Evolution and comparative genomics of the most common Trichoderma species

Abstract

Background The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution. Many Trichoderma species are used as biofertilizers and biofungicides and T. reesei is the model organism for industrial production of cellulolytic enzymes. In addition, some highly opportunistic species devastate mushroom farms and can become pathogens of humans. A comparative analysis of the first three whole genomes revealed mycoparasitism as the innate feature of Trichoderma . However, the evolution of these traits is not yet understood. Results We selected 12 most commonly occurring Trichoderma species and studied the evolution of their genome sequences. Trichoderma evolved in the time of the Cretaceous-Palaeogene extinction event 66 (±15) mya, but the formation of extant sections ( Longibrachiatum, Trichoderma ) or clades ( Harzianum/Virens ) happened in Oligocene. The evolution of the Harzianum clade and section Trichoderma was accompanied by significant gene gain, but the ancestor of section Longibrachiatum experienced rapid gene loss. The highest number of genes gained encoded ankyrins, HET domain proteins and transcription factors. We also identified the Trichoderma core genome, completely curated its annotation, investigated several gene families in detail and compared the results to those of other fungi. Eighty percent of those genes for which a function could be predicted were also found in other fungi, but only 67% of those without a predictable function. Conclusions Our study presents a time scaled pattern of genome evolution in 12 Trichoderma species from three phylogenetically distant clades/sections and a comprehensive analysis of their genes . The data offer insights in the evolution of a mycoparasite towards a generalist. Electronic supplementary material The online version of this article (10.1186/s12864-019-5680-7) contains supplementary material, which is available to authorized users.

“Integrative Genomic Analysis for the Bioprospection of Regulators and Accessory Enzymes Associated with Cellulose Degradation in a Filamentous Fungus (Trichoderma harzianum)”

“…The study of genomic regions is an important tool for providing a global view of the important genes and regulatory regions of a genome [24, 31]. The genomes of a few strains of T. harzianum are available [32, 33]. A complete genome draft sequenced in 1572 scaffolds is available for T. harzianum T6776 [32]; however, little is known about the ThIOC3844 genome, and as it is a strain with potential for hydrolytic enzymes, more genomic information regarding CAZyme sequences is needed.…”

Seeking the Roles for Fungal Small-Secreted Proteins in Affecting Saprophytic Lifestyles

“…An impressive portion of the SSPs (20-61%) is developmentally regulated, with ∼20% being conserved across all tested species, and are comprised of fungal cell wall-related families, such as hydrophobins, cerato-platanins, cupredoxins, lectins, Kre9/Knh1, GH12, and LysM domain proteins . Cerato-platanin proteins are believed to be important for plant-fungal interactions but are also present in saprophytes such as Trichoderma (Kubicek et al, 2019). Over 40 developmentally-regulated SSPs have yet to be functionally annotated and are currently regarded as speciesspecific .…”

Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp

“…Recent advances in next generation sequencing (NGS) lead to the publication of more and more high-quality full genomes from various fungal species and genera such as Aspergillus flavus or various Trichoderma spp. [12,13]. Today, fungi represent a vast and generally untapped pool for new lead compounds with pharmaceutical and agricultural applications [14].…”

“…The genus Trichoderma contains mycoparasitic, saprophytic and opportunistically pathogenic fungi. T. reesei is a well-studied saprobe and used industrially for the production of cellulases and hemicellulases [12]. T. harzianum is a ubiquitous species with agricultural applications, the opportunistically pathogenic T. citrinoviride is often isolated as endophyte and T. brevicompactum is a producer of antifungal metabolites [12,[19][20][21].…”

“…T. reesei is a well-studied saprobe and used industrially for the production of cellulases and hemicellulases [12]. T. harzianum is a ubiquitous species with agricultural applications, the opportunistically pathogenic T. citrinoviride is often isolated as endophyte and T. brevicompactum is a producer of antifungal metabolites [12,[19][20][21]. All mentioned Trichoderma species contain various classes of BGCs, Type 1 polyketide synthetases (T1pks), nonribosomal peptide synthases (NRPSs), terpene BGCs, fatty acid BGCs and various combined and putative clusters.…”