The complete mitochondrial genome of medicinal fungus Taiwanofungus camphoratus reveals gene rearrangements and intron dynamics of Polyporales

Abstract

Taiwanofungus camphoratus is a highly valued medicinal mushroom that is endemic to Taiwan, China. In the present study, the mitogenome of T. camphoratus was assembled and compared with other published Polyporales mitogenomes. The T. camphoratus mitogenome was composed of circular DNA molecules, with a total size of 114,922 bp. Genome collinearity analysis revealed large-scale gene rearrangements between the mitogenomes of Polyporales, and T. camphoratus contained a unique gene order. The number and classes of introns were highly variable in 12 Polyporales species we examined, which proved that numerous intron loss or gain events occurred in the evolution of Polyporales. The Ka/Ks values for most core protein coding genes in Polyporales species were less than 1, indicating that these genes were subject to purifying selection. However, the rps3 gene was found under positive or relaxed selection between some Polyporales species. Phylogenetic analysis based on the combined mitochondrial gene set obtained a well-supported topology, and T. camphoratus was identified as a sister species to Laetiporus sulphureus. This study served as the first report on the mitogenome in the Taiwanofungus genus, which will provide a basis for understanding the phylogeny and evolution of this important fungus.

The mitogenomes of two saprophytic Boletales species (Coniophora) reveals intron dynamics and accumulation of plasmid-derived and non-conserved genes

“…In the present study, we found the core PCGs [56] , [57] underwent non synonymous and synonymous mutations in Boletales, and different core PCGs showed differentiated mutation rate. The results were consistent with previous studies [58] , [59] . The rps3 gene was found differentiated greatly in Boletales species.…”

Comparative Mitogenomic Analysis Reveals Dynamics of Intron Within and Between Tricholoma Species and Phylogeny of Basidiomycota

“…The rps3 gene is an ancient gene in fungi, which evolved within the endosymbiotic model and presents varied evolutionary routes (Korovesi et al, 2018 ). The rps3 gene was frequently observed to experience positive selection or relaxed selection in fungi (Wang et al, 2020b , c ), and the selection pressure on rps3 gene needs to be further verified. Most mitochondrial genes have been transferred to the nuclear genome during the evolution of eukaryotic lineages, which is considered to have many advantages (Bjorkholm et al, 2015 ).…”

Comparative mitochondrial genome analysis reveals intron dynamics and gene rearrangements in two Trametes species

“…Generally, animal mitogenomes do not contain any introns, whereas plant mitogenomes mainly contain group II introns and fungal mitogenomes mainly contain group I introns 51,54 . The cox1 gene was found to be the main host gene of introns in mitogenomes of Basidiomycetes 55,56 . We divided the introns of cox1 genes of 14 Polyporales species into different position classes (Pcls) according to their insertion sites in the protein coding region.…”