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Comparative Large-Scale Mitogenomics Evidences Clade-Specific Evolutionary Trends in Mitochondrial DNAs of Bivalvia
Despite the figure of complete bivalve mitochondrial genomes keeps growing, an assessment of the general features of these genomes in a phylogenetic framework is still lacking, despite the fact that bivalve mitochondrial genomes are unusual under different aspects. In this work, we constructed a dat...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5010914/ https://www.ncbi.nlm.nih.gov/pubmed/27503296 http://dx.doi.org/10.1093/gbe/evw187 |
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author | Plazzi, Federico Puccio, Guglielmo Passamonti, Marco |
author_facet | Plazzi, Federico Puccio, Guglielmo Passamonti, Marco |
author_sort | Plazzi, Federico |
collection | PubMed |
description | Despite the figure of complete bivalve mitochondrial genomes keeps growing, an assessment of the general features of these genomes in a phylogenetic framework is still lacking, despite the fact that bivalve mitochondrial genomes are unusual under different aspects. In this work, we constructed a dataset of one hundred mitochondrial genomes of bivalves to perform the first systematic comparative mitogenomic analysis, developing a phylogenetic background to scaffold the evolutionary history of the class' mitochondrial genomes. Highly conserved domains were identified in all protein coding genes; however, four genes (namely, atp6, nad2, nad4L, and nad6) were found to be very divergent for many respects, notwithstanding the overall purifying selection working on those genomes. Moreover, the atp8 gene was newly annotated in 20 mitochondrial genomes, where it was previously declared as lacking or only signaled. Supernumerary mitochondrial proteins were compared, but it was possible to find homologies only among strictly related species. The rearrangement rate on the molecule is too high to be used as a phylogenetic marker, but here we demonstrate for the first time in mollusks that there is correlation between rearrangement rates and evolutionary rates. We also developed a new index (HERMES) to estimate the amount of mitochondrial evolution. Many genomic features are phylogenetically congruent and this allowed us to highlight three main phases in bivalve history: the origin, the branching of palaeoheterodonts, and the second radiation leading to the present-day biodiversity. |
format | Online Article Text |
id | pubmed-5010914 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-50109142016-09-06 Comparative Large-Scale Mitogenomics Evidences Clade-Specific Evolutionary Trends in Mitochondrial DNAs of Bivalvia Plazzi, Federico Puccio, Guglielmo Passamonti, Marco Genome Biol Evol Research Article Despite the figure of complete bivalve mitochondrial genomes keeps growing, an assessment of the general features of these genomes in a phylogenetic framework is still lacking, despite the fact that bivalve mitochondrial genomes are unusual under different aspects. In this work, we constructed a dataset of one hundred mitochondrial genomes of bivalves to perform the first systematic comparative mitogenomic analysis, developing a phylogenetic background to scaffold the evolutionary history of the class' mitochondrial genomes. Highly conserved domains were identified in all protein coding genes; however, four genes (namely, atp6, nad2, nad4L, and nad6) were found to be very divergent for many respects, notwithstanding the overall purifying selection working on those genomes. Moreover, the atp8 gene was newly annotated in 20 mitochondrial genomes, where it was previously declared as lacking or only signaled. Supernumerary mitochondrial proteins were compared, but it was possible to find homologies only among strictly related species. The rearrangement rate on the molecule is too high to be used as a phylogenetic marker, but here we demonstrate for the first time in mollusks that there is correlation between rearrangement rates and evolutionary rates. We also developed a new index (HERMES) to estimate the amount of mitochondrial evolution. Many genomic features are phylogenetically congruent and this allowed us to highlight three main phases in bivalve history: the origin, the branching of palaeoheterodonts, and the second radiation leading to the present-day biodiversity. Oxford University Press 2016-08-08 /pmc/articles/PMC5010914/ /pubmed/27503296 http://dx.doi.org/10.1093/gbe/evw187 Text en © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Research Article Plazzi, Federico Puccio, Guglielmo Passamonti, Marco Comparative Large-Scale Mitogenomics Evidences Clade-Specific Evolutionary Trends in Mitochondrial DNAs of Bivalvia |
title | Comparative Large-Scale Mitogenomics Evidences Clade-Specific Evolutionary Trends in Mitochondrial DNAs of Bivalvia |
title_full | Comparative Large-Scale Mitogenomics Evidences Clade-Specific Evolutionary Trends in Mitochondrial DNAs of Bivalvia |
title_fullStr | Comparative Large-Scale Mitogenomics Evidences Clade-Specific Evolutionary Trends in Mitochondrial DNAs of Bivalvia |
title_full_unstemmed | Comparative Large-Scale Mitogenomics Evidences Clade-Specific Evolutionary Trends in Mitochondrial DNAs of Bivalvia |
title_short | Comparative Large-Scale Mitogenomics Evidences Clade-Specific Evolutionary Trends in Mitochondrial DNAs of Bivalvia |
title_sort | comparative large-scale mitogenomics evidences clade-specific evolutionary trends in mitochondrial dnas of bivalvia |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5010914/ https://www.ncbi.nlm.nih.gov/pubmed/27503296 http://dx.doi.org/10.1093/gbe/evw187 |
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