Targeting lignocellulolytic gene clusters in novel Trichoderma atroviride and Trichoderma harzianum strains through bacterial artificial chromosome–guided analysis

Lignocellulosic biomass is a complex carbon source with recalcitrant properties whose degradation via industrial enzymatic hydrolysis is challenging, directly affecting the cost of reliable energy production. In nature, filamentous fungi, including Trichoderma species, degrade lignocellulose via an arsenal of hydrolytic and oxidative enzymes that act synergistically to process it into soluble sugar monomers. This work explored the genomic content of Trichoderma atroviride and Trichoderma harzianum strains with hydrolytic abilities by identifying regions possessing degradative enzyme–encoding genes, namely, hydrolytic clusters. We employed bacterial artificial chromosome (BAC) methodology to target specific genomic regions and explore their genetic organization, proximal gene context, and gene expression under degradative conditions. With this tool, it was possible to inspect the linear structure and expression profile of target hydrolytic-rich genomic regions. The present work offers a perspective on the organization of genome regions related to carbohydrate metabolism. This study revealed novel genes and genome regions that are positively regulated during cellulose degradation, contributing to elucidating differences in gene organization that potentially impact hydrolysis among Trichoderma species.