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. 2012;7(2):e30908.
doi: 10.1371/journal.pone.0030908. Epub 2012 Feb 27.

Development of genomic resources for Pacific Herring through targeted transcriptome pyrosequencing

Steven B Roberts  1 , Lorenz Hauser, Lisa W Seeb, James E Seeb
Affiliations

Development of genomic resources for Pacific Herring through targeted transcriptome pyrosequencing

Steven B Roberts et al. PLoS One. 2012.

Abstract

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.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Histogram of contig sequence length.
Contig sequences were generated from de novo assembly of both libraries (n = 42,953) and average length is 728 bp. Note logarithmic scale for frequency axis.
Figure 2
Figure 2. Functional categorization of contig sequences.
Contig sequences were generated from de novo assembly of both libraries (n = 42,953) and annotations performed using BLASTx with Swiss-Prot and Gene Ontology databases.
Figure 3
Figure 3. Relative expression (RPKM) of 454 sequenced transcriptome across liver and gonad tissue.
Diagonal line represents equal expression in both tissue types. Note both axes are on the logarithmic scale.
Figure 4
Figure 4. Rarefaction analysis of quality trimmed reads from each library.
Rarefaction analysis was used to determine level of contig discovery relative to sequencing effort. Reads were sequentially sampled in 1×105 sequence read increments and de novo assembled.
Figure 5
Figure 5. Variance components from a locus-by-locus AMOVA.
Five loci (green) showed differentiation between the two ocean basins (high FBT), while a single locus (yellow) significantly differentiated between Prince William Sound and Kodiak Island within the Gulf of Alaska (high FSB, yellow).
See this image and copyright information in PMC

References

    1. EVOSTC. Prince William Sound Integrated Herring Restoration Program. Exxon Valdez Oil Spill Trust Council website. 2008. Available: http://www.evostc.state.ak.us/Universal/Documents/Publications/IHRP%20-%.... Accessed 2012 Jan 1.
    1. Hulson PJF, Miller SE, Quinn TJ, Marty GD, Moffitt SD, et al. Data conflicts in fishery models: incorporating hydroacoustic data into the Prince William Sound Pacific herring assessment model. ICES Journal of Marine Science. 2008;65:25–43.
    1. Thorne RE, Thomas GL. Herring and the “Exxon Valdez” oil spill: an investigation into historical data conflicts. ICES Journal of Marine Science. 2008;65:44–50.
    1. Carls MG, Marty GD, Hose JE. Synthesis of the toxicological impacts of the Exxon Valdez oil spill on Pacific herring (Clupea pallasi) in Prince William Sound, Alaska, USA. Canadian Journal of Fisheries and Aquatic Sciences. 2002;59:153–172.
    1. Marty GD, Quinn TJ, Carpenter G, Meyers TR, Willits NH. Role of disease in abundance of a Pacific herring (Clupea pallasi) population. Canadian Journal of Fisheries and Aquatic Sciences. 2003;60:1258–1265.

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