{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T11:05:50Z","timestamp":1789470350450,"version":"build-2803163510"},"reference-count":48,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T00:00:00Z","timestamp":1789430400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>The genus Trichoderma comprises ecologically and biotechnologically important fungi that have been widely investigated and used in agriculture, industrial biotechnology, and biological control. However, publicly available genomes reveal substantial taxonomic inconsistencies across the genus, which can complicate strain identification, reproducibility, and the comparison and selection of strains for applied research and biotechnology. Here, we present a comprehensive phylogenomic and comparative genomic analysis integrating one of the largest collections of Trichoderma genomes analyzed to date. Phylogenomic reconstruction based on 920 conserved single-copy orthologs recovered four major evolutionary clades with strong statistical support and revealed widespread taxonomic inconsistencies affecting multiple species complexes, including T. harzianum, T. asperellum, T. viride, and T. longibrachiatum. Comparative analyses demonstrated marked clade-associated differences in genome size, GC content, repetitive DNA content, gene content, and whole-genome conservation patterns. Genome size was positively associated with repetitive-element accumulation and gene number, whereas GC content showed a negative association with genome size. We additionally characterized a novel Colombian isolate that clustered within a highly supported and divergent lineage together with three inconsistently annotated public genomes. This lineage, provisionally designated Trichoderma sp. \u201cCB2\u201d, formed a sister group to the Longibrachiatum complex and exhibited strong internal genomic cohesion and clear divergence from neighboring lineages. Orthology-based analyses identified lineage-associated proteins with predicted functions related to transcriptional regulation, plant biomass degradation, secondary metabolism, and detoxification. Overall, this study provides a genome-scale framework for resolving Trichoderma diversity and highlights the extent of taxonomic inconsistencies in public genomic resources. Improved phylogenomic characterization of strains can facilitate more reliable strain identification, reproducibility, comparative genomic studies, and the selection and evaluation of Trichoderma strains for agricultural and biotechnological applications.<\/jats:p>","DOI":"10.3390\/ijms27188204","type":"journal-article","created":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T10:32:01Z","timestamp":1789468321000},"page":"8204","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Phylogenomic and Comparative Genomic Analyses Reveal Deep Evolutionary Structure and Cryptic Diversity in the Genus Trichoderma"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8966-0405","authenticated-orcid":false,"given":"Felipe","family":"Cabarcas","sequence":"first","affiliation":[{"name":"Centro Nacional de Secuenciaci\u00f3n Gen\u00f3mica\u2014CNSG, Sede de Investigaci\u00f3n Universitaria\u2014SIU, Universidad de Antioquia UdeA, Calle 67 No. 53-108, Medell\u00edn 050010, Colombia"},{"name":"Facultad de Ingenier\u00eda, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medell\u00edn 050010, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"given":"Juliana","family":"Lopez-Jimenez","sequence":"additional","affiliation":[{"name":"Centro Nacional de Secuenciaci\u00f3n Gen\u00f3mica\u2014CNSG, Sede de Investigaci\u00f3n Universitaria\u2014SIU, Universidad de Antioquia UdeA, Calle 67 No. 53-108, Medell\u00edn 050010, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Maria Patricia","family":"Ricardo","sequence":"additional","affiliation":[{"name":"Bioorigen, Grupo Greenland, Apartado 057840, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"}]},{"given":"Isabel","family":"Luna","sequence":"additional","affiliation":[{"name":"Bioorigen, Grupo Greenland, Apartado 057840, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2578-4609","authenticated-orcid":false,"given":"Juan F.","family":"Alzate","sequence":"additional","affiliation":[{"name":"Centro Nacional de Secuenciaci\u00f3n Gen\u00f3mica\u2014CNSG, Sede de Investigaci\u00f3n Universitaria\u2014SIU, Universidad de Antioquia UdeA, Calle 67 No. 53-108, Medell\u00edn 050010, Colombia"},{"name":"Departamento de Microbiolog\u00eda y Parasitolog\u00eda, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medell\u00edn 050010, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1080\/03235408.2026.2650353","article-title":"Trichoderma: A versatile microbe from basic to nanotechnology","volume":"59","author":"Singh","year":"2026","journal-title":"Arch. 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