The 256 kb mitochondrial genome of Clavaria fumosa is the largest among phylum Basidiomycota and is rich in introns and intronic ORFs

Abstract

In the present study, the complete mitogenome of Clavaria fumosa, was sequenced, assembled, and compared. The complete mitogenome of C. fumosa is 256,807 bp in length and is the largest mitogenomes among all Basidiomycota mitogenomes reported. Comparative mitogenomic analysis indicated that the C. fumosa mitogenome contained the most introns and intronic ORFs among all fungal mitogenomes. Large intergenic regions, intronic regions, accumulation of repeat sequences and plasmid-derived genes together promoted the size expansion of the C. fumosa mitogenome. In addition, the rps3 gene was found subjected to positive selection between some Agaricales species. We found frequent intron gain/loss events in Agaricales mitogenomes, and four novel intron classes were detected in the C. fumosa mitogenome. Large-scale gene rearrangements were found occurred in Agaricales species and the C. fumosa mitogenome had a unique gene arrangement which differed from other Agaricales species. Phylogenetic analysis for 76 Basidiomycetes based on combined mitochondrial gene sets indicated that mitochondrial genes could be used as effective molecular markers for reconstructing evolution of Basidiomycota. The study served as the first report on the mitogenomes of the family Clavariaceae, which will promote the understanding of the genetics, evolution and taxonomy of C. fumosa and related 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 ).…”

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

“…The information inferred from mitogenome analyses promoted better understanding of the origin and population genetics of Basidiomycota [18] , [19] . It has been reported that the mitogenomes of Basidiomycota vary greatly in size, genome structure, gene content, gene arrangement, repeat sequence content and intron type [20] , [21] , [22] , [23] . So far, there are less than 120 complete mitogenomes available in public database ( https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/ ), far less than the number of Basidiomycete nuclear genomes available.…”

Characterization of the Complete Mitochondrial Genome of Basidiomycete Yeast Hannaella oryzae: Intron Evolution, Gene Rearrangement, and Its Phylogeny

“…Besides, the arrangement of mitochondrial genes, their transfer RNA (tRNA) structure, their codon usage, and the dynamic changes of introns can also be used to infer the evolutionary status of eukaryotes (Li et al, 2018a;Wang et al, 2018Wang et al, , 2020bWu et al, 2021). With the rapid development of next-generation sequencing technologies in recent years, more and more mitochondrial genomes have been obtained (du Toit et al, 2017;Yang et al, 2018;Zhang et al, 2018;Wang et al, 2020c). However, the mitochondrial genomes of fungi are less studied than those of animals.…”