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Genetic diversity across the mitochondrial genome of eastern oysters (Crassostrea virginica) in the northern Gulf of Mexico
The eastern oyster, Crassostrea virginica, is divided into four populations along the western North Atlantic, however, the only published mitochondrial genome sequence was assembled using one individual in Delaware. This study aimed to (1) assemble C. virginica mitochondrial genomes from Texas with...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8485835/ https://www.ncbi.nlm.nih.gov/pubmed/34692250 http://dx.doi.org/10.7717/peerj.12205 |
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author | Rue, Chani R. Selwyn, Jason D. Cockett, Patricia M. Gillis, Bryan Gurski, Lauren Jose, Philip Kutil, Brandi L. Magnuson, Sharon F. Ángela López de Mesa, Luz Overath, R Deborah Smee, Delbert Lee Bird, Christopher E. |
author_facet | Rue, Chani R. Selwyn, Jason D. Cockett, Patricia M. Gillis, Bryan Gurski, Lauren Jose, Philip Kutil, Brandi L. Magnuson, Sharon F. Ángela López de Mesa, Luz Overath, R Deborah Smee, Delbert Lee Bird, Christopher E. |
author_sort | Rue, Chani R. |
collection | PubMed |
description | The eastern oyster, Crassostrea virginica, is divided into four populations along the western North Atlantic, however, the only published mitochondrial genome sequence was assembled using one individual in Delaware. This study aimed to (1) assemble C. virginica mitochondrial genomes from Texas with pooled restriction-site-associated DNA sequencing (ezRAD), (2) evaluate the validity of the mitochondrial genome assemblies including comparison with Sanger sequencing data, and (3) evaluate genetic differentiation both between the Delaware and Texas genomes, as well as among three bays in Texas. The pooled-genome-assembled-genomes (PAGs) from Texas exhibited several characteristics indicating that they were valid, including elevated nucleotide diversity in non-coding and the third position of codons, placement as the sister haplotype of the genome from Delaware in a phylogenetic reconstruction of Crassostrea mitochondrial genomes, and a lack of genetic structure in the ND4 gene among the three Texas bays as was found with Sanger amplicons in samples from the same bays several years prior. In the comparison between the Delaware and Texas genome, 27 of 38 coding regions exhibited variability between the two populations, which were differentiated by 273 mutations, versus 1–13 mutations among the Texas samples. Using the full PAGs, there was no additional evidence for population structure among the three Texas bays. While population genetics is rapidly moving towards larger high-density datasets, studies of mitochondrial DNA (and genomes) can be particularly useful for comparing historic data prior to the modern era of genomics. As such, being able to reliably compile mitochondrial genomes from genomic data can improve the ability to compare results across studies. |
format | Online Article Text |
id | pubmed-8485835 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-84858352021-10-22 Genetic diversity across the mitochondrial genome of eastern oysters (Crassostrea virginica) in the northern Gulf of Mexico Rue, Chani R. Selwyn, Jason D. Cockett, Patricia M. Gillis, Bryan Gurski, Lauren Jose, Philip Kutil, Brandi L. Magnuson, Sharon F. Ángela López de Mesa, Luz Overath, R Deborah Smee, Delbert Lee Bird, Christopher E. PeerJ Genetics The eastern oyster, Crassostrea virginica, is divided into four populations along the western North Atlantic, however, the only published mitochondrial genome sequence was assembled using one individual in Delaware. This study aimed to (1) assemble C. virginica mitochondrial genomes from Texas with pooled restriction-site-associated DNA sequencing (ezRAD), (2) evaluate the validity of the mitochondrial genome assemblies including comparison with Sanger sequencing data, and (3) evaluate genetic differentiation both between the Delaware and Texas genomes, as well as among three bays in Texas. The pooled-genome-assembled-genomes (PAGs) from Texas exhibited several characteristics indicating that they were valid, including elevated nucleotide diversity in non-coding and the third position of codons, placement as the sister haplotype of the genome from Delaware in a phylogenetic reconstruction of Crassostrea mitochondrial genomes, and a lack of genetic structure in the ND4 gene among the three Texas bays as was found with Sanger amplicons in samples from the same bays several years prior. In the comparison between the Delaware and Texas genome, 27 of 38 coding regions exhibited variability between the two populations, which were differentiated by 273 mutations, versus 1–13 mutations among the Texas samples. Using the full PAGs, there was no additional evidence for population structure among the three Texas bays. While population genetics is rapidly moving towards larger high-density datasets, studies of mitochondrial DNA (and genomes) can be particularly useful for comparing historic data prior to the modern era of genomics. As such, being able to reliably compile mitochondrial genomes from genomic data can improve the ability to compare results across studies. PeerJ Inc. 2021-09-28 /pmc/articles/PMC8485835/ /pubmed/34692250 http://dx.doi.org/10.7717/peerj.12205 Text en ©2021 Rue 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 | Genetics Rue, Chani R. Selwyn, Jason D. Cockett, Patricia M. Gillis, Bryan Gurski, Lauren Jose, Philip Kutil, Brandi L. Magnuson, Sharon F. Ángela López de Mesa, Luz Overath, R Deborah Smee, Delbert Lee Bird, Christopher E. Genetic diversity across the mitochondrial genome of eastern oysters (Crassostrea virginica) in the northern Gulf of Mexico |
title | Genetic diversity across the mitochondrial genome of eastern oysters (Crassostrea virginica) in the northern Gulf of Mexico |
title_full | Genetic diversity across the mitochondrial genome of eastern oysters (Crassostrea virginica) in the northern Gulf of Mexico |
title_fullStr | Genetic diversity across the mitochondrial genome of eastern oysters (Crassostrea virginica) in the northern Gulf of Mexico |
title_full_unstemmed | Genetic diversity across the mitochondrial genome of eastern oysters (Crassostrea virginica) in the northern Gulf of Mexico |
title_short | Genetic diversity across the mitochondrial genome of eastern oysters (Crassostrea virginica) in the northern Gulf of Mexico |
title_sort | genetic diversity across the mitochondrial genome of eastern oysters (crassostrea virginica) in the northern gulf of mexico |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8485835/ https://www.ncbi.nlm.nih.gov/pubmed/34692250 http://dx.doi.org/10.7717/peerj.12205 |
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