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Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus

BACKGROUND: The order and orientation of genes encoded by animal mitogenomes are typically conserved, although there is increasing evidence of multiple rearrangements among mollusks. The mitogenome from a Brazilian brown mussel (hereafter named B1) classified as Perna perna Linnaeus, 1758 and assemb...

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Autores principales: Cunha, Regina L., Nicastro, Katy R., Zardi, Gerardo I., Madeira, Celine, McQuaid, Christopher D., Cox, Cymon J., Castilho, Rita
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9521344/
https://www.ncbi.nlm.nih.gov/pubmed/36187748
http://dx.doi.org/10.7717/peerj.13953
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author Cunha, Regina L.
Nicastro, Katy R.
Zardi, Gerardo I.
Madeira, Celine
McQuaid, Christopher D.
Cox, Cymon J.
Castilho, Rita
author_facet Cunha, Regina L.
Nicastro, Katy R.
Zardi, Gerardo I.
Madeira, Celine
McQuaid, Christopher D.
Cox, Cymon J.
Castilho, Rita
author_sort Cunha, Regina L.
collection PubMed
description BACKGROUND: The order and orientation of genes encoded by animal mitogenomes are typically conserved, although there is increasing evidence of multiple rearrangements among mollusks. The mitogenome from a Brazilian brown mussel (hereafter named B1) classified as Perna perna Linnaeus, 1758 and assembled from Illumina short-length reads revealed an unusual gene order very different from other congeneric species. Previous mitogenomic analyses based on the Brazilian specimen and other Mytilidae suggested the polyphyly of the genus Perna. METHODS: To confirm the proposed gene rearrangements, we sequenced a second Brazilian P. perna specimen using the “primer-walking” method and performed the assembly using as reference Perna canaliculus. This time-consuming sequencing method is highly effective when assessing gene order because it relies on sequentially-determined, overlapping fragments. We also sequenced the mitogenomes of eastern and southwestern South African P. perna lineages to analyze the existence of putative intraspecific gene order changes as the two lineages show overlapping distributions but do not exhibit a sister relationship. RESULTS: The three P. perna mitogenomes sequenced in this study exhibit the same gene order as the reference. CREx, a software that heuristically determines rearrangement scenarios, identified numerous gene order changes between B1 and our P. perna mitogenomes, rejecting the previously proposed gene order for the species. Our results validate the monophyly of the genus Perna and indicate a misidentification of B1.
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spelling pubmed-95213442022-09-30 Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus Cunha, Regina L. Nicastro, Katy R. Zardi, Gerardo I. Madeira, Celine McQuaid, Christopher D. Cox, Cymon J. Castilho, Rita PeerJ Evolutionary Studies BACKGROUND: The order and orientation of genes encoded by animal mitogenomes are typically conserved, although there is increasing evidence of multiple rearrangements among mollusks. The mitogenome from a Brazilian brown mussel (hereafter named B1) classified as Perna perna Linnaeus, 1758 and assembled from Illumina short-length reads revealed an unusual gene order very different from other congeneric species. Previous mitogenomic analyses based on the Brazilian specimen and other Mytilidae suggested the polyphyly of the genus Perna. METHODS: To confirm the proposed gene rearrangements, we sequenced a second Brazilian P. perna specimen using the “primer-walking” method and performed the assembly using as reference Perna canaliculus. This time-consuming sequencing method is highly effective when assessing gene order because it relies on sequentially-determined, overlapping fragments. We also sequenced the mitogenomes of eastern and southwestern South African P. perna lineages to analyze the existence of putative intraspecific gene order changes as the two lineages show overlapping distributions but do not exhibit a sister relationship. RESULTS: The three P. perna mitogenomes sequenced in this study exhibit the same gene order as the reference. CREx, a software that heuristically determines rearrangement scenarios, identified numerous gene order changes between B1 and our P. perna mitogenomes, rejecting the previously proposed gene order for the species. Our results validate the monophyly of the genus Perna and indicate a misidentification of B1. PeerJ Inc. 2022-09-26 /pmc/articles/PMC9521344/ /pubmed/36187748 http://dx.doi.org/10.7717/peerj.13953 Text en © 2022 Cunha et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Evolutionary Studies
Cunha, Regina L.
Nicastro, Katy R.
Zardi, Gerardo I.
Madeira, Celine
McQuaid, Christopher D.
Cox, Cymon J.
Castilho, Rita
Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus
title Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus
title_full Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus
title_fullStr Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus
title_full_unstemmed Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus
title_short Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus
title_sort comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus
topic Evolutionary Studies
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9521344/
https://www.ncbi.nlm.nih.gov/pubmed/36187748
http://dx.doi.org/10.7717/peerj.13953
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