Whole Genome Sequencing Reveals Major Deletions in the Genome of M7, a Gamma Ray-Induced Mutant of Trichoderma virens That Is Repressed in Conidiation, Secondary Metabolism, and Mycoparasitism

Shikha Pachauri; Pramod D Sherkhane; Vinay Kumar; Prasun K Mukherjee

doi:10.3389/fmicb.2020.01030

Whole Genome Sequencing Reveals Major Deletions in the Genome of M7, a Gamma Ray-Induced Mutant of Trichoderma virens That Is Repressed in Conidiation, Secondary Metabolism, and Mycoparasitism

Front Microbiol. 2020 Jun 12:11:1030. doi: 10.3389/fmicb.2020.01030. eCollection 2020.

Authors

Shikha Pachauri^{1

2}, Pramod D Sherkhane¹, Vinay Kumar^{2

3}, Prasun K Mukherjee^{1

2}

Affiliations

¹ Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India.
² Homi Bhabha National Institute, Mumbai, India.
³ Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India.

Abstract

Trichoderma virens is a commercial biofungicide used in agriculture. We have earlier isolated a mutant of T. virens using gamma ray-induced mutagenesis. This mutant, designated as M7, is defective in morphogenesis, secondary metabolism, and mycoparasitism. The mutant does not produce conidia, and the colony is hydrophilic. M7 cannot utilize cellulose and chitin as a sole carbon source and is unable to parasitize the plant pathogens Rhizoctonia solani and Pythium aphanidermatum in confrontation assay. Several volatile (germacrenes, beta-caryophyllene, alloaromadendrene, gamma-muurolene) and non-volatile (viridin, viridiol, gliovirin, heptelidic acid) metabolites are not detected in M7. In transcriptome analysis, many genes related to secondary metabolism, carbohydrate metabolism, hydrophobicity, and transportation, among others, were found to be downregulated in the mutant. Using whole genome sequencing, we identified five deletions in the mutant genome, totaling about 250 kb (encompassing 71 predicted ORFs), which was confirmed by PCR. This study provides novel insight into genetics of morphogenesis, secondary metabolism, and mycoparasitism and eventually could lead to the identification of novel regulators of beneficial traits in plant beneficial fungi Trichoderma spp. We also suggest that this mutant can be developed as a microbial cell factory for the production of secondary metabolites and proteins.

Keywords: NGS; Trichoderma virens; mutant; secondary metabolism; transcriptome.