Nearly Telomere-to-telomere Genome Assembly of Lentinula edodes Diploid Genome (hap 1)

This study reports the near telomere-to-telomere (T2T) assembly of the complete diploid genome of Lentinula edodes (shiitake mushroom), a commercially important Japanese strain XR1. We employed PacBio HiFi long-read sequencing technology combined with single-cell genotyping data and manual curation. The assembled diploid genome comprises 20 chromosomes (10 per haplotype) and significant inter-haplotype variations were found. We also identified a novel Penelope-like retrotransposon, Coprina-1_LeEd, localized specifically at telomeres, marking the first report of a long-terminal repeat (LTR)-containing element actively transposing in telomeric regions. Our findings provide a high-resolution genome resource for L. edodes, advancing our understanding of its evolution, genomic structure, and breeding potential, while establishing a foundation for further research on edible mushroom genetics and biotechnology. Haplotype 1