Comparative genome and transcriptome analysis of the endophytic fungus Epichloë sibirica reveals biological control mechanism in host Achnatherum sibiricum

• Endophytic genome reveals antibiotics and mycelial-enzyme biocontrol potential. • Transcriptomics show pathogens do not alter endophytes’ transcriptional activity. • Endophytes enhance host defense via trehalose- and effector-triggered immunity. • Ecological niche competitiveness underpins endophytes’ ability to suppress pathogens. • Endophytes exhibit superior antibiotic tolerance compared to pathogens. Endophytic fungi of the genus Epichloë can bolster the host’s immune defenses against phytopathogens. However, the underlying mechanisms by which the endophytes regulate host responses remain poorly understood. This study elucidates the tripartite strategy employed by Epichloë sibirica to protect Achnatherum sibiricum through comparative genomics and transcriptomics. First, genomic and transcriptomic analyses revealed that E. sibirica can synthesize antibiotics (e.g., ε-poly-L-lysine) and mycelial degrading enzymes. Second, ecological niche occupation was supported by (1) minimal transcriptomic alterations in E. sibirica during pathogen challenge, (2) superior antimicrobial activity in fungal fermentation assays (superior antimicrobial activity of E. sibirica against four pathogens, while pathogen-derived broths had negligible effects on E. sibirica growth), and (3) comparative antibiotic susceptibility testing demonstrated E. sibirica ’s significantly higher tolerance to strobilurin A, tetracycline, streptomycin sulphate, and penicillin sodium compared to pathogens. Third, host resistance induction involved gene clusters encoding effector proteins, cell wall-modifying enzymes, and trehalose. These findings identify E. sibirica as a multifaceted biocontrol agent through metabolite-mediated antagonism, ecological niche occupation, and host priming. Our results provide omics-level evidence of endophyte-driven tripartite defense mechanisms.