Genomes and Genomics of the Genus Trichoderma

The genus Trichoderma comprises more than 400 species and fungi from diverse ecological niches as well as model fungi for different phenomena, such as plant cell wall degradation, biocontrol, or light response. The widespread uses that arise from these characteristics initiated applications in industry and agriculture, but also development of a plethora of molecular tools for genome manipulation and strain improvement with Trichoderma. Analysis of evolution with high-quality genome sequences revealed the acquisition of an important share of enzymes by horizontal gene transfer (HGT). The “core genome” of Trichoderma was narrowed down to 7000 genes and repeat-induced point mutation (RIP) was discovered as one mechanism for evolutionary genome modification. Genome sequencing studies further revealed numerous mitochondrial genomes and the presence of a surprising diversity of mycoviruses in Trichoderma genomes. Moreover, discoveries on the relevance of long non-coding RNA (lncRNA) and small RNAs as well as selected transcriptome and proteome studies are discussed. Besides new insights from comparative analysis of genomes, genome mining yielded new enzymes, pathways, and progress in the investigation of secondary metabolism of diverse species of the genus.