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.
Highlights
The DNAse treatment of the whole mitochondrial pellets and the extraction of mtDNA were dependent on the instructions from the DNeasy Plant Mini Kit (Qiagen, Hilden, Germany) and Lang’s protocol [48]; nuclear DNA interference was assessed by polymerase chain reaction (PCR) for the target regions of ITS rDNA [49]
The mitochondrial genome of S. bambusicola was sequenced using Illumina Hiseq 2000, and eight scaffolds were assembled into a typical circular DNA molecule with a length of 39,030 bp using PCR amplification to successfully span all gaps
We found a number of repeats in the intergenic spacer (IGS) and coding sequence (CDS) regions of S. bambusicola, which were classified as 17 forward, 22 inverted, 6 reverse and 25 tandem repeats (S4 Table)
Summary
S. bambusicola is a highly specific pathogen, usually confining infection to Brachystachyum densiflorum and related species in China and Bambusa species in Japan [1,2]. The corresponding position of S. bambusicola has been reclassified several times over one hundred years of taxonomic research. Shiraia was anchored in the Hypocreaceae family based on the base of the larger fleshy stroma [14]. This viewpoint was popular for several decades, until the ascus was observed to not be unitunicate but was instead bitunicate, and Shiraia was transferred to the Loculoascomycetes class, the Pleosporales order, and the Pleosporaceae family [15]. It is noticeable that whether regarded as a genus or a family, there is only one representative species present in this group, and no distinct differences were found among fungal isolates from different bamboo hosts [17]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
