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Mitochondrial genome evolution in species belonging to the Phialocephala fortinii s.l. - Acephala applanata species complex
BACKGROUND: Mitochondrial (mt) markers are successfully applied in evolutionary biology and systematics because mt genomes often evolve faster than the nuclear genomes. In addition, they allow robust phylogenetic analysis based on conserved proteins of the oxidative phosphorylation system. In the pr...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3434094/ https://www.ncbi.nlm.nih.gov/pubmed/22559219 http://dx.doi.org/10.1186/1471-2164-13-166 |
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author | Duò, Angelo Bruggmann, Rémy Zoller, Stefan Bernt, Matthias Grünig, Christoph R |
author_facet | Duò, Angelo Bruggmann, Rémy Zoller, Stefan Bernt, Matthias Grünig, Christoph R |
author_sort | Duò, Angelo |
collection | PubMed |
description | BACKGROUND: Mitochondrial (mt) markers are successfully applied in evolutionary biology and systematics because mt genomes often evolve faster than the nuclear genomes. In addition, they allow robust phylogenetic analysis based on conserved proteins of the oxidative phosphorylation system. In the present study we sequenced and annotated the complete mt genome of P. subalpina, a member of the Phialocephala fortinii s.l. – Acephala applanata 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. RESULTS: The mt genome of P. subalpina is 43,742 bp long and codes for 14 mt genes associated with the oxidative phosphorylation. In addition, a GIY-YIG endonuclease, the ribosomal protein S3 (Rps3) 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 P. subalpina deviated from the gene order in Sclerotinia sclerotiorum, 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. CONCLUSIONS: The combination of non-interrupted ORFs and EST sequences resulted in a high quality annotation of the mt genome of P. subalpina, 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. |
format | Online Article Text |
id | pubmed-3434094 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-34340942012-09-06 Mitochondrial genome evolution in species belonging to the Phialocephala fortinii s.l. - Acephala applanata species complex Duò, Angelo Bruggmann, Rémy Zoller, Stefan Bernt, Matthias Grünig, Christoph R BMC Genomics Research Article BACKGROUND: Mitochondrial (mt) markers are successfully applied in evolutionary biology and systematics because mt genomes often evolve faster than the nuclear genomes. In addition, they allow robust phylogenetic analysis based on conserved proteins of the oxidative phosphorylation system. In the present study we sequenced and annotated the complete mt genome of P. subalpina, a member of the Phialocephala fortinii s.l. – Acephala applanata 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. RESULTS: The mt genome of P. subalpina is 43,742 bp long and codes for 14 mt genes associated with the oxidative phosphorylation. In addition, a GIY-YIG endonuclease, the ribosomal protein S3 (Rps3) 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 P. subalpina deviated from the gene order in Sclerotinia sclerotiorum, 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. CONCLUSIONS: The combination of non-interrupted ORFs and EST sequences resulted in a high quality annotation of the mt genome of P. subalpina, 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. BioMed Central 2012-05-04 /pmc/articles/PMC3434094/ /pubmed/22559219 http://dx.doi.org/10.1186/1471-2164-13-166 Text en Copyright ©2012 Duò et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Duò, Angelo Bruggmann, Rémy Zoller, Stefan Bernt, Matthias Grünig, Christoph R Mitochondrial genome evolution in species belonging to the Phialocephala fortinii s.l. - Acephala applanata species complex |
title | Mitochondrial genome evolution in species belonging to the Phialocephala fortinii s.l. - Acephala applanata species complex |
title_full | Mitochondrial genome evolution in species belonging to the Phialocephala fortinii s.l. - Acephala applanata species complex |
title_fullStr | Mitochondrial genome evolution in species belonging to the Phialocephala fortinii s.l. - Acephala applanata species complex |
title_full_unstemmed | Mitochondrial genome evolution in species belonging to the Phialocephala fortinii s.l. - Acephala applanata species complex |
title_short | Mitochondrial genome evolution in species belonging to the Phialocephala fortinii s.l. - Acephala applanata species complex |
title_sort | mitochondrial genome evolution in species belonging to the phialocephala fortinii s.l. - acephala applanata species complex |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3434094/ https://www.ncbi.nlm.nih.gov/pubmed/22559219 http://dx.doi.org/10.1186/1471-2164-13-166 |
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