Table 3 Table showing the differential expression of the PR genes and various defense-related transcription factors expressed differentially during the Trichoderma-tomato interaction (T1, T2, and T3) vs un-inoculated control (C1, C2, and C3). The significant genes have been sorted based on p_cal-value < 0.05. The identified and characterized proteins were further validated using the Sol Genomics BLASTp tool to find the first and topmost hit related to the specific isoform of the protein

Les.122

Acidic 26-kDa endochitinase

Solyc04g009900.4.1

0.955

6.00E-03

-6.61E-02

Chitinolytic antifungal activities

[103, 104]

Les.3406

Basic 30-kDa endochitinase

Solyc10g055810.2.1

1.032

2.82E-03

4.49E-02

Chitin degradation, plant defense against fungal pathogens

[103, 104]

Les.3779

Acidic 27-kDa endochitinase

Solyc02g082930.3.1

1.053

1.32E-02

7.50E-02

acidic 27-kDa endochitinase cleaves the β-1,4 glycosidic bonds in chitin,

[103, 104]

Les.2591

glucan endo-1,3-beta-glucosidase B precursor

Solyc01g060020.4.1

1.04

1.45E-02

5.60E-02

Plant defense through hydrolytic clevage of β (1 → 3)-glucosidic linkages in β (1 → 3)-d-glucan, present in fungal cell walls

[104,105,106]

Les.3673

Beta-1,3 Glucanase

Solyc01g008620.4.1

0.848

3.39E-02

-2.37E-01

Plant defense through hydrolytic clevage of β (1 → 3)-glucosidic linkages in β (1 → 3)-d-glucan, present in fungal cell walls

[104,105,106]

Les.4307

Pathogenesis-related 5(PR-5)/thaumatin-like proteins (TLPs)

Solyc08g080670.1.1

1.132

2.77E-02

1.79E-01

Plant Defense

[104]

Les.4693

Pathogenesis-related 4(PR-4)

Solyc09g007010.1.1

0.94

4.15E-03

-8.94E-02

Plant Defense against fungal pathogen

[106]

Les.4460

Pathogenesis-related precursor 2(PR2)

Solyc01g097240.3.1

0.977

4.08E-02

-3.35E-02

Plant Defense

[107]

LesAffx.5691

Pathogenesis-related 4(PR-4)

Solyc09g006005.1.1

1.06

1.83E-02

8.46E-02

Plant Defense

[106]

Les.4496.1

Pathogenesis-related protein STH-2-like (PRSTH2)

Solyc09g090970.4.1

1.039

8.79E-03

5.52E-02

PR-10 like protein provide defense against abiotic and biotic stress

[104]

LesAffx.4763

MADS-box transcription factor(LOC101247413)

Solyc12g087830.2.1

0.92

7.32E-03

-1.20E-01

floral transition, floral patterning, and other reproductive development

[104,105,106, 108, 109]

Les.4450.1

MADS-box transcription factor RIN(RIN)

Solyc05g012020.4.1

0.956

2.14E-02

-6.53E-02

Key regulator of fruit ripening gene-expression network

[110, 111]

Les.3716.1

SANT/MYB domain protein

Solyc10g052470.1.1

0.958

1.01E-02

-6.23E-02

Early stages of fruit development

[112]

Les.5091.1

MYB4 transcription factor

Solyc09g090130.3.1

1.031

4.78E-03

4.38E-02

Plant growth and Development and tolerance to various abiotic stresses

[113, 114]

LesAffx.65724

transcription factor MYB20(LOC101252939)

Solyc02g093730.4.1

1.021

2.96E-02

3.01E-02

Regulating the phenylpropanoid metabolism during secondary cell wall formation

[115]

LesAffx.53591

Transcription factor MYB13-like(LOC101260654)

Solyc06g083900.3.1

1.081

1.82E-03

1.13E-01

Auxin response and flavonoid biosynthesis

[116, 117]

LesAffx.62138

Transcription factor MYB78-like(LOC101265734)

Solyc05g053330.3.1

0.975

2.74E-02

-3.68E-02

Abscission Zone-Specific Modulation of Key Meristem Activity Genes

[118]

LesAffx.21940

MYB family transcription factor (LOC101243935)

Solyc01g108300.3.1

1.03

1.58E-02

4.23E-02

Plant growth and Development

[118]

Les.3512.1

WRKY transcription factor 2(WRKY2)

Solyc07g066220.3.1

0.988

1.05E-02

-1.79E-02

Abiotic and Biotic Response

[119, 120]

LesAffx.9910

Probable WRKY transcription factor 40 (LOC101246812)

Solyc03g116890.3.1

0.988

1.86E-02

-1.80E-02

Biotic Response

[119, 121,122,123,124]

Les.3964.1

Probable WRKY transcription factor 17 (LOC543855)

Solyc12g096350.2.1

0.952

1.72E-02

-7.04E-02

Negative regulator of basal resistance in Arabidopsis

[125]

Les.5219.1

NAC domain-containing protein NACMTF3(NACMTF3)

Solyc06g073050.2.1

0.99

1.45E-02

-1.45E-02

Biotic interaction

[126]