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...
Published in: | PLoS ONE |
---|---|
Main Authors: | , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Public Library of Science (PLoS)
2012
|
Subjects: | |
Online Access: | https://doi.org/10.1371/journal.pone.0030908 https://doaj.org/article/4248c8b9ff8c4d10883615c17993c6e3 |
id |
ftdoajarticles:oai:doaj.org/article:4248c8b9ff8c4d10883615c17993c6e3 |
---|---|
record_format |
openpolar |
spelling |
ftdoajarticles:oai:doaj.org/article:4248c8b9ff8c4d10883615c17993c6e3 2023-05-15T15:43:46+02:00 Development of genomic resources for Pacific Herring through targeted transcriptome pyrosequencing. Steven B Roberts Lorenz Hauser Lisa W Seeb James E Seeb 2012-01-01T00:00:00Z https://doi.org/10.1371/journal.pone.0030908 https://doaj.org/article/4248c8b9ff8c4d10883615c17993c6e3 EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC3288011?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0030908 https://doaj.org/article/4248c8b9ff8c4d10883615c17993c6e3 PLoS ONE, Vol 7, Iss 2, p e30908 (2012) Medicine R Science Q article 2012 ftdoajarticles https://doi.org/10.1371/journal.pone.0030908 2022-12-31T02:30:10Z 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. Article in Journal/Newspaper Bering Sea Kodiak Alaska Directory of Open Access Journals: DOAJ Articles Bering Sea Gulf of Alaska Pacific PLoS ONE 7 2 e30908 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Medicine R Science Q |
spellingShingle |
Medicine R Science Q Steven B Roberts Lorenz Hauser Lisa W Seeb James E Seeb Development of genomic resources for Pacific Herring through targeted transcriptome pyrosequencing. |
topic_facet |
Medicine R Science Q |
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 |
Article in Journal/Newspaper |
author |
Steven B Roberts Lorenz Hauser Lisa W Seeb James E Seeb |
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. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2012 |
url |
https://doi.org/10.1371/journal.pone.0030908 https://doaj.org/article/4248c8b9ff8c4d10883615c17993c6e3 |
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 |
PLoS ONE, Vol 7, Iss 2, p e30908 (2012) |
op_relation |
http://europepmc.org/articles/PMC3288011?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0030908 https://doaj.org/article/4248c8b9ff8c4d10883615c17993c6e3 |
op_doi |
https://doi.org/10.1371/journal.pone.0030908 |
container_title |
PLoS ONE |
container_volume |
7 |
container_issue |
2 |
container_start_page |
e30908 |
_version_ |
1766377970871566336 |