodes a temperature sensitive plastidic fatty acid desaturase.
mediumpurple3 Gbar_A09G017280 AT3G09270 Encodes glutathione transferase belonging to the tau class of GSTs
mediumpurple3 Gbar_A12G023890 AT4G11820 Encodes a protein with hydroxymethylglutaryl-CoA synthase activity which was characterized by phenotypical complementation of the S. cerevisiae mutant.
mediumpurple3 Gbar_D11G013690 AT4G02670 Indeterminate(ID)-domain 12
mediumpurple3 Gbar_A10G001130 AT4G05530 Encodes a peroxisomal member of the short-chain dehydrogenase/reductase (SDR) family of enzymes
mediumpurple3 Gbar_D07G009160 AT3G22160 JAV1 is a repressor of jasmonate-mediated defense responses.
mediumpurple3 Gbar_D13G003050 AT5G11880 Meso-diaminopimelate decarboxylase which catalyzes the decarboxylation of mesodiaminopimelate
mediumpurple3 Gbar_A10G014630 AT2G43120 Encodes a member of the functionally diverse cupin protein superfamily that is involved in susceptibility to the bacterial plant pathogen Ralstonia solanacearum
mediumpurple3 Gbar_D05G025610 AT4G10050 Esterase/lipase/thioesterase family protein
mediumpurple3 Gbar_D02G009200 AT5G26780 Encodes a protein with serine hydroxymethyltransferase activity which is thought to be localized in the mitochondrial matrix
mediumpurple3 Gbar_D04G005270 AT5G39950 Encodes a cytosolic thioredoxin that reduces disulfide bridges of target proteins by the reversible formation of a disulfide bridge between two neighboring Cys residues present in the active site
mediumpurple3 Gbar_D12G029450 AT5G17990 Encodes the tryptophan biosynthetic enzyme phosphoribosylanthranilate transferase (PAT1, called trpD in bacteria)
plum3 Gbar_A12G021030 AT5G07610 F-box family protein
plum3 Gbar_D12G026230 AT5G53220 Hypothetical protein
plum3 Gbar_D12G022690 AT4G16720 Ribosomal protein L23/L15e family protein
plum3 Gbar_A10G024460 AT5G05960 Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein
plum3 Gbar_D10G023440 AT4G10720 Ankyrin repeat family protein
plum3 Gbar_D01G011220 AT1G19530 DNA polymerase epsilon catalytic subunit A
plum3 Gbar_D11G009060 AT2G45590 Protein kinase superfamily protein
plum3 Gbar_D07G007700 AT1G53540 HSP20-like chaperones superfamily protein
plum3 Gbar_D07G005520 AT5G50790 Encodes a member of the SWEET sucrose efflux transporter family proteins.
plum3 Gbar_D13G015090 AT3G25585 Amino alcohol phosphor transferase (AAPT2)
plum3 Gbar_D11G009450 AT2G45760 Encodes a protein that is similar to BONZAI1-binding protein BAP1.
plum3 Gbar_D05G023580 AT1G24620 Encodes an EF-hand calcium-binding protein family member
plum3 Gbar_D09G001430 AT5G39670 Calmodulin like protein involved in negative regulation of pattern triggered immunity.
plum3 Gbar_A11G016050 AT2G32530 Encodes a gene similar to cellulose synthase
plum3 Gbar_A10G004080 AT1G29160 Encodes a DOF transcription factor involved in seed coat development.
plum3 Gbar_D11G011430 AT1G48300 Cytosolic iron-sulfur protein
plum3 Gbar_D07G005040 AT5G51190 Encodes a member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family
plum3 Gbar_D03G017340 AT5G47230 Encodes a member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family (ATERF-5)
plum3 Gbar_D11G017170 AT3G51550 Encodes a synergid-expressed, plasma-membrane localized receptor-like kinase that accumulates asymetrically in the synergid membrnane at the filiform apparatus and mediates male-female gametophyte interactions during pollen tube reception
plum3 Gbar_D08G023540 AT5G27320 Encodes a gibberellin (GA) receptor ortholog of the rice GA receptor gene (OsGID1)
plum3 Gbar_D13G019370 AT5G20090 MPC1 negatively regulates ABA enhanced slow anion channel function during stomatal closure.
plum3 Gbar_D08G017720 AT5G16770 Member of the R2R3 factor gene family.
plum3 Gbar_D03G012490 AT3G46980 Encodes an inorganic phosphate transporter (PHT4;3).
plum3 Gbar_D12G022500 AT4G16820 Encodes a lipase that hydrolyzes phosphatidylcholine, glycolipids as well as triacylglycerols.
plum3 Gbar_D05G005280 AT2G25180 Encodes an Arabidopsis response regulator (ARR) protein that acts in concert with other type-B ARRs in the cytokinin signaling pathway
plum3 Gbar_D12G010820 AT3G60220 Encodes a putative RING-H2 zinc finger protein ATL4 (ATL4).
plum3 Gbar_D11G004590 AT2G18060 Encodes a NAC-domain transcription factor that is expressed in developing vessels and protoxylem
plum3 Gbar_D05G028190 AT3G56400 Function as activator of SA-dependent defense genes and a repressor of JA-regulated genes

Fig. 7

Expression analysis of the hub genes a: expression analysis by qRT-PCR, the bars indicate standard deviation of three replications. b: heat map of the hub genes. *: p < 0.05, **: p < 0.01. "

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