Genomic Characterization of Novel Endophyte Strains from Tall Fescue Shows Genome Fragmentation Post-Hybridization

Interspecific hybridization in fungi has gained attention for its role in fungal evolution and potential commercial applications. Successful hybridization can enhance fitness and facilitate adaptation to new ecological niches. However, the genomic consequences of hybridization in fungi remain poorly understood. Epichloë is a genus of fungi that includes both non-hybrid and hybrid species, with the hybrids forming through parasexual hybridization and reproducing asexually. Some Epichloë hybrids are of commercial significance, as they colonize Lolium arundinaceum (Schreb.) Darbysh., a crucial forage and turf grass species. In this study, we sought to generate high-quality genome assemblies for two previously uncharacterized Epichloë hybrid strains, both of which are similar to Epichloë sp. FaTG-3. We aimed to characterize their genomes and examine the effects of parasexual interspecific hybridization on fungal genome structure. Our results reveal that the genomes of both strains are rich in AT-rich blocks and repetitive elements. Upon comparison with putative progenitor genomes, we observed significant fragmentation and rearrangement. Despite the genomic instability, more than 85% of gene homologs from each progenitor species were retained. This study demonstrates that while parasexual hybridization dramatically alters genome structure, it does not significantly affect gene content.