Comprehensive Genomic Analysis of Penicillium Species

Genes related to cellulose and hemicellulose degradation: Carbohydrate-active enzymes (CAZymes) in the three Penicillium species were annotated using BLAST (Johnson M. et al., 2008 (link)). The dbCAN annotation program HMMER 3 (Finn et al., 2011 (link)) was used to search against the CAZy (carbohydrate-active enzyme) database (Lombard et al., 2014 (link)). The results were combined when e values ≤1e–5. The class II peroxidases and dye-decolorizing peroxidases were further confirmed by BLAST searches against PeroxiBase (Fawal et al., 2012 (link)).
Secondary metabolism genes: Candidate transporter genes in the three Penicillium species were identified based on searches of the Transporter Classification Database (TCDB) (Saier et al., 2014 (link)) with e values ≤1e–5 and identity values ≥40%. The secondary metabolism biosynthesis genes and gene clusters in the genomes of the three Penicillium species were predicted with AntiSMASH 6.0 (Blin et al., 2021 (link)). The Comprehensive Antibiotic Research Database (CARD) (McArthur et al., 2013 (link)) was used to compare coding genes (of the three Penicillium species) involved in antimicrobial resistance.
Virulence associated genes: Candidate pathogen-host interactions (PHI) genes within the genome of the three Penicillium species were identified using BLASTp to search against PHI-base v4.3⁷, and protein alignments were performed to identify putative virulence-associated genes in the three Penicillium species with identity ≥40% and query coverage ≥70%.