Characterization and Phylogenetic Analysis of the Mitochondrial Genome of Shiraia bambusicola Reveals Special Features in the Order of Pleosporales

Abstract

Shiraia bambusicola P. Henn. is a pathogenic fungus of bamboo, and its fruiting bodies are regarded as folk medicine. We determined and analyzed its complete mitochondrial DNA sequence (circular DNA molecule of 39,030 bp, G + C content of 25.19%). It contains the typical genes encoding proteins involved in electron transport and coupled oxidative phosphorylation (nad1-6 and nad4L, cob and cox1-3), one ATP synthase subunit (atp6), 4 hypothetical proteins, and two genes for large and small rRNAs (rnl and rns). There is a set of 32 tRNA genes comprising all 20 amino acids, and these genes are evenly distributed on the two strands. Phylogenetic analyses based on concatenated mitochondrial proteins indicated that S. bambusicola clustered with members of the order Pleosporales, which is in agreement with previous results. The gene arrangements of Dothideomycetes species contained three regions of gene orders partitioned in their mitochondrial genomes, including block 1 (nad6-atp6), block 2 (nad1-cox3) and block 3 (genes around rns). S. bambusicola displayed unique special features that differed from the other Pleosporales species, especially in the coding regions around rns (trnR-trnY). Moreover, a comparison of gene orders in mitochondrial genomes from Pezizomycotina revealed that although all encoded regions are located on the same strand in most Pezizomycotina mtDNAs, genes from Dothideomycetes species had different orientations, as well as diverse positions and colocalization of genes (such as cox3, cox1-cox2 and nad2–nad3); these distinctions were regarded as class-specific features. Interestingly, two incomplete copies of the atp6 gene were found on different strands of the mitogenomic DNA, a finding that has not been observed in the other analyzed fungal species. In our study, mitochondrial genomes from Dothideomycetes species were comprehensively analyzed for the first time, including many species that have not appeared in previous reports.

Genome Sequencing and Analysis of the Hypocrellin-Producing Fungus Shiraia bambusicola S4201

“…In order to determine the classification of S. bambusicola, nine fungal species were used for phylogenetic construction using the complete genome sequencing data downloaded from the NCBI database. The results from the phylogenetic analysis were basically consistent with previous studies (Liu et al, 2013;Shen et al, 2015), which showed that S. bambusicola is located in the order Pleosporales. The inferred phylogeny indicated that Stagonospora sp.…”

The complete mitochondrial genome of the conifer needle endophyte, Phialocephala scopiformis DAOMC 229536 confirms evolutionary division within the fungal Phialocephala fortinii s.l. – Acephala appalanata species complex

“…Given that the mitochondrial (mt) genome evolves more rapidly than the nuclear genome and has been shown to produce reliable phylogenetic trees, it has been established as an effective evolutionary marker in fungi (Wu et al 2009, Duò et al 2012, Youssar et al 2013, Shen et al 2015. Fungal mt genomes are frequently circular molecules consisting of 14 highly conserved protein coding genes related to oxidative phosphorylation (OXPHOS), one large (rrnL) and one small (rrnS) ribosomal RNA (rRNA) gene, and a set of transfer RNA (tRNA or trn) genes which can vary between species (Gray et al 1999, Lavín et al 2008.…”

Comparative genomics in plant fungal pathogens (Mycosphaerellaceae): variation in mitochondrial composition due to at least five independent intron invasions

“…Two incomplete copies of atp6 were found on different strands of the mitogenomic DNA of Shiraia bambusicola, a Pleosporales member used as outgroup in this study (Shen et al, 2015). Three hypotheses can be drawn regarding mitochondrial gene duplications: First, copies could be undergoing subfunctionalization (Conant and Wolfe, 2008) where recombination events of fission and fusion are the drivers of such a process (Burger, Gray and Lang, 2003), however we did not see two functional copies of any ETC genes in any genome.…”

“…One hundred bootstrapped trees were generated and used to assign bootstrap support values to the consensus trees. The species Didymella pinodes (Okorski et al, 2016), Pseudovirgaria hyperparasítica (Braun et al, 2011), Phaeosphaeria nodorum (Hane et al, 2007) and Shiraia bambusicola (Shen et al, 2015) were used as outgroup.…”