Transcriptome analysis and annotation of Trichoderma virens, a beneficial plant fungal endophyte

Abstract

Trichoderma is a ubiquitous, culturable genus of soil-borne fungi. Many species in the Trichoderma genus possess the ability to colonise plant roots and form mutualistic endophytic relationships. In particular, Trichoderma virens is of agricultural and environmental importance. T. virens is a useful model organism for exploring plant-fungi interactions and biological control. The genome of T. virens was sequenced in 2007 and made publically available by the Joint Genome Institute which provides a context for investigating plant-endophyte interactions. However, this annotation was prepared before transcriptome data was available. This project aims to reannotate the current T. virens genome with the advantage of a transcriptome assembly. In this work, mRNA and ncRNA populations based on ~100 x deep sequencing were obtained from T. virens strain Gv29-8 under nutrient-rich and minimal-nutrient growth conditions. Differential expression analysis between the differing conditions revealed transcripts related to a predicted thiamine-regulated TPP riboswitch. The prediction was experimentally validated to regulate gene expression in response to the presence of exogenous thiamine. Computational prediction for the presence, structure and functions of ncRNA, protein coding genes and functional elements was also performed. Some considerable improvements were made to the gene structure annotations for predicted ncRNA and protein coding genes. The subsequent annotation is presented here. The results contribute to the understanding of the T. virens genome and regulated expression, which has the potential to aid the development of biocontrol and growth enhancing strains, as well as controlled expression regulation systems in agricultural applications.