Development of Genomic Resources for Pacific Herring through Targeted Transcriptome Pyrosequencing
Pacific herring (Clupea pallasii) support commercially and culturally important fisheries but have experienced significant additional pressure from a variety of anthropogenic and environmental sources. In order to provide genomic resources to facilitate organismal and population level research, high...
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ftpubmed:oai:pubmedcentral.nih.gov:3288011 2023-05-15T15:43:45+02:00 Development of Genomic Resources for Pacific Herring through Targeted Transcriptome Pyrosequencing Roberts, Steven B. Hauser, Lorenz Seeb, Lisa W. Seeb, James E. 2012-02-27 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3288011 http://www.ncbi.nlm.nih.gov/pubmed/22383979 https://doi.org/10.1371/journal.pone.0030908 en eng Public Library of Science http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3288011 http://www.ncbi.nlm.nih.gov/pubmed/22383979 http://dx.doi.org/10.1371/journal.pone.0030908 Roberts et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. CC-BY Research Article Text 2012 ftpubmed https://doi.org/10.1371/journal.pone.0030908 2013-09-04T03:09:16Z Pacific herring (Clupea pallasii) support commercially and culturally important fisheries but have experienced significant additional pressure from a variety of anthropogenic and environmental sources. In order to provide genomic resources to facilitate organismal and population level research, high-throughput pyrosequencing (Roche 454) was carried out on transcriptome libraries from liver and testes samples taken in Prince William Sound, the Bering Sea, and the Gulf of Alaska. Over 40,000 contigs were identified with an average length of 728 bp. We describe an annotated transcriptome as well as a workflow for single nucleotide polymorphism (SNP) discovery and validation. A subset of 96 candidate SNPs chosen from 10,933 potential SNPs, were tested using a combination of Sanger sequencing and high-resolution melt-curve analysis. Five SNPs supported between-ocean-basin differentiation, while one SNP associated with immune function provided high differentiation between Prince William Sound and Kodiak Island within the Gulf of Alaska. These genomic resources provide a basis for environmental physiology studies and opportunities for marker development and subsequent population structure analysis. Text Bering Sea Kodiak Alaska PubMed Central (PMC) Bering Sea Gulf of Alaska Pacific PLoS ONE 7 2 e30908 |
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Research Article |
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Research Article Roberts, Steven B. Hauser, Lorenz Seeb, Lisa W. Seeb, James E. Development of Genomic Resources for Pacific Herring through Targeted Transcriptome Pyrosequencing |
topic_facet |
Research Article |
description |
Pacific herring (Clupea pallasii) support commercially and culturally important fisheries but have experienced significant additional pressure from a variety of anthropogenic and environmental sources. In order to provide genomic resources to facilitate organismal and population level research, high-throughput pyrosequencing (Roche 454) was carried out on transcriptome libraries from liver and testes samples taken in Prince William Sound, the Bering Sea, and the Gulf of Alaska. Over 40,000 contigs were identified with an average length of 728 bp. We describe an annotated transcriptome as well as a workflow for single nucleotide polymorphism (SNP) discovery and validation. A subset of 96 candidate SNPs chosen from 10,933 potential SNPs, were tested using a combination of Sanger sequencing and high-resolution melt-curve analysis. Five SNPs supported between-ocean-basin differentiation, while one SNP associated with immune function provided high differentiation between Prince William Sound and Kodiak Island within the Gulf of Alaska. These genomic resources provide a basis for environmental physiology studies and opportunities for marker development and subsequent population structure analysis. |
format |
Text |
author |
Roberts, Steven B. Hauser, Lorenz Seeb, Lisa W. Seeb, James E. |
author_facet |
Roberts, Steven B. Hauser, Lorenz Seeb, Lisa W. Seeb, James E. |
author_sort |
Roberts, Steven B. |
title |
Development of Genomic Resources for Pacific Herring through Targeted Transcriptome Pyrosequencing |
title_short |
Development of Genomic Resources for Pacific Herring through Targeted Transcriptome Pyrosequencing |
title_full |
Development of Genomic Resources for Pacific Herring through Targeted Transcriptome Pyrosequencing |
title_fullStr |
Development of Genomic Resources for Pacific Herring through Targeted Transcriptome Pyrosequencing |
title_full_unstemmed |
Development of Genomic Resources for Pacific Herring through Targeted Transcriptome Pyrosequencing |
title_sort |
development of genomic resources for pacific herring through targeted transcriptome pyrosequencing |
publisher |
Public Library of Science |
publishDate |
2012 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3288011 http://www.ncbi.nlm.nih.gov/pubmed/22383979 https://doi.org/10.1371/journal.pone.0030908 |
geographic |
Bering Sea Gulf of Alaska Pacific |
geographic_facet |
Bering Sea Gulf of Alaska Pacific |
genre |
Bering Sea Kodiak Alaska |
genre_facet |
Bering Sea Kodiak Alaska |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3288011 http://www.ncbi.nlm.nih.gov/pubmed/22383979 http://dx.doi.org/10.1371/journal.pone.0030908 |
op_rights |
Roberts et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1371/journal.pone.0030908 |
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PLoS ONE |
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7 |
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2 |
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e30908 |
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1766377948689989632 |