Abstract
The cosmopolitan fungal genus Trichoderma contains species commonly found in other fungi, on plant litter, or living plants, showing parasitic, saprophytic, or symbiotic lifestyles. Such versatility results from its genomic repertoire giving rise to great species diversity. Currently, there are many accepted Trichoderma species, and probably many remain to be discovered and described. Here, we report the whole-genome sequence and functional analysis of a new endophytic Trichoderma species isolated from orchid roots and insights into genome evolution, especially regarding carbohydrate-active enzymes related to plant cell wall degradation (pcwdCAZymes). Phylogenetic analysis indicated that this Trichoderma isolate was a new species, proposed in this study as Trichoderma orchidacearum sp. nov. We detected evidence of genome simplification in T. orchidacearum evolution, such as the reduced repertoire of protein-coding genes (8,903 genes) and the contraction of many gene families related to gene expression regulation, signal transduction, oxidoreductases, and hydrolases. Similar evolutionary events also occurred for other species, such as T. reesei and T. longibrachiatum, and were related to shifts from mycoparasitism to other nutritional strategies. The exoproteome analysis combined with plant cell wall-degrading enzyme activities evidenced the ability of T. orchidacearum to feed on plant biomass, despite the large imbalance between cellulolytic and xylanolytic enzymes. The results obtained here increase the knowledge about the evolution of Trichoderma species and contribute to a better understanding of the phenotypic diversity within the genus.
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Data availability
This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JAAOZV000000000. The predicted protein sequences from the genome mentioned above and raw LC-MS/MS data are available from the corresponding author on reasonable request.
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Acknowledgements
The authors thank the “Diretoria de Tecnologia de Informação” (DTI) at “Universidade Federal de Viçosa” for availability of the computational cluster and software used in this work, and the Mass Spectrometry Facility at Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas, Brazil, for their support on mass spectrometry analysis.
Funding
This work was supported by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq/PROTAX 441384/2020-0), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), and Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG). The authors thank the “Diretoria de Tecnologia de Informação” (DTI) at “Universidade Federal de Viçosa” for availability of the computational cluster and software used in this work and the “Núcleo de Pesquisa e Conservação de Orquídeas” (NPCO) at “Universidade Federal de Viçosa” for maintenance of studied plants.
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Túlio Morgan conducted fungal cultivation, enzymatic and saccharification assays, genome sequencing and bioinformatic analysis, proteomic analysis, data interpretation, and discussion. Fábio Alex Custódio performed the morphological analysis. Murillo Peterlini Tavares participated in proteomic analysis and data interpretation, and discussion. Olinto Liparini Pereira, Valéria Monteze Guimarães, and Tiago Antônio de Oliveira Mendes guided and supervised the experiments. Túlio Morgan, Fábio Alex Custódio, and Tiago Antônio de Oliveira Mendes wrote the text. All authors revised and approved the text.
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Morgan, T., Custódio, F.A., Tavares, M.P. et al. Genome sequencing and evolutionary analysis of a new endophytic Trichoderma species isolated from orchid roots with reduced repertoire of protein-coding genes. Mycol Progress 21, 60 (2022). https://doi.org/10.1007/s11557-022-01811-2
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DOI: https://doi.org/10.1007/s11557-022-01811-2