Whole-genome sequencing and analysis of the symbiotic Mycena sp. L02 with Gastrodia Elata.

BACKGROUND: Mycena is a widespread genus of mushroom capable of decomposing various dead plant substrates. Gastrodia elata is a fully mycoheterotrophic orchid whose seed germination depends on specific Mycena strains. However, only a few Mycena species are capable of inducing germination, necessitating the identification of novel germinating fungal resources. RESULTS: The genome of Mycena sp. L02 was sequenced using the Illumina NovaSeq and Oxford Nanopore Technologies (ONT) platforms. The final assembly spanned 160.06 Mb, with 36,246 genes predicted and repetitive sequences accounting for 31.90% (46,496,154 bp) of the genome. A total of 1,339 CAZyme genes were annotated, along with 3,772 genes involved in host-pathogen interactions, 88.33% of which were associated with loss of pathogenicity, reduced virulence, or unaffected pathogenicity. Comparative genomic analysis between germinating and non-germinating Mycena strains revealed that their CAZymes and PHI gene characteristics represent common traits shared across the Mycena genus, with no distinctive features identified. Furthermore, pathways enriched in unique gene families of the germinating fungi-such as glutathione metabolism, sulfur metabolism, phosphatidylinositol signaling system, and inositol phosphate metabolism-may contribute to the germination of G. elata seeds. CONCLUSIONS: The abundance of CAZymes and low-virulence genes in L02 ensures sufficient nutrient acquisition and may facilitate hyphal penetration of the lignin-rich seed coat of G. elata, thereby enabling successful symbiosis. Additionally, KEGG pathways enriched in the unique gene families of the germinating fungi may contribute to the stimulation of seed germination in G. elata. Overall, this study provides a valuable genomic foundation for screening high-performance germinating fungi and further investigating the molecular mechanisms underlying the symbiosis with G. elata.