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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ftciteseerx:oai:CiteSeerX.psu:10.1.1.271.5992 2023-05-15T15:43:45+02:00 Development of Genomic Resources for Pacific Herring through Targeted Transcriptome Pyrosequencing Steven B. Roberts Lorenz Hauser Lisa W. Seeb James E. Seeb The Pennsylvania State University CiteSeerX Archives 2012 application/zip http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.271.5992 en eng http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.271.5992 Metadata may be used without restrictions as long as the oai identifier remains attached to it. ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/f8/10/PLoS_One_2012_Feb_27_7(2)_e30908.tar.gz text 2012 ftciteseerx 2016-01-07T20:40:12Z 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 Unknown Bering Sea Gulf of Alaska Pacific |
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ftciteseerx |
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English |
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. |
author2 |
The Pennsylvania State University CiteSeerX Archives |
format |
Text |
author |
Steven B. Roberts Lorenz Hauser Lisa W. Seeb James E. Seeb |
spellingShingle |
Steven B. Roberts Lorenz Hauser Lisa W. Seeb James E. Seeb Development of Genomic Resources for Pacific Herring through Targeted Transcriptome Pyrosequencing |
author_facet |
Steven B. Roberts Lorenz Hauser Lisa W. Seeb James E. Seeb |
author_sort |
Steven B. Roberts |
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 |
publishDate |
2012 |
url |
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.271.5992 |
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_source |
ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/f8/10/PLoS_One_2012_Feb_27_7(2)_e30908.tar.gz |
op_relation |
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.271.5992 |
op_rights |
Metadata may be used without restrictions as long as the oai identifier remains attached to it. |
_version_ |
1766377950853201920 |