Comparative Phenotypic, Genomic, and Transcriptomic Analyses of Two Contrasting Strains of the Plant Beneficial Fungus .

Trichoderma virens is a beneficial fungus that helps plants fight pathogens and abiotic stresses and thereby enhances crop yields. Unlike other spp., there are two well-defined strains (P and Q) of T. virens, classified by secondary metabolites profiling, primarily the biosynthesis of the nonribosomal, strong antimicrobial agents gliotoxin (Q) and gliovirin (P). We have studied the phenotypic and biocontrol properties of two well-studied representative isolates ( Gv29-8 and GvW/IMI304061) that represent a Q strain and a P strain of , respectively. We refined the genome assembly of the P strain using nanopore technology, and we compared it with the Q strain. The differences between the genomes include gene expansion in the Q strain. Gv29-8 is weaker than GvW as a mycoparasite on the broad host-range plant pathogen Sclerotium rolfsii, and it is ineffective as a biocontrol agent when applied to pathogen-infested soil. Gv29-8 proved to be phytotoxic to seedlings, whereas the effect of GvW was not major. Both strains colonized the surface and outer cortex layer of tomato roots, with about 40% higher colonization by Gv29-8. Gv29-8 induced the expression of a larger set of tomato genes than did GvW, although some tomato genes were uniquely induced in response to GvW. We studied the comparative transcriptome response of Gv29-8 and GvW to S. rolfsii. A larger set of genes was regulated in GvW than in Gv29-8 in the presence of the plant pathogen. populations that were earlier classified into two strains (P and Q) based on secondary metabolites profiling are also phenotypically and genetically distinct, with the latter being ineffective in controlling the devastating, broad host range plant pathogen . The two strains also provoke distinct as well as overlapping transcriptional responses to the presence of the plant and the pathogen. This study enriches our knowledge of -plant-pathogen interactions and identifies novel candidate genes for further research and deployment in agriculture.