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Background  Unveiling fungal genome structure and function reveals the potential biotechnological use of fungi.  Trichoderma harzianum  is a powerful CAZyme-producing fungus. We studied the genomic regions in  T. harzianum  IOC3844 containing CAZyme genes, transcription factors and transporters.    Results  We used bioinformatics tools to mine the  T. harzianum  genome 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 in  T. harzianum  IOC3844. 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 in  Trichoderma  spp., 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.    Conclusions  Our results provide new insights into the relationship between genomic organization and hydrolytic enzyme expression and regulation in  T. harzianum  IOC3844. Our results can improve plant biomass degradation, which is fundamental for developing more efficient strains and/or enzymatic cocktails to produce hydrolytic enzymes.    Supplementary information   Supplementary information  accompanies this paper at 10.1186/s12864-020-07158-w.

bmc genomics

“Integrative genomic analysis of the bioprospection of regulators and accessory enzymes associated with cellulose degradation in a filamentous fungus (Trichoderma harzianum)”