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Comparative mitochondrial genomic analyses of three chemosynthetic vesicomyid clams from deep‐sea habitats

Vesicomyid clams of the subfamily Pliocardinae are among the dominant chemosymbiotic bivalves found in sulfide‐rich deep‐sea habitats. Plastic morphologies and present molecular data could not resolve taxonomic uncertainties. The complete mitochondrial (mt) genomes will provide more data for compara...

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Autores principales: Liu, Helu, Cai, Shanya, Liu, Jun, Zhang, Haibin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6106168/
https://www.ncbi.nlm.nih.gov/pubmed/30151147
http://dx.doi.org/10.1002/ece3.4153
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author Liu, Helu
Cai, Shanya
Liu, Jun
Zhang, Haibin
author_facet Liu, Helu
Cai, Shanya
Liu, Jun
Zhang, Haibin
author_sort Liu, Helu
collection PubMed
description Vesicomyid clams of the subfamily Pliocardinae are among the dominant chemosymbiotic bivalves found in sulfide‐rich deep‐sea habitats. Plastic morphologies and present molecular data could not resolve taxonomic uncertainties. The complete mitochondrial (mt) genomes will provide more data for comparative studies on molecular phylogeny and systematics of this taxonomically uncertain group, and help to clarify generic classifications. In this study, we analyze the features and evolutionary dynamics of mt genomes from three Archivesica species (Archivesica sp., Ar. gigas and Ar. pacifica) pertaining to subfamily Pliocardinae. Sequence coverage is nearly complete for the three newly sequenced mt genomes, with only the control region and some tRNA genes missing. Gene content, base composition, and codon usage are highly conserved in these pliocardiin species. Comparative analysis revealed the vesicomyid have a relatively lower ratio of Ka/Ks, and all 13 protein‐coding genes (PGCs) are under strong purifying selection with a ratio of Ka/Ks far lower than one. Minimal changes in gene arrangement among vesicomyid species are due to the translocation trnaG in Isorropodon fossajaponicum. Additional tRNA genes were detected between trnaG and nad2 in Abyssogena mariana (trnaL3), Ab. phaseoliformis (trnaS3), and Phreagena okutanii (trnaM2), and display high similarity to other pliocardiin sequences at the same location. Single base insertion in multiple sites of this location could result in new tRNA genes, suggesting a possible tRNA arising from nongeneic sequence. Phylogenetic analysis based on 12 PCGs (excluding atp8) supports the monophyly of Pliocardiinae. These nearly complete mitogenomes provide relevant data for further comparative studies on molecular phylogeny and systematics of this taxonomically uncertain group of chemosymbiotic bivalves.
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spelling pubmed-61061682018-08-27 Comparative mitochondrial genomic analyses of three chemosynthetic vesicomyid clams from deep‐sea habitats Liu, Helu Cai, Shanya Liu, Jun Zhang, Haibin Ecol Evol Original Research Vesicomyid clams of the subfamily Pliocardinae are among the dominant chemosymbiotic bivalves found in sulfide‐rich deep‐sea habitats. Plastic morphologies and present molecular data could not resolve taxonomic uncertainties. The complete mitochondrial (mt) genomes will provide more data for comparative studies on molecular phylogeny and systematics of this taxonomically uncertain group, and help to clarify generic classifications. In this study, we analyze the features and evolutionary dynamics of mt genomes from three Archivesica species (Archivesica sp., Ar. gigas and Ar. pacifica) pertaining to subfamily Pliocardinae. Sequence coverage is nearly complete for the three newly sequenced mt genomes, with only the control region and some tRNA genes missing. Gene content, base composition, and codon usage are highly conserved in these pliocardiin species. Comparative analysis revealed the vesicomyid have a relatively lower ratio of Ka/Ks, and all 13 protein‐coding genes (PGCs) are under strong purifying selection with a ratio of Ka/Ks far lower than one. Minimal changes in gene arrangement among vesicomyid species are due to the translocation trnaG in Isorropodon fossajaponicum. Additional tRNA genes were detected between trnaG and nad2 in Abyssogena mariana (trnaL3), Ab. phaseoliformis (trnaS3), and Phreagena okutanii (trnaM2), and display high similarity to other pliocardiin sequences at the same location. Single base insertion in multiple sites of this location could result in new tRNA genes, suggesting a possible tRNA arising from nongeneic sequence. Phylogenetic analysis based on 12 PCGs (excluding atp8) supports the monophyly of Pliocardiinae. These nearly complete mitogenomes provide relevant data for further comparative studies on molecular phylogeny and systematics of this taxonomically uncertain group of chemosymbiotic bivalves. John Wiley and Sons Inc. 2018-06-27 /pmc/articles/PMC6106168/ /pubmed/30151147 http://dx.doi.org/10.1002/ece3.4153 Text en © 2018 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Research
Liu, Helu
Cai, Shanya
Liu, Jun
Zhang, Haibin
Comparative mitochondrial genomic analyses of three chemosynthetic vesicomyid clams from deep‐sea habitats
title Comparative mitochondrial genomic analyses of three chemosynthetic vesicomyid clams from deep‐sea habitats
title_full Comparative mitochondrial genomic analyses of three chemosynthetic vesicomyid clams from deep‐sea habitats
title_fullStr Comparative mitochondrial genomic analyses of three chemosynthetic vesicomyid clams from deep‐sea habitats
title_full_unstemmed Comparative mitochondrial genomic analyses of three chemosynthetic vesicomyid clams from deep‐sea habitats
title_short Comparative mitochondrial genomic analyses of three chemosynthetic vesicomyid clams from deep‐sea habitats
title_sort comparative mitochondrial genomic analyses of three chemosynthetic vesicomyid clams from deep‐sea habitats
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6106168/
https://www.ncbi.nlm.nih.gov/pubmed/30151147
http://dx.doi.org/10.1002/ece3.4153
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