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

Abstract

In the present study, we assembled and analyzed the mitogenomes of two Ramaria species. The assembled mitogenomes of Ramaria cfr. rubripermanens and R. rubella were 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 of Ramaria mitogenomes. The genetic contents, gene length, tRNAs, and codon usages of the two Ramaria mitogenomes varied greatly. In addition, the evolutionary rates of different core protein coding genes (PCGs) in Phallomycetidae mitogenomes varied. We detected large-scale gene rearrangements between Phallomycetidae mitogenomes, including gene displacement and tRNA doubling. A total of 4499 bp and 7746 bp aligned fragments were detected between the mitochondrial and nuclear genomes of R. cfr. rubripermanens and R. rubella, respectively, indicating possible gene transferring events. We further found frequent intron loss/gain and potential intron transfer events in Phallomycetidae mitogenomes during the evolution, and the mitogenomes of R. rubella contained 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 for Basidiomycota, wherein R. cfr. rubripermanens and Turbinellus floccosus are sister species. This study served as the first report on mitogenomes from the genus Ramaria, which provides a basis for understanding the evolution, genetics, and taxonomy of this important fungal group.

Analysis of synonymous codon usage patterns in mitochondrial genomes of nine Amanita species

“…Based on the RSCU values of the nine Amanita species, we used SPSS v19.0 software based on the hierarchical clustering method to draw the relationship tree between different species. We then used the combined mitochondrial gene datasets to construct phylogenetic trees of the 9 Amanita species according to the method described by our previous studies ( Li et al, 2022a , b ). Briefly, individual mitochondrial genes were first aligned using MAFFT v7.037( Katoh et al, 2019 ), and then the aligned mitochondrial sequences were concatenated into a combined mitochondrial gene set based on Sequence Matrix v1.7.8 ( Vaidya et al, 2011 ).…”

Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

“…Eukaryotes rely on the mitochondrial genome, which is often referred to as the ‘second genome’, for their growth, development, and ability to adjust to the environment ( Latorre-Pellicer et al, 2016 ). Fungi possess a set of 15 core protein-coding genes (PCGs), namely, atp6 , atp8 , atp9 , cob , cox1 , cox2 , cox3 , nad1 , nad2 , nad3 , nad4 , nad4 L, nad5 , nad6 , and rps3 ( Li et al, 2020a , 2022a , b ). Variations in the mitochondrial genome are essential for the stability, resilience, and adaptability of eukaryotic cells, in addition to their development ( Hayashi et al, 2016 ; Chen et al, 2020 ; Cai et al, 2021 ).…”

Comparative Mitogenomics Analysis Revealed Evolutionary Divergence among Neopestalotiopsis Species Complex (Fungi: Xylariales)

“…Mitogenome-related investigations across different species revealed a considerable diversity, allowing for a sturdy foundation for taxonomic clarity [ 3 ]. The high copy numbers and evolutionary rates of fungal mtDNFA make it an exceptional tool for evolutionary biology, taxonomy, and molecular phylogenetics [ 4 , 5 , 6 , 7 , 8 , 9 ]. Mitochondrial genomes possess distinct characteristics, such as a condensed size, constrained recombination rates, autonomous evolutionary path, and the abundance of analogous genes, which equip them with remarkable analytical capabilities when examining the subjects of population genetics and evolutionary biology [ 10 , 11 , 12 , 13 ].…”