Comparative Genomics Analysis Reveals the Genomic Basis of S8 Proteases, CAZymes, and Secondary Metabolism Associated with Nematode Biocontrol in Purpureocillium lilacinum

Biological control fungi play an important role in the management of plant-parasitic nematodes; however, the molecular basis underlying their diverse biocontrol strategies remains incompletely understood. In this study, a comparative genomic analysis was performed on four representative biocontrol fungi: Purpureocillium lilacinum PLFJ-1, Trichoderma harzianum CBS 226.95, Pochonia chlamydosporia 170, and Aspergillus niger CBS 513.88. Genome comparison revealed substantial variation: genome size ranged from 34.0 Mb (A. niger) to 44.2 Mb (P. chlamydosporia), GC content from 47.5% (T. harzianum) to 58.5% (P. lilacinum), and predicted gene models also differed markedly among the four fungi. Phylogenetic analysis based on the Internal Transcribed Spacer divided these fungi into two major clades corresponding to distinct evolutionary lineages. Orthogroup analysis identified both a conserved core gene set and species-specific gene repertoires. Functional annotation using KEGG, KOG, and GO indicated a high degree of conservation across core metabolic processes, catalytic activities, and cellular components, with distinct differences within specific functional categories. Further comparative analyses demonstrated pronounced variation in the composition and abundance of carbohydrate-active enzymes (CAZymes) and peptidases, as well as a notable expansion and enrichment of S8 subtilisin-like serine peptidases in the nematode-parasitic fungi P. lilacinum and P. chlamydosporia. Secondary metabolite analysis revealed lineage-specific biosynthetic gene clusters (BGCs). Notably, P. lilacinum and P. chlamydosporia carried PKS/NRPS clusters potentially linked to nematicidal activity, while A. niger and T. harzianum displayed broader but less infection-specific metabolic profiles. Together, these findings suggest that distinct enzymatic and metabolic gene repertoires, particularly expansions of S8 serine peptidases and specific CAZyme families, may contribute to the biocontrol potential of these fungi.