Evolution and comparative genomics of the most common Trichoderma species

Christian P Kubicek,Qirong Shen,Igor V Grigoriev,Sabrina Sarrocco,Feng Cai,Irina S Druzhinina,Alexey G Kopchinskiy,Eliane Ferreira Noronha,Riccardo Baroncelli,Komal Chenthamara,Bernard Henrissat,Gelsomina Manganiello,Alan Kuo,Andrei S Steindorff,Jian Zhang,Giovanni Vannacci,Eva M Kubicek

doi:10.1186/s12864-019-5680-7

Abstract

BackgroundThe 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.ResultsWe 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.ConclusionsOur 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.

Highlights

The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution
This was followed by T. asperellum, T. atroviride, T. longibrachiatum, T. gamsii, and T. virens that were represented by > 1000 sequences each and frequent
We identified 10–25 polyketide synthase (PKS), 12–34 non-ribosomal polypeptide synthetase (NRPS), and 6–14 terpenoid synthase (TS) encoding genes in the 12 species, of which 6 PKS, 10 NRPS and 3 TS genes were present in the core genome

Summary

Introduction

The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution. The Sordariomycetes, one of the largest classes in the Division Ascomycota, display a wide range of nutritional strategies including saprotrophy and biotrophic interactions with bacteria, plants, animals, fungi or other organisms [1]. Mycoparasitic fungi can be found in species from several fungal taxa [5], but only the Hypocreales contain exclusively fungicolous genera, i.e. Hypomyces, Escovopsis, and Trichoderma. The ancestor of these mycoparasitic fungi likely evolved at the same time as the entomoparasites, but the time and events of Trichoderma evolution are not known

Methods

Results

Discussion

Conclusion