Unveiling the carbohydrate-active enzyme repertoire of Trichoderma caribbaeum IHBT through whole-genome analysis and...

Carbohydrate-active enzymes (CAZymes) play an important role in the efficient deconstruction of lignocellulosic biomass (LCB) and chitin, which is essential for sustainable bioenergy production and for the development of industrially important value-added products. Fungi, especially members of Trichoderma spp., are known as efficient degraders of biomass and represent valuable resources for expanding the known repertoire of CAZymes. This study presents the first report of the sequencing and annotation of a high-quality hybrid genome assembly of Trichoderma caribbaeum IHBT, isolated from the western Himalayan region, along with RNA-seq analysis to identify CAZyme-encoding genes potentially involved in the biomass degradation process. The assembled genome was 36.2 Mb in size, with a N50 value of 1.2 Mb and a GC content of 48%, indicating a high-quality genome assembly. Genome mining enabled the identification and functional annotation of 362 putative CAZyme-encoding genes. Time-course transcriptome profiling of T. caribbaeum IHBT grown on sugarcane bagasse (SB) revealed an upregulation of several genes involved in carbohydrate metabolism, including members of the glycoside hydrolase (GH; XP_013945330.1, UKZ69522.1, UKZ67968.1, XP_013947289.1, XP_013940790.1, and UKZ68144.1) and auxiliary activity (AA; UKZ70991.1, XP_013940326.1, XP_013944427.1, UKZ71564, and UKZ60083.1) families, including lytic polysaccharide monooxygenases (LPMOs). Weighted Gene Co-Expression Network Analysis (WGCNA) identified eight potential Hub genes, of which XP_013943413.1, XP_013940723.1, XP_013945605, and XP_013942713 are directly implicated in biomass deconstruction. Overall, the identified CAZyme-encoding genes offer significant potential for further functional characterization and application in biomass valorization, thereby supporting the development of sustainable circular economic strategies in prospective studies.