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Linkage Mapping and Comparative Genomics of Red Drum (Sciaenops ocellatus) Using Next-Generation Sequencing

Developments in next-generation sequencing allow genotyping of thousands of genetic markers across hundreds of individuals in a cost-effective manner. Because of this, it is now possible to rapidly produce dense genetic linkage maps for nonmodel species. Here, we report a dense genetic linkage map f...

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Autores principales: Hollenbeck, Christopher M., Portnoy, David S., Wetzel, Dana, Sherwood, Tracy A., Samollow, Paul B., Gold, John R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Genetics Society of America 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5345714/
https://www.ncbi.nlm.nih.gov/pubmed/28122951
http://dx.doi.org/10.1534/g3.116.036350
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author Hollenbeck, Christopher M.
Portnoy, David S.
Wetzel, Dana
Sherwood, Tracy A.
Samollow, Paul B.
Gold, John R.
author_facet Hollenbeck, Christopher M.
Portnoy, David S.
Wetzel, Dana
Sherwood, Tracy A.
Samollow, Paul B.
Gold, John R.
author_sort Hollenbeck, Christopher M.
collection PubMed
description Developments in next-generation sequencing allow genotyping of thousands of genetic markers across hundreds of individuals in a cost-effective manner. Because of this, it is now possible to rapidly produce dense genetic linkage maps for nonmodel species. Here, we report a dense genetic linkage map for red drum, a marine fish species of considerable economic importance in the southeastern United States and elsewhere. We used a prior microsatellite-based linkage map as a framework and incorporated 1794 haplotyped contigs derived from high-throughput, reduced representation DNA sequencing to produce a linkage map containing 1794 haplotyped restriction-site associated DNA (RAD) contigs, 437 anonymous microsatellites, and 44 expressed sequence-tag-linked microsatellites (EST-SSRs). A total of 274 candidate genes, identified from transcripts from a preliminary hydrocarbon exposure study, were localized to specific chromosomes, using a shared synteny approach. The linkage map will be a useful resource for red drum commercial and restoration aquaculture, and for better understanding and managing populations of red drum in the wild.
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spelling pubmed-53457142017-03-21 Linkage Mapping and Comparative Genomics of Red Drum (Sciaenops ocellatus) Using Next-Generation Sequencing Hollenbeck, Christopher M. Portnoy, David S. Wetzel, Dana Sherwood, Tracy A. Samollow, Paul B. Gold, John R. G3 (Bethesda) Investigations Developments in next-generation sequencing allow genotyping of thousands of genetic markers across hundreds of individuals in a cost-effective manner. Because of this, it is now possible to rapidly produce dense genetic linkage maps for nonmodel species. Here, we report a dense genetic linkage map for red drum, a marine fish species of considerable economic importance in the southeastern United States and elsewhere. We used a prior microsatellite-based linkage map as a framework and incorporated 1794 haplotyped contigs derived from high-throughput, reduced representation DNA sequencing to produce a linkage map containing 1794 haplotyped restriction-site associated DNA (RAD) contigs, 437 anonymous microsatellites, and 44 expressed sequence-tag-linked microsatellites (EST-SSRs). A total of 274 candidate genes, identified from transcripts from a preliminary hydrocarbon exposure study, were localized to specific chromosomes, using a shared synteny approach. The linkage map will be a useful resource for red drum commercial and restoration aquaculture, and for better understanding and managing populations of red drum in the wild. Genetics Society of America 2017-01-24 /pmc/articles/PMC5345714/ /pubmed/28122951 http://dx.doi.org/10.1534/g3.116.036350 Text en Copyright © 2017 Hollenbeck et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Investigations
Hollenbeck, Christopher M.
Portnoy, David S.
Wetzel, Dana
Sherwood, Tracy A.
Samollow, Paul B.
Gold, John R.
Linkage Mapping and Comparative Genomics of Red Drum (Sciaenops ocellatus) Using Next-Generation Sequencing
title Linkage Mapping and Comparative Genomics of Red Drum (Sciaenops ocellatus) Using Next-Generation Sequencing
title_full Linkage Mapping and Comparative Genomics of Red Drum (Sciaenops ocellatus) Using Next-Generation Sequencing
title_fullStr Linkage Mapping and Comparative Genomics of Red Drum (Sciaenops ocellatus) Using Next-Generation Sequencing
title_full_unstemmed Linkage Mapping and Comparative Genomics of Red Drum (Sciaenops ocellatus) Using Next-Generation Sequencing
title_short Linkage Mapping and Comparative Genomics of Red Drum (Sciaenops ocellatus) Using Next-Generation Sequencing
title_sort linkage mapping and comparative genomics of red drum (sciaenops ocellatus) using next-generation sequencing
topic Investigations
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5345714/
https://www.ncbi.nlm.nih.gov/pubmed/28122951
http://dx.doi.org/10.1534/g3.116.036350
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