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Table 2 Differentially expressed genes common to noninoculated and inoculated mj-far-1 -overexpressing root line and their functional categories

From: Meloidogyne javanica fatty acid- and retinol-binding protein (Mj-FAR-1) regulates expression of lipid-, cell wall-, stress- and phenylpropanoid-related genes during nematode infection of tomato

Functional categories Sub-category Gene ID OE1-KAN1 OE2-KAN2 OE3-KAN3 OE4-KAN4 Annotation
Cell Wall Proteins LLR Solyc07g053840.1.1 -2.44 -2.20 -9.83 -2.24 LRP receptor-like serine/threonine-protein kinase , RLP
Cellulose synthesis COBRA Solyc03g114900.2.1 -1.22 -1.19 -2.29 -1.46 COBRA-like protein
Degradation pectate lyase and polygalacturonases Solyc12g096750.1.1 -2.32 -3.37 -1.90 -7.01 Polygalacturonase 4
Modification Solyc10g086520.1.1 -1.23 -1.49 -1.81 -1.02 Expansin-1
UDP glucosyl and glucoronyl transferase Solyc05g053400.1.1 2.20 2.57 1.15 3.53 Glucosyltransferase
Cell organization Chloroplast location Solyc06g062400.1.1 2.12 1.65 2.26 1.70 Cloroplast unusual positioning 1A
Development Nodule formation Solyc05g055540.1.1 2.94 1.64 2.54 1.99 Nodulin family protein
unkown Solyc06g082460.1.1 -1.90 -1.29 -1.11 -1.46 Plant-specific domain TIGRO1568 family protein
Hormone metabolism Auxin induced/regulated/responsive Solyc02g092820.2.1 -2.99 -1.80 -4.29 -5.59 Indole-3-acetic acid-amido synthetase GH3.8
Solyc12g005310.1.1 -2.75 -1.18 -3.60 -4.05 Auxin-responsive GH3-like
Ethylene synthesis/degradation Solyc09g010000.2.1 1.42 1.80 1.87 1.11 1-aminocyclopropane-1-carboxylate oxidase-like protein
Solyc11g072310.1.1 1.51 1.45 1.41 1.72 Gibberellin 20 -oxidase-3
Solyc06g073580.2.1 -3.78 -1.50 -1.01 1.16 1-aminocyclopropane-1-carboxylate oxidase-like protein
Jasmonic acid induced/regulated/responsive Solyc03g098710.1.1 -4.38 -1.50 -2.09 2.49 Kunitz-type proteinase inhibitor A4 (Fragment)
Solyc03g098720.2.1 -10.39 -1.72 -10.48 4.26 Kunitz trypsin inhibitor
Lipid metabolism FA Synthesis and FA Elongation Solyc08g008310.2.1 -3.21 -2.93 -3.52 -3.27 Long-chain-fatty-acid-CoA ligase
Phospholipid synthesis Solyc12g040790.1.1 -1.07 -1.19 -1.40 2.19 Menaquinone biosynthesis methyltransfere ubiE
Lipid modification Solyc05g018770.1.1 -2.58 -12.08 -10.93 -4.19 Esterase/lipase/thioesterase (Fragment)
N-metabolism/degradation Glutamate dehydrogenase Solyc05g052100.2.1 -5.33 -11.68 -2.12 -1.56 Glutamate dehydrogenase
Phosphotransfer and Pyrophoshatases guanylate kinase Solyc10g79140.1.1 1.30 1.75 2.57 2.48 Guanylate kinase
NUDIX hydrolases Solyc07g045430.2.1 2.34 2.61 1.62 -2.97 Nudix hydrolase 2
Polyamine metabolism SAM/decarboxylase Solyc06g054460.1.1 -1.37 -2.12 -1.17 -1.96 S-adenosylmethionine decarboxylase proenzyme
Spermidine/synthase Solyc06g053510.2.1 -5.21 -2.87 -1.88 1.21 Spermidine synthase
Protein metabolism Protease Solyc05g016250.2.1 -11.21 -11.18 -11.08 -9.72 Cysteine-type peptidase
Solyc07g066500.1.1 11.02 9.87 4.88 11.14 U1p1 protease family C-terminal catalytic domain containing protein
Solyc01g057880.1.1 -4.10 -5.48 -3.35 -4.10 U1p1 protease family C-terminal catalytic domain containing protein
Postranslational modification Solyc08g066400.1.1 -10.91 -10.97 -10.39 -10.64 Protein kinase (Fragment)
Solyc03g083800.1.1 5.01 10.74 5.59 11.45 Serine/threonine-protein phosphatase 7 long form homolog
Targeting Solyc12g096550.1.1 1.20 1.10 1.23 1.11 Pheophorbide a oxygenase family
Transcription factor GeBP like Solyc07g052900.1.1 1.21 1.55 1.66 1.96 Os09g0451700 protein (Fragment)
Solyc07g052700.2.1 2.84 2.57 4.21 2.30 MADS-box transcription factor 1
MADS box transcription factor/family Solyc02g089200.2.1 4.79 3.11 5.74 4.14 MADS-box transcription factor
Solyc07g052720.2.1 3.67 2.31 4.65 2.99 MADS-box protein AGL66
Putative transcription regulator Solyc10g051140.1.1 -1.94 -2.58 -1.90 -1.81 Genomic DNA chromosome 5 P1 clone MTE17
WRKY domain transcription factor family Solyc05g053380.2.1 -2.30 -1.99 1.60 -2.02 WRKY transcription factor 31
unknown Solyc01g100440.1.1 2.07 1.33 1.89 2.42 Transcription regulatory protein SNF5
Secondary metabolism Isoflavone reductase Solyc10g052500.1.1 -4.36 -510 -3.32 -4.16 Phenylcoumaran benzylic ether reductase 3
Isoprenoids/terpenoids Solyc10g005390.2.1 1.86 1.47 2.96 2.67 Linalool synthase
Phenylpropanoids Solyc02g08100.1.1 2.24 2.86 3.13 1.41 Acyltransferase (Fragment)
Signaling Sugar and nutrien phisiology Solyc12g099780.1.1 -1.69 -1.48 1.91 1.05 Unknown Protein
Receptor kinase leucine rich repeat XI Solyc12g009780.1.1 8.74 3.37 3.18 8.43 LRR receptor-like serine/ threonine-protein kinase, RLP
Abiotic stress Heat stress Solyc06g011400.2.1 4.54 2.57 4.40 2.45 ATP-dependent chaperone c1pB
Solyc06g11380.2.1 5.99 3.67 4.70 2.51 Chaperone C1pB
Solyc06g011370.2.1 3.86 3.46 3.52 2.25 Chaperone protein clpB 2
Plant defence Pathogen attack response Solyc09g007020.1.1 1.70 1.24 1.07 1.14 Pathogenesis-related protein
Pathogen resistance Solyc07g009510.1.1 2.56 2.44 1.76 1.05 Chitinase
Gene to gene resistance/recognation Solyc12g044190.1.1 1.07 1.33 2.37 2.18 Nbs-lrr, resistance protein
Redox state Solyc01g081250.2.1 1.22 1.02 1.34 1.08 Glutathione-S-transferase
Solyc03g116120.1.1 2.80 1.87 2.18 1.99 Glutathione S-transferase 12
Solyc08g014330.2.1 -2.24 -1.19 -1.06 1.08 Primary amine oxidase
unknown Solyc01g017600.2.1 -2.17 -5.86 -10.57 1.48 Plant viral-response family protein
Transport Amino acids Solyc01g100390.2.1 2.12 2.04 2.63 1.21 Pyrophosphate-energized proton pump
Peptides and oligopeptides Solyc03g113430.2.1 1.63 1.24 3.70 1.28 Peptide transporter
unknown Solyc01g73670.2.1 -1,60 -1.63 -1.98 1.22 Uncharacterized MFS-type transporter C19orf28
Protease inhibitor/seed storage /lipid transfer protein (LTP) family protein Solyc03g083990.1.1 -2.08 1.15 1.25 -2.66 Cortical cell-delineating protein
Not assigned unknown Solyc04g015610.2.1 -1.89 -1.27 -1.50 -3.73 Os01g0611000 protein (Fragment)
Solyc10g080380.1.1 -1.53 -3.73 -3.61 -1.55 Unknown Protein
Solyc07g007770.1.1 -6.36 -5.19 -5.23 -4.54 Unknown Protein
Solyc09g091810.1.1 -2.80 -1.29 -1.62 -2.78 Unknown Protein
Solyc01g056370.2.1 12.79 12.99 13.67 13.64 Unknown Protein
Solyc05g052880.2.1 1.93 1.37 1.89 3.33 Unknown Protein
  1. Gene ID number and log2 values at each time point before and after inoculation are indicated. All genes were considered to be differentially expressed with a threshold q-value < 0.05.