Chromosome-Level Assembly Reveals a Fifteen-Chromosome Aneuploid Genome and Environmental Adaptation Strategy of Chinese Traditional Medical Fungus .

The sclerotia of are one of the most important traditional Chinese medicines and foods commonly used in China, Japan, Korea, and other Asian countries. To provide a high-quality reference genome and deepen our understanding of the genome of to elucidate various biological phenomena. In this study, we assembled three genomes of using a combination of Nanopore and Illumina sequencing strategies. The fifteen-chromosome genome L7 of was assembled with two-sided telomere and rDNA sequences for the first time. The chromosome count was subsequently confirmed through collinearity analysis, correcting the previous belief that had only fourteen chromosomes. Moreover, the aneuploid genome was discovered in for the first time through sequencing depth analysis of different chromosomes, and only some strains of exhibit aneuploid genomes. According to the genome analysis of homokaryotic offspring and protoplast-isolated strains, a potential variation in chromosome allocation patterns was revealed. Moreover, the gene function enrichment analysis of genes on reduplicated chromosomes demonstrated that aneuploidy in the genome may be the result of environmental adaptation for . The discovery of an aneuploid genome also provides new ideas for genetic improvement of .