Year: 2019
Type: article
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.
Source: BMC Genomics
Authors: Christian P. Kubicek, Andrei S. Steindorff, Komal Chenthamara, Gelsomina Manganiello, Bernard Henrissat, Jian Zhang, Feng Cai, Alexey G. Kopchinskiy, Eva M. Kubicek, Alan Kuo, Riccardo Baroncelli, Sabrina Sarrocco, Eliane Ferreira Noronha, Giovanni Vannacci, Qirong Shen, Igor V. Grigoriev, Irina S. Druzhinina
Institutions: TU Wien, United States Department of Energy, Universidade de Brasília, Joint Genome Institute, University of Campania "Luigi Vanvitelli", University of Naples Federico II, Centre National de la Recherche Scientifique, King Abdulaziz University, Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, Nanjing Agricultural University, Universidad de Salamanca, Instituto de Investigación en Agrobiotecnología, University of Pisa, University of California, Berkeley
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,145
Funders: U.S. Department of Energy, Joint Genome Institute, University of Exeter, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Austrian Science Fund, Conselho Nacional de Desenvolvimento Científico e Tecnológico, Österreichische Forschungsförderungsgesellschaft, Nanjing Agricultural University, Office of Science, National Key Research and Development Program of China
Awards: G1164920944, G1189359547, G1270460216, G1286236842, G1414775356, G1816284028, Genomic / transcriptomic approaches to fungus-pest interactions and biological control, G2620055207, Trichoderma proteins with an ankyrin domain, G3083819904, G3114243037, G365575497, G419881185, G42916606, G4501827968, G498139845, G5397131259, G5397860597, G5594613725, G6652958823, G7205239661, G805243471, G834277795, G969889393
OpenAlex ID: W2949926205