Comparative Genomics and Transcriptomics Analyses Reveal Divergent Plant Biomass-Degrading Strategies in Fungi

Abstract

Plant biomass is one of the most abundant renewable carbon sources, which holds great potential for replacing current fossil-based production of fuels and chemicals. In nature, fungi can efficiently degrade plant polysaccharides by secreting a broad range of carbohydrate-active enzymes (CAZymes), such as cellulases, hemicellulases, and pectinases. Due to the crucial role of plant biomass-degrading (PBD) CAZymes in fungal growth and related biotechnology applications, investigation of their genomic diversity and transcriptional dynamics has attracted increasing attention. In this project, we systematically compared the genome content of PBD CAZymes in six taxonomically distant species, Aspergillus niger, Aspergillus nidulans, Penicillium subrubescens, Trichoderma reesei, Phanerochaete chrysosporium, and Dichomitus squalens, as well as their transcriptome profiles during growth on nine monosaccharides. Considerable genomic variation and remarkable transcriptomic diversity of CAZymes were identified, implying the preferred carbon source of these fungi and their different methods of transcription regulation. In addition, the specific carbon utilization ability inferred from genomics and transcriptomics was compared with fungal growth profiles on corresponding sugars, to improve our understanding of the conversion process. This study enhances our understanding of genomic and transcriptomic diversity of fungal plant polysaccharide-degrading enzymes and provides new insights into designing enzyme mixtures and metabolic engineering of fungi for related industrial applications.

Genome Mining Reveals a Surprising Number of Sugar Reductases in Aspergillus niger

“…iTOL V6.8.1 [18] was used to visualize the tree. The transcriptome data were obtained from previous liquid culture studies in our group [19] for A. niger, A. nidulans, P. subrubescens, and T. reesei, while the N. crassa data were from Wu et al [20].…”

“…The reads from each of the transcriptome sequencing (RNA-seq) were previously published [19] and samples were deposited in the Sequence Read Archive at NCBI under the accession numbers: A. niger SRP448993, SRP449003-SRP449007, SRP449023, SRP449039, SRP449049, SRP449062, SRP449079-SRP449081, SRP449083-SRP449085, SRP449089, SRP449068-SRP449070, SRP449098, SRP449125, SRP449138, SRP449141, SRP449142, SRP449151, and SRP449193; A. nidulans SRP262827-SRP262853; P. subrubescens SRP246823-SRP246849; and T. reesei SRP378720-SRP378745. N. crassa transcriptome data was used from Wu et al, 2020 [20] and have been deposited National Center for Biotechnology Information (NCBI) Sequence Read Archive (ID SRP133337).…”