Mitogenomes of Two Phallus Mushroom Species Reveal Gene Rearrangement, Intron Dynamics, and Basidiomycete Phylogeny

Abstract

Phallus indusiatus and Phallus echinovolvatus are edible bamboo mushrooms with pharmacological properties. We sequenced, assembled, annotated, and compared the mitogenomes of these species. Both mitogenomes were composed of circular DNA molecules, with sizes of 89,139 and 50,098 bp, respectively. Introns were the most important factor in mitogenome size variation within the genus Phallus. Phallus indusiatus, P. echinovolvatus, and Turbinellus floccosus in the subclass Phallomycetidae have conservative gene arrangements. Large-scale gene rearrangements were observed in species representing 42 different genera of Basidiomycetes. A variety of intron position classes were found in the 44 Basidiomycete species analyzed. A novel group II intron from the P. indusiatus mitogenome was compared with other fungus species containing the same intron, and we demonstrated that the insertion sites of the intron had a base preference. Phylogenetic analyses based on combined gene datasets yielded well-supported Bayesian posterior probability (BPP = 1) topologies. This indicated that mitochondrial genes are reliable molecular markers for analyzing the phylogenetic relationships of the Basidiomycetes. This is the first study of the mitogenome of the genus Phallus, and it increases our understanding of the population genetics and evolution of bamboo mushrooms and related species.

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

“…It is reported that the mitogenome of basidiomycetes varies greatly in gene content, repeat sequence, genome structure and genome size, which makes it difficult to obtain the complete mitogenome of fungi (Basse 2010 ; Fonseca et al 2021 ; Mendoza et al 2020 ). In the family Phallomycetidae , the largest mitogenome (152,722 bp) (Ye et al 2020 ) is three times larger than the smallest one (50,098 bp) (Chen et al 2020a ). Great genome size variation has also occurred in Ramaria species.…”

“…Mitochondrial genomes (mitogenomes) have been reported to be an effective tool for analyzing the phylogeny of basidiomycetes. Up to now, we have reported four complete mitogenomes from Phallomycetidae , including Turbinellus floccosus (Cheng et al 2021 ), Sphaerobolus stellatus (Ye et al 2020 ), Dictyophora indusiate , and Phallus echinovolvatus (Chen et al 2020a ). However, the characteristics of mitogenomes from the genus Ramaria are still unknown, which limits our comprehensive understanding of mitochondrial evolutionary pattern and genetics of Ramaria species.…”

A Distinct Tobamovirus Associated With Trichosanthes kirilowii Mottle Mosaic Disease

“…Phylogenetic analyses based on amino acid sequences were performed by the neighbor-joining method using MEGA X software ( Kumar et al, 2018 ). Phylogenetic trees of the complete genome sequences of viruses were constructed as described ( Chen et al, 2020 ). Briefly, MAFFT v7.037 software ( Katoh and Standley, 2013 ) was used to align the gene sequence, and then SequenceMatrix v1.7.8 software ( Lanfear et al, 2017 ) was used to convert the aligned sequences into NEXUS (non-interleaved) format file.…”