A Transcriptomic Analysis of Cave, Surface, and Hybrid Isopod Crustaceans of the Species Asellus aquaticus
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{"title"=>"A transcriptomic analysis of cave, surface, and hybrid isopod crustaceans of the species Asellus aquaticus", "type"=>"journal", "authors"=>[{"first_name"=>"Bethany A.", "last_name"=>"Stahl", "scopus_author_id"=>"55585377700"}, {"first_name"=>"Joshua B.", "last_name"=>"Gross", "scopus_author_id"=>"7402752134"}, {"first_name"=>"Daniel I.", "last_name"=>"Speiser", "scopus_author_id"=>"24478049200"}, {"first_name"=>"Todd H.", "last_name"=>"Oakley", "scopus_author_id"=>"7003604734"}, {"first_name"=>"Nipam H.", "last_name"=>"Patel", "scopus_author_id"=>"35594245200"}, {"first_name"=>"Douglas B.", "last_name"=>"Gould", "scopus_author_id"=>"22955549700"}, {"first_name"=>"Meredith E.", "last_name"=>"Protas", "scopus_author_id"=>"6508145182"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"doi"=>"10.1371/journal.pone.0140484", "pui"=>"607101770", "scopus"=>"2-s2.0-84948822905", "issn"=>"19326203", "pmid"=>"26462237", "sgr"=>"84948822905"}, "id"=>"6c5469cc-69de-3648-9215-9f49485857ce", "abstract"=>"Cave animals, compared to surface-dwelling relatives, tend to have reduced eyes and pig- ment, longer appendages, and enhanced mechanosensory structures. Pressing questions include how certain cave-related traits are gained and lost, and if they originate through the same or different genetic programs in independent lineages. An excellent system for explor- ing these questions is the isopod, Asellus aquaticus. This species includes multiple cave and surface populations that have numerous morphological differences between them. A key feature is that hybrids between cave and surface individuals are viable, which enables genetic crosses and linkage analyses. Here, we advance this system by analyzing single animal transcriptomes of Asellus aquaticus.We use high throughput sequencing of non- normalized cDNA derived from the head of a surface-dwelling male, the head of a cave- dwelling male, the head of a hybrid male (produced by crossing a surface individual with a cave individual), and a pooled sample of surface embryos and hatchlings. Assembling reads from surface and cave head RNA pools yielded an integrated transcriptome com- prised of 23,984 contigs. Using this integrated assembly as a reference transcriptome, we aligned reads from surface-, cave- and hybrid- head tissue and pooled surface embryos and hatchlings. Our approach identified 742 SNPs and placed four new candidate genes to an existing linkage map for A. aquaticus. In addition, we examined SNPs for allele-specific expression differences in the hybrid individual. All of these resources will facilitate identifica- tion of genes and associated changes responsible for cave adaptation in A. aquaticus and, in concert with analyses of other species, will inform our understanding of the evolutionary processes accompanying adaptation to the subterranean environment.", "link"=>"http://www.mendeley.com/research/transcriptomic-analysis-cave-surface-hybrid-isopod-crustaceans-species-asellus-aquaticus", "reader_count"=>24, "reader_count_by_academic_status"=>{"Researcher"=>8, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>2, "Student > Master"=>3, "Professor"=>1, "Student > Bachelor"=>1}, "reader_count_by_user_role"=>{"Researcher"=>8, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>2, "Student > Master"=>3, "Professor"=>1, "Student > Bachelor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>19}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>19}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"United States"=>1, "Finland"=>1, "United Kingdom"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2357440"], "description"=>"<p>Putative genes with allele specific differences.</p>", "links"=>[], "tags"=>["transcriptome", "snp", "surface embryos", "Asellus aquaticus", "Hybrid Isopod Crustaceans", "Species Asellus aquaticus Cave animals", "cave head RNA pools"], "article_id"=>1573569, "categories"=>["Uncategorised"], "users"=>["Bethany A. Stahl", "Joshua B. Gross", "Daniel I. Speiser", "Todd H. Oakley", "Nipam H. Patel", "Douglas B. Gould", "Meredith E. Protas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140484.t003", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Putative_genes_with_allele_specific_differences_/1573569", "title"=>"Putative genes with allele specific differences.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-13 03:12:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/2357443", "https://ndownloader.figshare.com/files/2357444", "https://ndownloader.figshare.com/files/2357445", "https://ndownloader.figshare.com/files/2357446", "https://ndownloader.figshare.com/files/2357447"], "description"=>"<div><p>Cave animals, compared to surface-dwelling relatives, tend to have reduced eyes and pigment, longer appendages, and enhanced mechanosensory structures. Pressing questions include how certain cave-related traits are gained and lost, and if they originate through the same or different genetic programs in independent lineages. An excellent system for exploring these questions is the isopod, <i>Asellus aquaticus</i>. This species includes multiple cave and surface populations that have numerous morphological differences between them. A key feature is that hybrids between cave and surface individuals are viable, which enables genetic crosses and linkage analyses. Here, we advance this system by analyzing single animal transcriptomes of <i>Asellus aquaticus</i>. We use high throughput sequencing of non-normalized cDNA derived from the head of a surface-dwelling male, the head of a cave-dwelling male, the head of a hybrid male (produced by crossing a surface individual with a cave individual), and a pooled sample of surface embryos and hatchlings. Assembling reads from surface and cave head RNA pools yielded an integrated transcriptome comprised of 23,984 contigs. Using this integrated assembly as a reference transcriptome, we aligned reads from surface-, cave- and hybrid- head tissue and pooled surface embryos and hatchlings. Our approach identified 742 SNPs and placed four new candidate genes to an existing linkage map for <i>A</i>. <i>aquaticus</i>. In addition, we examined SNPs for allele-specific expression differences in the hybrid individual. All of these resources will facilitate identification of genes and associated changes responsible for cave adaptation in <i>A</i>. <i>aquaticus</i> and, in concert with analyses of other species, will inform our understanding of the evolutionary processes accompanying adaptation to the subterranean environment.</p></div>", "links"=>[], "tags"=>["transcriptome", "snp", "surface embryos", "Asellus aquaticus", "Hybrid Isopod Crustaceans", "Species Asellus aquaticus Cave animals", "cave head RNA pools"], "article_id"=>1573572, "categories"=>["Uncategorised"], "users"=>["Bethany A. Stahl", "Joshua B. Gross", "Daniel I. Speiser", "Todd H. Oakley", "Nipam H. Patel", "Douglas B. Gould", "Meredith E. Protas"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0140484.s001", "https://dx.doi.org/10.1371/journal.pone.0140484.s002", "https://dx.doi.org/10.1371/journal.pone.0140484.s003", "https://dx.doi.org/10.1371/journal.pone.0140484.s004", "https://dx.doi.org/10.1371/journal.pone.0140484.s005"], "stats"=>{"downloads"=>6, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Transcriptomic_Analysis_of_Cave_Surface_and_Hybrid_Isopod_Crustaceans_of_the_Species_Asellus_aquaticus_/1573572", "title"=>"A Transcriptomic Analysis of Cave, Surface, and Hybrid Isopod Crustaceans of the Species <i>Asellus aquaticus</i>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-10-13 03:12:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/2357416"], "description"=>"<p>A. The BLAST results reveal a wide range in matches for the top hits for each contiguous sequence, which likely is a consequence of limited genomic resources for invertebrate systems. However, the crustacean <i>D</i>. <i>pulex</i> is the species most frequently detected in our dataset. B. Our integrated trancriptome assembly yielded contigs ranging in size from 21 bp to 3490 bp, with an average length of 500 bp. C. A sequence similarity analysis further confirms the identity of genes detected in our transcriptome owing to the high level of similarity (60–80%) for each contig to their respective top hit. D. The reliability of gene identification in our transcriptome is further supported by the expect (or “e”) value distribution.</p>", "links"=>[], "tags"=>["transcriptome", "snp", "surface embryos", "Asellus aquaticus", "Hybrid Isopod Crustaceans", "Species Asellus aquaticus Cave animals", "cave head RNA pools"], "article_id"=>1573557, "categories"=>["Uncategorised"], "users"=>["Bethany A. Stahl", "Joshua B. Gross", "Daniel I. Speiser", "Todd H. Oakley", "Nipam H. Patel", "Douglas B. Gould", "Meredith E. Protas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140484.g001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Descriptive_analyses_of_the_A_aquaticus_transcriptome_/1573557", "title"=>"Descriptive analyses of the <i>A</i>. <i>aquaticus</i> transcriptome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-13 03:12:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/2357430"], "description"=>"<p>A. Generally, gene ontology (GO) terms were assigned to sequences ranging in length from ~100 bp to ~2,500 bp. B. Over 23,000 gene ontology terms were associated with genes in the <i>A</i>. <i>aquaticus</i> transcriptome, with a median GO level of 6.921. C. The top 20 gene ontology terms represented in our transcriptome for each GO category: molecular function, biological process and cellular component.</p>", "links"=>[], "tags"=>["transcriptome", "snp", "surface embryos", "Asellus aquaticus", "Hybrid Isopod Crustaceans", "Species Asellus aquaticus Cave animals", "cave head RNA pools"], "article_id"=>1573559, "categories"=>["Uncategorised"], "users"=>["Bethany A. Stahl", "Joshua B. Gross", "Daniel I. Speiser", "Todd H. Oakley", "Nipam H. Patel", "Douglas B. Gould", "Meredith E. Protas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140484.g002", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_aquaticus_gene_ontology_GO_term_analysis_/1573559", "title"=>"<i>A</i>. <i>aquaticus</i> gene ontology (GO) term analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-13 03:12:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/2357436"], "description"=>"<p> A. Three SNPs were present for the contig corresponding to <i>Peroxiredoxin-1</i>. Written first is the surface nucleotide, then the position, and then the cave nucleotide. B. Shown are the number of reads for the cave, surface, and hybrid samples and the corresponding allele, either cave or surface, for each of the reads. The cave allele is shown in red and the surface allele in black. Below the reads is written whether the surface and cave alleles encode different amino acids. The first and third SNPs are sense mutations and the second results in an amino acid change.</p>", "links"=>[], "tags"=>["transcriptome", "snp", "surface embryos", "Asellus aquaticus", "Hybrid Isopod Crustaceans", "Species Asellus aquaticus Cave animals", "cave head RNA pools"], "article_id"=>1573565, "categories"=>["Uncategorised"], "users"=>["Bethany A. Stahl", "Joshua B. Gross", "Daniel I. Speiser", "Todd H. Oakley", "Nipam H. Patel", "Douglas B. Gould", "Meredith E. Protas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140484.g003", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Allele_specific_expression_of_Peroxiredoxin_1_in_a_hybrid_sample_reveals_bias_for_the_cave_dwelling_allele_/1573565", "title"=>"Allele-specific expression of <i>Peroxiredoxin-1</i> in a hybrid sample reveals bias for the cave-dwelling allele.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-13 03:12:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/2357437"], "description"=>"<p>Primers used for genotyping the candidate genes and in the case of <i>Ruby</i>, degenerate PCR.</p>", "links"=>[], "tags"=>["transcriptome", "snp", "surface embryos", "Asellus aquaticus", "Hybrid Isopod Crustaceans", "Species Asellus aquaticus Cave animals", "cave head RNA pools"], "article_id"=>1573566, "categories"=>["Uncategorised"], "users"=>["Bethany A. Stahl", "Joshua B. Gross", "Daniel I. Speiser", "Todd H. Oakley", "Nipam H. Patel", "Douglas B. Gould", "Meredith E. Protas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140484.t001", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Primers_used_for_genotyping_the_candidate_genes_and_in_the_case_of_Ruby_degenerate_PCR_/1573566", "title"=>"Primers used for genotyping the candidate genes and in the case of <i>Ruby</i>, degenerate PCR.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-13 03:12:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/2357438"], "description"=>"<p>Candidate gene placement on <i>Asellus aquaticus</i> linkage map.</p>", "links"=>[], "tags"=>["transcriptome", "snp", "surface embryos", "Asellus aquaticus", "Hybrid Isopod Crustaceans", "Species Asellus aquaticus Cave animals", "cave head RNA pools"], "article_id"=>1573567, "categories"=>["Uncategorised"], "users"=>["Bethany A. Stahl", "Joshua B. Gross", "Daniel I. Speiser", "Todd H. Oakley", "Nipam H. Patel", "Douglas B. Gould", "Meredith E. Protas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140484.t002", "stats"=>{"downloads"=>3, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Candidate_gene_placement_on_Asellus_aquaticus_linkage_map_/1573567", "title"=>"Candidate gene placement on <i>Asellus aquaticus</i> linkage map.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-13 03:12:02"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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