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In the present study we sequenced and annotated the complete mt genome of <jats:italic>P. subalpina<\/jats:italic>, a member of the <jats:italic>Phialocephala fortinii<\/jats:italic> s.l. <jats:italic>\u2013 Acephala applanata<\/jats:italic> species complex (PAC). PAC belongs to the Helotiales, which is one of the most diverse groups of ascomycetes including more than 2,000 species. The gene order was compared to deduce the mt genome evolution in the Pezizomycotina. Genetic variation in coding and intergenic regions of the mtDNA was studied for PAC to assess the usefulness of mt DNA for species diagnosis.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>The mt genome of <jats:italic>P. subalpina<\/jats:italic> is 43,742\u2009bp long and codes for 14 mt genes associated with the oxidative phosphorylation. In addition, a GIY-YIG endonuclease, the ribosomal protein S3 (<jats:italic>Rps3<\/jats:italic>) and a putative N-acetyl-transferase were recognized. A complete set of tRNA genes as well as the large and small rRNA genes but no introns were found. All protein-coding genes were confirmed by EST sequences. The gene order in <jats:italic>P. subalpina<\/jats:italic> deviated from the gene order in <jats:italic>Sclerotinia sclerotiorum<\/jats:italic>, the only other helotialean species with a fully sequenced and annotated mt genome. Gene order analysis within Pezizomycotina suggests that the evolution of gene orders is mostly driven by transpositions. Furthermore, sequence diversity in coding and non-coding mtDNA regions in seven additional PAC species was pronounced and allowed for unequivocal species diagnosis in PAC.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>The combination of non-interrupted ORFs and EST sequences resulted in a high quality annotation of the mt genome of <jats:italic>P. subalpina,<\/jats:italic> which can be used as a reference for the annotation of other mt genomes in the Helotiales. In addition, our analyses show that mtDNA loci will be the marker of choice for future analysis of PAC communities.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2164-13-166","type":"journal-article","created":{"date-parts":[[2012,9,5]],"date-time":"2012-09-05T12:14:58Z","timestamp":1346847298000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":36,"title":["Mitochondrial genome evolution in species belonging to the Phialocephala fortinii s.l. - Acephala applanata species complex"],"prefix":"10.1186","volume":"13","author":[{"given":"Angelo","family":"Du\u00f2","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"R\u00e9my","family":"Bruggmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Zoller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthias","family":"Bernt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christoph R","family":"Gr\u00fcnig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2012,5,4]]},"reference":[{"issue":"12","key":"4129_CR1","doi-asserted-by":"publisher","first-page":"1239","DOI":"10.1139\/b02-115","volume":"80","author":"CR Gr\u00fcnig","year":"2002","unstructured":"Gr\u00fcnig CR, Sieber TN, Rogers SO, Holdenrieder O: Genetic variability among strains of Phialocephala fortinii and phylogenetic analysis of the genus Phialocephala based on rDNA ITS sequence comparisons. 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