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.
Highlights
Clavaria fumosa, belonging to the family Clavariaceae and the order Agaricales, is a mushroom-forming fungus with dark basidiomata (Kautmanova et al 2012b)
A total of 121 Protein-coding gene (PCG) were detected in the C. fumosa mitogenome, including 46 non-intronic PCGs and 60 intronic ORFs
A total of 64 introns were detected in the C. fumosa mitogenome, 56 of which belonged to the group I, 2 belonged to the group II, with the remaining 6 introns containing unknown types
Summary
Clavaria fumosa, belonging to the family Clavariaceae and the order Agaricales, is a mushroom-forming fungus with dark basidiomata (Kautmanova et al 2012b). Species of the family Clavariaceae produce simple clubs, coralloid, lamellate-stipitate, hydnoid and resupinate sporocarps (Birkebak et al 2013). Morphological classification of Clavariaceae species was mostly based on spore characters and presence or absence of clamps (Kautmanova et al 2012a, b). The introduction of molecular markers, including LSU nrDNA, RNA polymerase II second largest subunit (rpb2), nuclear ribosomal 28S, and internal transcribed spacer region (ITS) has promoted the revision of taxonomic concept and phylogeny of Clavariaceae species (Birkebak et al 2016; Dentinger and McLaughlin 2006; Kautmanova et al 2012a; Olariaga et al 2015).
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