Genetic diversity across the mitochondrial genome of eastern oysters (Crassostrea virginica) in the northern Gulf of Mexico

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dc.contributor.authorBird, Christopher E.
dc.contributor.authorRue, Chani R.
dc.contributor.authorSelwyn, Jason D.
dc.contributor.authorCockett, Patricia M.
dc.contributor.authorGillis, Bryan S.
dc.contributor.authorGurski, Lauren M.
dc.contributor.authorJose, Philip D.
dc.contributor.authorKutil, Brandi L.
dc.contributor.authorMagnuson, Sharon F.
dc.contributor.authorLopez de Mesa, Luz Angela
dc.contributor.authorOverath, R. Deborah
dc.contributor.authorSmee, Delbert L.
dc.creator.orcidhttps://orcid.org/0000-0003-0228-3318en_US
dc.creator.orcidhttps://orcid.org/0000-0002-9100-217Xen_US
dc.creator.orcidhttps://orcid.org/0000-0003-0228-3318
dc.creator.orcidhttps://orcid.org/0000-0002-9100-217X
dc.creator.orcidhttps://orcid.org/0000-0003-0228-3318
dc.creator.orcidhttps://orcid.org/0000-0002-9100-217Xhttps://orcid.org/0000-0003-0228-3318
dc.creator.orcidhttps://orcid.org/0000-0002-9100-217X
dc.date.accessioned2021-10-13T16:57:26Z
dc.date.available2021-10-13T16:57:26Z
dc.date.issued2021-09-28
dc.description.abstractThe 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 sequence (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.en_US
dc.identifier.citatione Rue CR, Selwyn JD, Cockett PM, Gillis B, Gurski L, Jose P, Kutil BL, Magnuson SF, Ángela López de Mesa L, Overath RD, Smee DL, Bird CE. 2021. Genetic diversity across the mitochondrial genome of eastern oysters (Crassostrea virginica) in the northern Gulf of Mexico. PeerJ 9:e12205 http://doi.org/10.7717/peerj.12205en_US
dc.identifier.doihttp://doi.org/10.7717/peerj.12205
dc.identifier.urihttps://hdl.handle.net/1969.6/89826
dc.language.isoen_USen_US
dc.publisherPeerJen_US
dc.rightsAttribution 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.subjectezraden_US
dc.subjectmitochondrial genomeen_US
dc.subjectcrassostrea virginicaen_US
dc.subjectsanger sequencingen_US
dc.titleGenetic diversity across the mitochondrial genome of eastern oysters (Crassostrea virginica) in the northern Gulf of Mexicoen_US
dc.typeArticleen_US

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