AbstractBackgroundUnveiling fungal genome structure and function reveals the potential biotechnological use of fungi.Trichoderma harzianumis a powerful CAZyme-producing fungus. We studied the genomic regions inT. harzianumIOC3844 containing CAZyme genes, transcription factors and transporters.ResultsWe used bioinformatics tools to mine theT. harzianumgenome for potential genomics, transcriptomics, and exoproteomics data and coexpression networks. The DNA was sequenced by PacBio SMRT technology for multiomics data analysis and integration. In total, 1676 genes were annotated in the genomic regions analyzed; 222 were identified as CAZymes inT. harzianumIOC3844. When comparing transcriptome data under cellulose or glucose conditions, 114 genes were differentially expressed in cellulose, with 51 being CAZymes. CLR2, a transcription factor physically and phylogenetically conserved inTrichodermaspp., was differentially expressed under cellulose conditions. The genes induced/repressed under cellulose conditions included those important for plant biomass degradation, including CIP2 of the CE15 family and a copper-dependent LPMO of the AA9 family.ConclusionsOur results provide new insights into the relationship between genomic organization and hydrolytic enzyme expression and regulation inT. harzianumIOC3844. Our results can improve plant biomass degradation, which is fundamental for developing more efficient strains and/or enzymatic cocktails to produce hydrolytic enzymes.