Comparative genomics of endophytic fungi Apiospora malaysiana with related ascomycetes indicates adaptation attuned to lifestyle choices with potential sustainable cellulolytic activity.

Ascomycetes fungi produce carbohydrate-active enzymes that are prized in the biofuel industry. Comparative genome analysis of endophytic fungus Apiospora malaysiana with seven other closely related high quality genomes of endophytic and pathogenic organisms reveal that effectors and pathogenicity-related genes are predominantly localized within rapidly evolving gene-sparse regions rather than in the conserved region. This suggests bipartite genome architecture where the rapidly evolving region plays a role in host adaptation. Endophytic fungi adapt to plant invasion by enriching enzymes that degrade cellulose, hemicellulose, lignin, and pectin. In contrast, we observed that pathogenic fungi, especially N. oryzae, show a reduced number of secondary metabolites biosynthesis and catabolic genes, reflecting lifestyle adaptation. The presence of exclusive sporulating gene clusters in pathogen species could possibly indicate their pathogenic affiliation. Limited genome plasticity and low heterozygosity in A. malaysiana are in line with its predominant asexual life cycle choices in lab conditions. The secretome of A. malaysiana grown in cellulose-only media had more cellulase activities when compared to cultures grown in YPD media. Genes that were differentially up-regulated in cellulose-only media exhibited strong cellulose-degrading activity and genes involved in evading detection by the hosts surveillance system. Successful cloning and expression of selected CAZymes in bacterial expression systems with desirable physicochemical properties highlight the biotechnological potential of A. malaysiana for sustainable cellulolytic enzyme production. These findings position endophytes as valuable resources for cellulolytic enzyme research and broader bio-industrial applications.