TrichoBase: a standardized genomic resource for comparative genomics of Trichoderma species.

The ecological versatility of the fungal genus Trichoderma spans roles from mycoparasite to saprotroph, presenting a compelling model to investigate how genomic variation underpins niche adaptation. However, comparative genomic studies of Trichoderma are hampered by inconsistent annotation methods across independently sequenced genomes, complicating direct cross-species analysis. To address this, we developed and applied a unified, evidence-based annotation pipeline integrating RNA-seq and homology data to six key species spanning the genus's ecological range (T. asperellum, T. harzianum, T. virens, T. reesei, T. longibrachiatum, and T. citrinoviride). This work presents 'TrichoBase', a consistently annotated genomic resource comprising standardized gene models, functional annotations, and comparative profiles. Using this comparable dataset, we confirm and quantitatively refine the correlation between transposable element (TE) accumulation and genome size expansion. We further demonstrate that TE-rich genomes of mycoparasitic strains are enriched in carbohydrate-active enzymes (CAZymes) and biosynthetic gene clusters (BGCs), while saprotrophic opportunistic lineages show streamlined profiles. Notably, the resource reveals patchy phylogenetic distributions of specific BGC families, such as sorbicillinoid and brefeldin A-like clusters. We provide the complete resource including annotation files, analysis scripts, and a reproducible pipeline to serve as a foundational dataset for future functional genomics and ecological studies in Trichoderma.