Genomic insights into the transition from saprophytic to parasitic lifestyles in Hymenochaetales

Macrofungi play key roles in forest ecosystems by forming symbiotic, saprophytic, and parasitic associations with various plant species. Although previous genomic studies have investigated the transitions between these modes of nutrition, limited attention has been paid to the transition from saprophytic to parasitic ecological lifestyles. Hymenochaetales originated as a saprophytic species, and subsequently transitioned to parasitism on multiple occasions. In this study, we sequenced and compared 27 high-quality genomes of the Hymenochaetales. We identified differences in transposable element content and secretome composition between the saprophyte and parasite species. Specifically, the insertion of long-terminal repeat retrotransposons shortly after parasite speciation may drive the transition from saprophytic to parasitic ecological types. Additionally, the close genomic proximity of TEs to CAZymes and SSPs, along with the higher content in several CAZyme and protease families and SSPs in parasites may contribute to shaping host and substrate preferences. Notably, the Ser/Thr protein kinase was postulated to be crucial for the interaction between parasitic species and their host plants. In conclusion, we provide new insights into the molecular mechanisms underlying the transition from saprotrophy to parasitism in Hymenochaetales.