The first two mitochondrial genomes for the genus Ramaria reveal mitochondrial genome evolution of Ramaria and phylogeny of Basidiomycota

Abstract

AbstractIn the present study, we assembled and analyzed the mitogenomes of twoRamariaspecies. The assembled mitogenomes ofRamariacfr.rubripermanensandR. rubellawere circularized, with sizes of 126,497 bp and 143,271 bp, respectively. Comparative mitogenome analysis showed that intron region contributed the most (contribution rate, 43.74%) to the size variations ofRamariamitogenomes. The genetic contents, gene length, tRNAs, and codon usages of the twoRamariamitogenomes varied greatly. In addition, the evolutionary rates of different core protein coding genes (PCGs) inPhallomycetidaemitogenomes varied. We detected large-scale gene rearrangements betweenPhallomycetidaemitogenomes, including gene displacement and tRNA doubling. A total of 4499 bp and 7746 bp aligned fragments were detected between the mitochondrial and nuclear genomes ofR.cfr.rubripermanensandR. rubella, respectively, indicating possible gene transferring events. We further found frequent intron loss/gain and potential intron transfer events inPhallomycetidaemitogenomes during the evolution, and the mitogenomes ofR. rubellacontained a novel intron P44. Phylogenetic analyses using both Bayesian inference (BI) and Maximum Likelihood (ML) methods based on a combined mitochondrial gene dataset obtained an identical and well-supported phylogenetic tree forBasidiomycota, whereinR.cfr.rubripermanensandTurbinellus floccosusare sister species. This study served as the first report on mitogenomes from the genusRamaria, which provides a basis for understanding the evolution, genetics, and taxonomy of this important fungal group.