Development of Genomic Resources for Pacific Herring through Targeted Transcriptome Pyrosequencing
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{"title"=>"Development of genomic resources for pacific herring through targeted transcriptome pyrosequencing", "type"=>"journal", "authors"=>[{"first_name"=>"Steven B.", "last_name"=>"Roberts", "scopus_author_id"=>"55366464800"}, {"first_name"=>"Lorenz", "last_name"=>"Hauser", "scopus_author_id"=>"16222458400"}, {"first_name"=>"Lisa W.", "last_name"=>"Seeb", "scopus_author_id"=>"6603597807"}, {"first_name"=>"James E.", "last_name"=>"Seeb", "scopus_author_id"=>"6603771669"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84857550272", "sgr"=>"84857550272", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0030908", "pmid"=>"22383979", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pui"=>"364349965"}, "id"=>"0e345295-510f-36cd-bc5f-8b0475268372", "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.", "link"=>"http://www.mendeley.com/research/development-genomic-resources-pacific-herring-through-targeted-transcriptome-pyrosequencing", "reader_count"=>55, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>6, "Researcher"=>11, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>17, "Student > Postgraduate"=>1, "Student > Master"=>7, "Other"=>3, "Student > Bachelor"=>4, "Lecturer"=>1, "Professor"=>4}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>6, "Researcher"=>11, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>17, "Student > Postgraduate"=>1, "Student > Master"=>7, "Other"=>3, "Student > Bachelor"=>4, "Lecturer"=>1, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>5, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>39, "Social Sciences"=>1, "Computer Science"=>2, "Engineering"=>3}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>3}, "Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>39}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>5}}, "reader_count_by_country"=>{"United States"=>6, "Ireland"=>1, "Mexico"=>1, "Spain"=>1, "India"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/675138"], "description"=>"<p>Diagonal line represents equal expression in both tissue types. Note both axes are on the logarithmic scale.</p>", "links"=>[], "tags"=>["454", "sequenced", "transcriptome", "gonad"], "article_id"=>345632, "categories"=>["Inorganic Chemistry", "Biological Sciences", "Genetics"], "users"=>["Steven B. Roberts", "Lorenz Hauser", "Lisa W. Seeb", "James E. Seeb"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030908.g003", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_expression_RPKM_of_454_sequenced_transcriptome_across_liver_and_gonad_tissue_/345632", "title"=>"Relative expression (RPKM) of 454 sequenced transcriptome across liver and gonad tissue.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-27 01:33:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/675510"], "description"=>"a<p>\n <b>From </b><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030908#pone.0030908-Seeb2\" target=\"_blank\">[<b>26</b>]</a><b>.</b></p>", "links"=>[], "tags"=>["locus", "amova", "snps", "compared", "microsatellite"], "article_id"=>345991, "categories"=>["Inorganic Chemistry", "Biological Sciences", "Genetics"], "users"=>["Steven B. Roberts", "Lorenz Hauser", "Lisa W. Seeb", "James E. Seeb"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030908.t006", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Locus_by_locus_AMOVA_of_SNPS_compared_to_allozyme_microsatellite_and_mtDNA_/345991", "title"=>"Locus by locus AMOVA of SNPS compared to allozyme, microsatellite and mtDNA.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-02-27 01:39:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/675433"], "description"=>"<p>Annotation of selected loci based top BLAST hit and GO ontology.</p>", "links"=>[], "tags"=>["loci"], "article_id"=>345928, "categories"=>["Inorganic Chemistry", "Biological Sciences", "Genetics"], "users"=>["Steven B. Roberts", "Lorenz Hauser", "Lisa W. Seeb", "James E. Seeb"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030908.t003", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Annotation_of_selected_loci_based_top_BLAST_hit_and_GO_ontology_/345928", "title"=>"Annotation of selected loci based top BLAST hit and GO ontology.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-02-27 01:38:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/675472"], "description"=>"<p>Characteristics of Pacific herring hepatic and testicular transcriptome sequencing.</p>", "links"=>[], "tags"=>["pacific", "herring", "hepatic", "testicular", "transcriptome"], "article_id"=>345958, "categories"=>["Inorganic Chemistry", "Biological Sciences", "Genetics"], "users"=>["Steven B. Roberts", "Lorenz Hauser", "Lisa W. Seeb", "James E. Seeb"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030908.t001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characteristics_of_Pacific_herring_hepatic_and_testicular_transcriptome_sequencing_/345958", "title"=>"Characteristics of Pacific herring hepatic and testicular transcriptome sequencing.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-02-27 01:39:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/345519"], "description"=>"<div><p>Pacific herring (<em>Clupea pallasii</em>) 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.</p> </div>", "links"=>[], "tags"=>["genomic", "resources", "pacific", "herring", "targeted", "transcriptome", "pyrosequencing"], "article_id"=>128291, "categories"=>["Inorganic Chemistry", "Biological Sciences", "Genetics"], "users"=>["Steven B. Roberts", "Lorenz Hauser", "Lisa W. Seeb", "James E. Seeb"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030908", "stats"=>{"downloads"=>1, "page_views"=>49, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Development_of_Genomic_Resources_for_Pacific_Herring_through_Targeted_Transcriptome_Pyrosequencing/128291", "title"=>"Development of Genomic Resources for Pacific Herring through Targeted Transcriptome Pyrosequencing", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-02-27 02:18:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/675205"], "description"=>"<p>Rarefaction analysis was used to determine level of contig discovery relative to sequencing effort. Reads were sequentially sampled in 1×10<sup>5</sup> sequence read increments and <i>de novo</i> assembled.</p>", "links"=>[], "tags"=>["trimmed", "reads"], "article_id"=>345698, "categories"=>["Inorganic Chemistry", "Biological Sciences", "Genetics"], "users"=>["Steven B. Roberts", "Lorenz Hauser", "Lisa W. Seeb", "James E. Seeb"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030908.g004", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Rarefaction_analysis_of_quality_trimmed_reads_from_each_library_/345698", "title"=>"Rarefaction analysis of quality trimmed reads from each library.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-27 01:34:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/674965"], "description"=>"<p>Contig sequences were generated from <i>de novo</i> assembly of both libraries (n = 42,953) and average length is 728 bp. Note logarithmic scale for frequency axis.</p>", "links"=>[], "tags"=>["contig"], "article_id"=>345455, "categories"=>["Inorganic Chemistry", "Biological Sciences", "Genetics"], "users"=>["Steven B. Roberts", "Lorenz Hauser", "Lisa W. Seeb", "James E. Seeb"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030908.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Histogram_of_contig_sequence_length_/345455", "title"=>"Histogram of contig sequence length.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-27 01:30:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/675588"], "description"=>"a<p>the ratio between the two values (Gulf of Alaska/Bering Sea).</p>", "links"=>[], "tags"=>["heterozygosity", "markers", "pacific", "haplotype", "was"], "article_id"=>346077, "categories"=>["Inorganic Chemistry", "Biological Sciences", "Genetics"], "users"=>["Steven B. Roberts", "Lorenz Hauser", "Lisa W. Seeb", "James E. Seeb"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030908.t005", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Unbiased_heterozygosity_of_four_genetic_markers_from_Pacific_herring_haplotype_diversity_was_used_for_mtDNA_/346077", "title"=>"Unbiased heterozygosity of four genetic markers from Pacific herring; haplotype diversity was used for mtDNA.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-02-27 01:41:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/675283"], "description"=>"<p>Five loci (green) showed differentiation between the two ocean basins (high <i>F<sub>BT</sub></i>), while a single locus (yellow) significantly differentiated between Prince William Sound and Kodiak Island within the Gulf of Alaska (high <i>F<sub>SB</sub></i>, yellow).</p>", "links"=>[], "tags"=>["components", "locus-by-locus"], "article_id"=>345774, "categories"=>["Inorganic Chemistry", "Biological Sciences", "Genetics"], "users"=>["Steven B. Roberts", "Lorenz Hauser", "Lisa W. Seeb", "James E. Seeb"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030908.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Variance_components_from_a_locus_by_locus_AMOVA_/345774", "title"=>"Variance components from a locus-by-locus AMOVA.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-27 01:36:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/675551"], "description"=>"<p>Numbers in bold represent values that deviated significantly from HWE.</p>", "links"=>[], "tags"=>["allele", "inbreeding", "coefficient", "loci", "pacific", "herring"], "article_id"=>346035, "categories"=>["Inorganic Chemistry", "Biological Sciences", "Genetics"], "users"=>["Steven B. Roberts", "Lorenz Hauser", "Lisa W. Seeb", "James E. Seeb"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030908.t004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Minor_allele_frequency_expected_heterozygosity_and_inbreeding_coefficient_F_IS_for_select_loci_in_three_Pacific_herring_populations_/346035", "title"=>"Minor allele frequency, expected heterozygosity, and inbreeding coefficient (<i>F<sub>IS</sub></i>) for select loci in three Pacific herring populations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-02-27 01:40:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/675047"], "description"=>"<p>Contig sequences were generated from <i>de novo</i> assembly of both libraries (n = 42,953) and annotations performed using BLASTx with Swiss-Prot and Gene Ontology databases.</p>", "links"=>[], "tags"=>["categorization", "contig"], "article_id"=>345537, "categories"=>["Inorganic Chemistry", "Biological Sciences", "Genetics"], "users"=>["Steven B. Roberts", "Lorenz Hauser", "Lisa W. Seeb", "James E. Seeb"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030908.g002", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Functional_categorization_of_contig_sequences_/345537", "title"=>"Functional categorization of contig sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-27 01:32:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/675392"], "description"=>"<p>Loci selected for HRMA and associated primers.</p>", "links"=>[], "tags"=>["hrma"], "article_id"=>345887, "categories"=>["Inorganic Chemistry", "Biological Sciences", "Genetics"], "users"=>["Steven B. Roberts", "Lorenz Hauser", "Lisa W. Seeb", "James E. Seeb"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030908.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Loci_selected_for_HRMA_and_associated_primers_/345887", "title"=>"Loci selected for HRMA and associated primers.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-02-27 01:38:07"}

PMC Usage Stats | Further Information

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Relative Metric

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