Table 2 List of top most significant genes encountered in all the probability groups (pcal < 0.05, pcal < 0.01, and padj < 0.05) and were differentially expressed and down-regulated (pcal-value < 0.05; FC <1) in all the biological replicates (T1, T2, and T3) of Trichoderma-tomato interaction samples compared to all the un-inoculated (C1, C2, and C3) control samples. The results were further validated using the Sol Genomics BLAST tool for the identification and characterization of the specific isoform of the protein
Table 2 Probe ID | Putative Identity | Sol Genomics ID | Fold Change | p-value | Functional Category | Putative function |
|---|---|---|---|---|---|---|
Les.1413 | Malate dehydrogenase, chloroplastic(LOC101258932) | Solyc03g115990.3.1 | 0.982 | 1.50E-03 | Carbohydrate metabolism | Citric acid cycle and energy production in plants |
Les.3975 | Sulfite reductase(LOC101055609) sir | Solyc11g065620.2.1 | 0.981 | 6.40E-03 | Sulphur metabolism | Sulphur assimilation |
LesAffx.47717 | Uncharacterized protein | Solyc01g081480.3.1 | 0.98 | 8.17E-03 | Not Known | Not Known |
Les.5690 | Soluble inorganic pyrophosphatase 6, chloroplastic(LOC101264469) | Solyc10g047950.2.1 | 0.978 | 3.60E-04 | Plant Growth and Development | ATP synthesis, Photophosphorylation |
Les.5189 | Asparagine synthetase [glutamine-hydrolyzing] 2(LOC101259236) | Solyc04g055200.3.1 | 0.978 | 9.04E-03 | Nitrogen Metabolism | Biosynthesis of asparagine from the glutamine |
Les.5161 | Interactor of constitutive active ROPs 2, chloroplastic(LOC101255915) | Solyc09g007360.3.1 | 0.978 | 4.50E-03 | Stress Response | Plant-specific GTPases playing a critical role in cytoskeleton organization, hormone signaling, preventing photooxidative damage to chloroplast |
Les.14 | Subtilisin-like protease SBT2(SBT2) | Solyc03g006970.1.1 | 0.977 | 5.66E-03 | Plant Growth, Development, and Defense | Processing and activation of several precursor proteins required for plant development |
LesAffx.13831 | Plastid division protein PDV2(LOC101261370) | Solyc01g109260.3.1 | 0.977 | 3.08E-03 | Plant Growth and Development | Division of plastids |
Les.98.1 | MAR-binding filament-like protein 1(MFP1) | Solyc03g120230.3.1 | 0.976 | 6.96E-03 | Plant Growth and Development | Nuclear architecture and genome organization |
Les.1230 | L-ascorbate peroxidase 3(LOC101264282) | Solyc02g083630.3.1 | 0.968 | 5.29E-04 | Stress Response | ROS scavenging and Cellular Homeostasis |
Les.3579 | Type 2 metallothionein MT3(MT3) | Solyc04g058100.3.1 | 0.968 | 4.99E-03 | Cellular Homeostasis | Metal ion homeostasis, detoxification, and regulation of gene expression |
Les.64 | Gibberellin 20-oxidase-1(GA20ox1) | Solyc03g006880.3.1 | 0.966 | 1.58E-03 | Plant Growth and Development | Biosynthesis of Gibbrellins, seed germination, stem elongation, and flower and fruit development |
Les.386 | Probable protein phosphatase 2C 52(LOC101259375) | Solyc10g008490.3.1 | 0.966 | 2.93E-03 | Plant Growth, Development and Stress response | Regulation of cell cycle, hormonal signaling, and stress response |
Les.561 | Protein PIN-LIKES 3-like(LOC101247117) | Solyc12g095750.2.1 | 0.962 | 7.56E-03 | Cell Metabolism and Hormonal signaling | Auxin transport and signaling |
Les.702 | S-adenosylmethionine decarboxylase 2(LOC101260400) | Solyc02g089610.2.1 | 0.961 | 4.37E-04 | Plant Growth and Development | Chromatin remodeling and RNA processing, and biosynthesis of polyamines and spermidines |
Les.122 | Acidic 26Â kDa endochitinase (Chitinase CHI3) | Solyc02g082920.4.1 | 0.955 | 6.00E-03 | Plant Defense | Plant defense against fungal pathogens |
Les.1379 | Hop-interacting protein THI116(LOC101055532) | Solyc03g117250.4.1 | 0.954 | 3.61E-03 | Stress Response | Co-chaperon regulating the activity of molecular chaperones Hsp70 and Hsp90 |
Les.642 | Probable alkaline/neutral invertase B(LOC101253328) | Solyc01g111100.5.1 | 0.942 | 5.10E-03 | Carbohydrate metabolism | Seed germination and fruit ripening |
Les.3981 | UDP-glycosyltransferase 76E1(UGT76E1) | Solyc10g085230.2.1 | 0.942 | 3.12E-03 | Plant cell Metabolism and Defense | Glycosylation of various natural compounds, including flavonoids, alkaloids, and terpenoids |
LesAffx.67427 | Protein RESPONSE TO LOW SULFUR 3-like(LOC101243684) | Solyc03g096770.1.1 | 0.941 | 4.86E-04 | Plant Growth and Development | Sulphur metabolism |
Les.3045 | Adenylyl-sulfate reductase(LOC544267)/Cystathionine beta-synthase | Solyc08g014340.3.1 | 0.94 | 3.29E-03 | Amino acid metabolism | Biosynthesis of suphur containing amino acids |
Les.4693 | Pathogenesis-related protein P4(P4) | Solyc09g007010.1.1 | 0.94 | 4.15E-03 | Plant defense | Plant defense against pathogens and stress response |
LesAffx.62690 | Cytokinin riboside 5'-monophosphate phosphoribohydrolase LOG8(LOC101252798) | Solyc08g062820.3.1 | 0.938 | 2.16E-04 | Plant Growth and Development | Cytokinin metabolism |
LesAffx.22812 | probable E3 ubiquitin-protein ligase RNF217(LOC101250202) | Solyc03g117860.3.1 | 0.931 | 8.27E-04 | Protein Metabolism | RING finger family of E3 ubiquitin ligases involved in protein-turnover |
Les.3034 | Wound-induced proteinase inhibitor 2(LOC101255652) | Solyc11g020960.2.1 | 0.927 | 4.37E-04 | Plant Defense | Plant defense against herbivores and pathogens |
LesAffx.4763 | MADS-box transcription factor(LOC101247413) | Solyc12g087830.2.1 | 0.92 | 7.32E-03 | Plant Growth and Development | Flower development, fruit development, and ripening |
Les.2909 | Phosphoenolpyruvate carboxylase(PEPC2) | Solyc07g055060.3.1 | 0.912 | 1.37E-03 | Plant Growth and Development | Photosynthetic Carbon fixation |
LesAffx.17150 | Nitrite reductase(Nii1) | Solyc01g108630.3.1 | 0.898 | 6.89E-03 | Plant Growth and Development | Â Nitrogen Metabolism |
Les.3700.1 | Non-symbiotic hemoglobin class 1(Glb1) | Solyc07g008240.3.1 | 0.868 | 2.33E-03 | Cell Metabolism and Stress Response | nitrate assimilation, carbon metabolism, and the plant defense against oxidative stress |
Les.3539 | Phosphoenolpyruvate carboxylase kinase 1(PPCK1) | Solyc04g009900.4.1 | 0.801 | 6.58E-03 | Plant Growth and Development | Photosynthetic Carbon fixation |