Table 1 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 upregulated (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
Probe ID | Putative Identity | Sol Genomics ID | Fold Change | p-value | Functional Category | Putative Function |
|---|---|---|---|---|---|---|
Les.1077 | ATP dependent Clp protease | Solyc02g078160.3.1 | 1.297 | 1.45E-04 | Stress Response | Protein Degradation through ATP dependent ATPases |
Les.415 | Neryl diphosphate synthase 1(CPT1) | Solyc08g005680.4.1 | 1.224 | 5.63E-04 | Secondary Metabolism | Terpene Biosynthesis |
Les.4488 | Threonine dehydratase biosynthetic, chloroplastic(TD2) | Solyc09g008670.3.1 | 1.137 | 3.93E-03 | Protein Metabolism | Isoleucine Biosynthesis |
Les.4885 | BAHD acyltransferase DCR(LOC101256185) | Solyc05g052670.1.1 | 1.131 | 2.90E-03 | Secondary Metabolism | Biosyntheiss of Hydrocinnamic esters |
Les.2460 | organ-specific protein S2(LOC101245207) | Solyc10g009150.3.1 | 1.129 | 1.98E-03 | Defense Response | Serine proteases degrading peptide bonds from pathogen proteins |
LesAffx.32379 | polygalacturonate 4-alpha-galacturonosyltransferase (pectin synthase) | Solyc04g079860.1.1 | 1.128 | 2.38E-03 | Carbohydrate metabolism | Biosyntheis of Pectic compounds |
Les.3980 | lipoxygenase (loxC) | Solyc01g006540.4.1 | 1.128 | 3.52E-03 | Plant Growth, Development, and Defense | Generation of Fatty Acid-Derived Flavor Compounds |
LesAffx.9007 | Uncharacterized | Unknown | 1.126 | 5.24E-03 | Not Known | Not Known |
Les.4288 | pyruvate kinase 1, cytosolic (LOC101248036) | Solyc09g008840.4.1 | 1.124 | 3.78E-03 | Carbohydrate metabolism | Glycolytic pathway |
LesAffx.71065 | Protein Early Flowering 2-like (ELF2-like) | Solyc04g064870.3.1 | 1.112 | 1.32E-03 | Flower development and Stress reponse | AP2/ERF type transcription factor involved in flower development, hormonal signaling and stress response |
LesAffx.3388 | Plant cell wall protein SlTFR88 | Solyc10g074730.3.1 | 1.112 | 2.69E-03 | Stress response and Plant Defense | hydroxyproline-rich glycoproteins (HRGPs) involved in cell expansion, differentiation,cell structure, and plant microbe interactions |
Les.1783 | kirola(LOC101262669)/Bet v I/Major latex protein domain-containing protein | Solyc10g048030.2.1 | 1.109 | 1.47E-03 | Plant Defense and Stress Response | Plant Defense and Stress Response |
Les.4457 | Sesquiterpene synthase 1 (SSTLE1) | Solyc06g059930.4.1 | 1.104 | 7.42E-04 | Secondary Metabolism | Biosynthesis of Terpenes involved in Plant Defense against pathogens, and herbivores |
Les.275 | formate dehydrogenase(fdh) | Solyc02g086880.4.1 | 1.103 | 2.81E-03 | Energy Metabolism and Cellular Homeostasis | Formate metabolism and CO2 fixation |
Les.361 | Beta-phellandrene synthase(chloroplastic) | Solyc08g005677.1.1 | 1.098 | 3.57E-03 | Plant Defense, Stress Response | Biosynthesis of beta-phellandrene(terpene synthase) |
LesAffx.30145 | Plant Cadmium Resistance 2 (PCR2) | Solyc01g005470.3.1 | 1.094 | 3.82E-03 | Plant Defense, Stress Response | Cd detoxification and sequesteration, defense against oxidative stress |
LesAffx.32379 | Probable galacturonosyltransferase-like 1(LOC101247911) | Solyc04g079860.1.1 | 1.092 | 3.53E-03 | Carbohydrate metabolism | Biosyntheis of Pectic compounds |
Les.5139 | Epidermis-specific secreted glycoprotein EP1(LOC101268888) | Solyc07g062490.1.1 | 1.087 | 5.61E-03 | Cell adhesion, signaling, and/or immune responses | member of the Beta-microseminoprotein family involve in cell structure, adhesion and immune response |
LesAffx.28505 | Perakine reductase(LOC101256520) | Solyc09g082720.3.1 | 1.086 | 6.17E-03 | Secondary Metabolism | Biosynthesis of the alkaloid perakine |
Les.1900 | Kirola (LOC101264616) | Solyc04g007760.3.1 | 1.084 | 7.58E-04 | Plant Defense and Stress Response | Plant Defense and Stress Response |
Les.3035 | Aspartic protease inhibitor 1(LOC101262903) | Solyc03g098780.2.1 | 1.084 | 5.41E-03 | Protein Metabolism | Protein degradation |
LesAffx.53591 | Transcription factor MYB13-like (LOC101260654) | Solyc06g083900.3.1 | 1.081 | 1.82E-03 | Secondary Metabolism | Anthocyanin Biosynthesis |
LesAffx.4763 | MADS-box transcription factor(LOC101247413) | Solyc12g087830.2.1 | 1.08 | 8.26E-03 | Plant growth and Development | Flower formation, fruit ripening, and seed germination |
Les.3286 | Inducible plastid-lipid associated protein | Solyc07g064600.3.1 | 1.078 | 4.23E-03 | Lipid Metabolism | Synthesis and accumulation of lipids in response to stress response |
Les.2460 | Organ-specific protein S2(LOC101245207) | Solyc10g009150.3.1 | 1.071 | 6.26E-04 | Protein Metabolism | Seine proteases function as a scaffold protein for cellular structure re-organization |
Les.5685 | High-affinity nitrate transporter | Solyc02g083120.3.1 | 1.071 | 3.85E-03 | Nitrogen metabolism | Nitrate uptake and transport |
Les.1015 | Dehydrodolichyl diphosphate synthase 2(CPT7) | Solyc06g076920.3.1 | 1.07 | 7.83E-03 | Protein Metabolism | Biosynthesis of Dolichol, a polyisoprenoid alcohal for protein glycosylation |
LesAffx.35587 | Vacuolar processing enzyme VPE3 precursor | Solyc08g065610.2 | 1.069 | 6.82E-03 | Programmed cell Death and Apotosis | cysteine proteases involved in processing of stored food during seed germination |
Les.3267 | Bifunctional UDP-glucose 4-epimerase and UDP-xylose 4-epimerase 1(LOC101266745) | Solyc08g080570.4.1 | 1.064 | 9.90E-03 | Carbohydrate metabolism | Biosynthesis of various cell wall polysaccharides, including xyloglucan and xylan |
LesAffx.1.1.S1_at | Arginase 2 | Solyc01g091170.3.1 | 1.064 | 3.39E-03 | Protein and Nitrogen metabolism | Degradation of protein and other nitrogen compounds |
Les.2971 | Wound-induced proteinase inhibitor 1(LOC101246961) | Solyc09g084440.2.1 | 1.063 | 4.64E-03 | Plant Defense against herbivores and pathogen | Kunitz-type inhibitors function as proteinase inhibitor |
Les.1175 | Uncharacterized protein | Solyc03g025670.3.1 | 1.062 | 6.48E-03 | Unknown | Unknown |
LesAffx.4779 | Peroxidase 12(LOC101253377) | Solyc04g071890.3.1 | 1.058 | 9.54E-03 | Plant Defense | Degradation of toxic substances and host defense |
LesAffx.71532 | NBS-LRR type receptor like protein33(RLP33) | Solyc10g052880.1.1 | 1.053 | 9.29E-03 | Plant Defense | Plant defense. particularly, against fungal pathogens |
Les.3436 | Metallocarboxypeptidase inhibitor | Solyc06g061230.3.1 | 1.051 | 5.74E-03 | Protein Metabolism | Breakdown of proteins and peptides |
LesAffx.9438 | WD repeat-containing protein 43(LOC101255780) | Solyc03g116380.4.1 | 1.049 | 2.20E-03 | DNA and RNA metabolism | RNA metabolism, protein transport, and chromatin remodeling |
Les.3757 | Glutaminase domain-containing protein(LOC544312) | Solyc03g006490.3.1 | 1.049 | 6.91E-04 | Amino acid metabolism | Plant growth and development, nitrogen assimilation, and stress response |
Les.5499 | Probable nucleoredoxin 2 | Solyc04g081900.4.1 | 1.049 | 1.42E-03 | Plant Growth and Development | Photosynthesis, plant growth, and responses to environmental stress |
LesAffx.29801 | Fe2OG dioxygenase domain-containing protein | Solyc03g080190.3.1 | 1.049 | 8.22E-03 | DNA and RNA metabolism | DNA repair, RNA metabolism, binding of iron and oxygen molecule, and synthesis of various metabolites |
Les.1724 | Glutathione S-transferase L3 isoform | Solyc10g084400.2.1 | 1.047 | 9.27E-03 | Plant defense and Stress Response | Detoxification and metabolism of various toxins, and environmental factors leading to oxidative stress |
Les.5710 | BTB/POZ domain-containing protein | Solyc11g012840.2.1 | 1.046 | 6.05E-03 | Stress Response | Fruit development and response to stress |
LesAffx.9824 | DMR6-LIKE OXYGENASE 2-like (LOC101260084) | Solyc01g105660.4.1 | 1.045 | 4.45E-03 | Cell Death and Stress Response | Regulation of the jasmonic acid (JA) signaling pathway |
Les.3608 | Peroxidase(CEVI-1) | Solyc01g006300.3.1 | 1.043 | 1.01E-03 | Plant Stress Response | Cellular redox balance and protection against oxidative stress |
Les.413 | Glutathione S-transferase/peroxidase(BI-GST/GPX) | Solyc07g056480.3.1 | 1.042 | 6.40E-03 | Plant Defense | Defense against Geminiviruses |
Les.5601 | Protein SRG1 | Solyc02g071380.2.1 | 1.041 | 7.25E-03 | Plant Defense | Plant defense against both Biotic and Abiotic stress |
LesAffx.42701 | Nicotinamidase 1 | Solyc01g106000.4.1 | 1.041 | 7.97E-03 | Plant Defense | Plant Defense |
Les.4496 | Pathogenesis-related protein STH-2-like(LOC101246381) | Solyc09g090980.3.1 | 1.039 | 8.79E-03 | Cellular Homeostasis | Protein folding and molecular chaperon |
LesAffx.9815 | DNAJ-like protein(DNAJ) | Solyc04g081530.1.1 | 1.039 | 8.96E-04 | Plant growth and Development | Seed Dormancy and Germination |
LesAffx.15284 | Auxin repressed/dormancy associated protein(LOC101258429)/DRM1/ARP | Solyc02g077880.3.1 | 1.037 | 5.76E-03 | Plant Growth, Development and Defense | Defense response to biotic stress, including salicylic acid (SA) and methyl jasmonate (MeJA) signaling |
Les.4834 | Serine decarboxylase(LOC101262912) | Solyc04g071140.3.1 | 1.026 | 4.94E-04 | Amino acid metabolism | Phospholipid and amino acid metabolism in A. thaliana |
LesAffx.10299 | Polyol transporter 5-like(PMT5) | Solyc01g109460.3.1 | 1.024 | 5.42E-05 | Plant growth and Development | plasma membrane hexose sugar transporters in A. thaliana |