Genome Resequencing and Transcriptome Analysis Reveal the Genetic Diversity of Wolfiporia cocos Germplasm and Genes Related to High Yield.

Wolfiporia cocos is a saprophytic fungus belonging to the phylum Basidiomycota. The dried sclerotium of this organism has been widely used in traditional Chinese medicine for several thousand years and it is prescribed in many formulations. The W. cocos germplasm resources are complex and diverse, and the molecular mechanisms underlying the growth and development of its sclerotia are unclear. In this study, we used genome resequencing and transcriptome analysis to evaluate the genetic diversity of W. cocos germplasm resources in China and the mechanism of sclerotium growth and development. Phylogenetic and population structure analyses revealed that all the 39 tested strains were divided into three major groups. Most of the strains were clustered into one group, and the remaining strains were clustered into the other two groups. There may be a shared origin of cultivated W. cocos in the main production areas. Transcriptome analysis and quantitative reverse transcription-polymerase chain reaction confirmed that candidate genes related to the yield of W. cocos were mainly enriched in oxidation-reduction and carbohydrate metabolism and highly expressed in the ShenChuan strain, which had the highest comprehensive cultivation score. The findings will be helpful for further understanding the evolution and population structure of W. cocos and determining the functional genes that contribute to the high yield of sclerotia.