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Background   Trichoderma  spp. are effective biocontrol agents for many plant pathogens, thus the mechanism of  Trichoderma -induced plant resistance is not fully understood. In this study, a novel  Trichoderma  strain was identified, which could promote plant growth and reduce the disease index of gray mold caused by  Botrytis cinerea  in cucumber. To assess the impact of  Trichoderma  inoculation on the plant response, a multi-omics approach was performed in the  Trichoderma -inoculated cucumber plants through the analyses of the plant transcriptome, proteome, and phytohormone content.    Results  A novel  Trichoderma  strain was identified by morphological and molecular analysis, here named  T. longibrachiatum  H9. Inoculation of  T. longibrachiatum  H9 to cucumber roots promoted plant growth in terms of root length, plant height, and fresh weight. Root colonization of  T. longibrachiatum  H9 in the outer layer of epidermis significantly inhibited the foliar pathogen  B. cinerea  infection in cucumber. The plant transcriptome and proteome analyses indicated that a large number of differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were identified in cucumber plants 96 h post  T. longibrachiatum  H9 inoculation. Up-regulated DEGs and DEPs were mainly associated with defense/stress processes, secondary metabolism, and phytohormone synthesis and signaling, including jasmonic acid (JA), ethylene (ET) and salicylic acid (SA), in the  T. longibrachiatum  H9-inoculated cucumber plants in comparison to untreated plants. Moreover, the JA and SA contents significantly increased in cucumber plants with  T. longibrachiatum  H9 inoculation.    Conclusions  Application of  T. longibrachiatum  H9 to the roots of cucumber plants effectively promoted plant growth and significantly reduced the disease index of gray mold caused by  B. cinerea . The analyses of the plant transcriptome, proteome and phytohormone content demonstrated that  T. longibrachiatum  H9 mediated plant systemic resistance to  B. cinerea  challenge through the activation of signaling pathways associated with the phytohormones JA/ET and SA in cucumber.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5513-8) contains supplementary material, which is available to authorized users.

bmc genomics

Involvement of jasmonic acid, ethylene and salicylic acid signaling pathways behind the systemic resistance induced by Trichoderma longibrachiatum H9 in cucumber