Characterization and comparison of the mitochondrial genomes from two Lyophyllum fungal species and insights into phylogeny of Agaricomycetes

Lyophyllum decastes and Lyophyllum shimeji are the two primary species within the L. decastes complex, and they differ considerably in their nutritional lifestyles and preferred growth environments. However, differences in their mitogenomes have not yet been investigated. In this study, the mitogenomes of the two species were sequenced by next-generation sequencing technology, successfully assembled, and compared. The two mitogenomes of L. decastes and L. shimeji comprised circular DNA molecules of sizes 50,643 bp and 73,678 bp, respectively. The lengths and base compositions of their core protein coding genes (PCGs) and tRNA genes varied considerably between the two mitogenomes. Further, gene collinearity analysis indicated a large-scale gene rearrangement between the two mitogenomes. Of the 15 core PCGs, the genetic distance of the atp9 gene was the smallest between the two species, indicating that this gene was highly conserved in the two Lyophyllum species. Phylogenetic analysis based on a combined mitochondrial gene dataset resulted in a well-supported topology, wherein the two Lyophyllum species were most closely related to Tricholoma matsutake. This study represents the first report of mitogenomes for the Lyophyllum genus. As such, the results will provide a basis for understanding the differentiation and evolution of mitogenomes in the Lyophyllum genus.