Trichoderma – genomes and genomics as treasure troves for research towards biology, biotechnology and agriculture

Abstract

The genus Trichoderma is among the best studied groups of filamentous fungi, largely because of its high relevance in applications from agriculture to enzyme biosynthesis to biofuel production. However, the physiological competences of these fungi, that led to these beneficial applications are intriguing also from a scientific and ecological point of view. This review therefore summarizes recent developments in studies of fungal genomes, updates on previously started genome annotation efforts and novel discoveries as well as efforts towards bioprospecting for enzymes and bioactive compounds such as cellulases, enzymes degrading xenobiotics and metabolites with potential pharmaceutical value. Thereby insights are provided into genomes, mitochondrial genomes and genomes of mycoviruses of Trichoderma strains relevant for enzyme production, biocontrol and mycoremediation. In several cases, production of bioactive compounds could be associated with responsible genes or clusters and bioremediation capabilities could be supported or predicted using genome information. Insights into evolution of the genus Trichoderma revealed large scale horizontal gene transfer, predominantly of CAZyme genes, but also secondary metabolite clusters. Investigation of sexual development showed that Trichoderma species are competent of repeat induced point mutation (RIP) and in some cases, segmental aneuploidy was observed. Some random mutants finally gave away their crucial mutations like T. reesei QM9978 and QM9136 and the fertility defect of QM6a was traced back to its gene defect. The Trichoderma core genome was narrowed down to 7000 genes and gene clustering was investigated in the genomes of multiple species. Finally, recent developments in application of CRISPR/Cas9 in Trichoderma, cloning and expression strategies for the workhorse T. reesei as well as the use genome mining tools for bioprospecting Trichoderma are highlighted. The intriguing new findings on evolution, genomics and physiology highlight emerging trends and illustrate worthwhile perspectives in diverse fields of research with Trichoderma.

Plant recognition byTrichoderma harzianumelicits upregulation of a novel secondary metabolite cluster required for colonization

“…One striking example of horizontal gene transfer (HGT) was described for the sorbicillin biosynthetic cluster in T. reesei, which was acquired from other fungi, but also other cases are known from this genus (Druzhinina et al, 2018;Druzhinina et al, 2016;Schalamun & Schmoll, 2022). An unexpectedly high .…”

“…Fungi of the genus Trichoderma (Schalamun & Schmoll, 2022;Woo et al, 2022) are typical inhabitants of the rhizosphere and are found in soils worldwide (Druzhinina et al, 2011). They belong to the most versatile microorganisms for both agricultural and industrial applications (Mukherjee et al, 2013).…”

Targeting lignocellulolytic gene clusters in novelTrichoderma atrovirideandTrichoderma harzianumstrains through Bac-guided analysis

“…Additionally, gene families such as ankyrin, heterokaryon incompatibility domain protein (HET), TF, carbohydrate degradative, and secondary metabolism genes all present high polymorphism rates (Kubicek et al, 2011, 2019; Mukherjee et al, 2013). The intraspecific diversity of the Harzianum clade poses a challenge to even modern molecular genetics because this species aggregate has multiple infra groups and great complexity (Druzhinina et al, 2010; Kubicek et al, 2019; Schalamun and Schmoll, 2022), which can partially explain the limited CAZyme transfer.…”

“…Their remarkable capacities at the intraspecific level are greatly influenced by lateral gene transfer and other complex evolutionary processes contributing to genomic variations, even those observed in closely related species. Interestingly, carbohydrate metabolism and biocontrol gene families seem to be especially influenced by evolutionary processes (Kubicek et al, 2011; Kubicek et al, 2019; Hewedy et al, 2020; Sood et al, 2020; Schalamun and Schmoll, 2022; Tyśkiewicz et al, 2022; Guzmán-Guzmán et al, 2023).…”

MAPkinases regulate secondary metabolism, sexual development and light dependent cellulase regulation in Trichoderma reesei

“…The genus Trichoderma comprises a diverse array of mostly bene cal fungi, which comprise plant symbionts and industrial workhorses for enzyme production [35][36][37][38][39][40] .…”