Abstract
Trametes species are efficient wood decomposers that are widespread throughout the world. Mitogenomes have been widely used to understand the phylogeny and evolution of fungi. Up to now, two mitogenomes from the Trametes genus have been revealed. In the present study, the complete mitogenomes of two novel Trametes species, Trametes versicolor and T. coccinea, were assembled and compared with other Polyporales mitogenomes. Both species contained circular DNA molecules, with sizes of 67,318 bp and 99,976 bp, respectively. Comparative mitogenomic analysis indicated that the gene number, length and base composition varied between the four Trametes mitogenomes we tested. In addition, all of the core protein coding genes in Trametes species were identified and subjected to purifying selection. The mitogenome of T. coccinea contained the largest number of introns among the four Trametes species tested, and introns were considered the main factors contributing to size variations of Polyporales. Several novel introns were detected in the Trametes species we assembled, and introns identified in Polyporales were found to undergo frequent loss/gain events. Large-scale gene rearrangements were detected between closely related Trametes species, including gene inversions, insertions, and migrations. A well-supported phylogenetic tree for 77 Basidiomycetes was obtained based on the combined mitochondrial gene set using 2 phylogenetic inference methods. The results showed that mitochondrial genes are effective molecular markers for understanding the phylogeny of Basidiomycetes. This study is the first to report the mitogenome rearrangement and intron dynamics of Trametes species, which shed light on the evolution of Trametes and other related species.
Highlights
Trametes species are efficient wood decomposers that are widespread throughout the world
Intronic open reading frames (ORFs) in the two Trametes mitogenomes mainly encoded LAGLIDADG endonucleases, GIY-YIG endonucleases, and intron-encoded RNA maturase bI4; we found two and three intronic ORFs with unknown functions in the T. versicolor and T. coccinea mitogenomes, respectively
Comparative mitogenomic analysis showed that the novel mitogenome of T. coccinea was largest among the four Trametes mitogenomes reported[10,11]
Summary
Trametes species are efficient wood decomposers that are widespread throughout the world. The complete mitogenomes of two novel Trametes species, Trametes versicolor and T. coccinea, were assembled and compared with other Polyporales mitogenomes. Both species contained circular DNA molecules, with sizes of 67,318 bp and 99,976 bp, respectively. The goals of this study were to: (1) characterize Trametes mitogenomes; (2) reveal the variations or similarities in genome size, structure, and gene content of the Trametes mitogenomes; (3) reveal the dynamic changes of introns in Polyporales mitogenomes; and (4) shed light on the phylogenetic relationships of Trametes in the phylum Basidiomycota based on the combined mitochondrial gene set. The results of this study will promote improved understanding of the origin, evolution, and taxonomy of Trametes species and other related fugal species
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