De novo Transcriptome Assemblies of Rana (Lithobates) catesbeiana and Xenopus laevis Tadpole Livers for Comparative Genomics without Reference Genomes
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{"title"=>"De novo transcriptome assemblies of Rana (Lithobates) catesbeiana and Xenopus laevis tadpole livers for comparative genomics without reference genomes", "type"=>"journal", "authors"=>[{"first_name"=>"Inanc", "last_name"=>"Birol", "scopus_author_id"=>"35298470000"}, {"first_name"=>"Bahar", "last_name"=>"Behsaz", "scopus_author_id"=>"55402133800"}, {"first_name"=>"S. Austin", "last_name"=>"Hammond", "scopus_author_id"=>"15745546700"}, {"first_name"=>"Erdi", "last_name"=>"Kucuk", "scopus_author_id"=>"56764145800"}, {"first_name"=>"Nik", "last_name"=>"Veldhoen", "scopus_author_id"=>"6603158219"}, {"first_name"=>"Caren C.", "last_name"=>"Helbing", "scopus_author_id"=>"7004291628"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"26121473", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0130720", "pui"=>"605481270", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "scopus"=>"2-s2.0-84938588236", "sgr"=>"84938588236"}, "id"=>"6bbe9bb3-7fbf-342d-944c-c168d7773bf7", "abstract"=>"In this work we studied the liver transcriptomes of two frog species, the American bullfrog (Rana (Lithobates) catesbeiana) and the African clawed frog (Xenopus laevis). We used high throughput RNA sequencing (RNA-seq) data to assemble and annotate these transcriptomes, and compared how their baseline expression profiles change when tadpoles of the two species are exposed to thyroid hormone. We generated more than 1.5 billion RNA-seq reads in total for the two species under two conditions as treatment/control pairs. We de novo assembled these reads using Trans-ABySS to reconstruct reference transcriptomes, obtaining over 350,000 and 130,000 putative transcripts for R. catesbeiana and X. laevis, respectively. Using available genomics resources for X. laevis, we annotated over 97% of our X. laevis transcriptome contigs, demonstrating the utility and efficacy of our methodology. Leveraging this validated analysis pipeline, we also annotated the assembled R. catesbeiana transcriptome. We used the expression profiles of the annotated genes of the two species to examine the similarities and differences between the tadpole liver transcriptomes. We also compared the gene ontology terms of expressed genes to measure how the animals react to a challenge by thyroid hormone. Our study reports three main conclusions. First, de novo assembly of RNA-seq data is a powerful method for annotating and establishing transcriptomes of non-model organisms. Second, the liver transcriptomes of the two frog species, R. catesbeiana and X. laevis, show many common features, and the distribution of their gene ontology profiles are statistically indistinguishable. Third, although they broadly respond the same way to the presence of thyroid hormone in their environment, their receptor/signal transduction pathways display marked differences.", "link"=>"http://www.mendeley.com/research/novo-transcriptome-assemblies-rana-lithobates-catesbeiana-xenopus-laevis-tadpole-livers-comparative", "reader_count"=>40, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Student > Doctoral Student"=>2, "Researcher"=>11, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>2, "Student > Master"=>4, "Other"=>3, "Student > Bachelor"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Student > Doctoral Student"=>2, "Researcher"=>11, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>2, "Student > Master"=>4, "Other"=>3, "Student > Bachelor"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>12, "Agricultural and Biological Sciences"=>20, "Medicine and Dentistry"=>1, "Chemistry"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>20}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>12}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>2}}, "reader_count_by_country"=>{"Canada"=>1, "Netherlands"=>1, "Argentina"=>1, "Korea (South)"=>1, "Denmark"=>1, "Australia"=>2}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2154778"], "description"=>"<p>Top 25 impacted pathways after TH treatment for <i>R. catesbeiana</i> ranked by the highest proportion of overall observed genes. The pathway names are indicated in the center of the figure with the total number of genes known in each IGA pathway indicated. The asterisk indicates those pathways that are found in the top 25 list of <i>X. laevis</i>. The colour coded bar plots illustrate the percentage of the total number of gene transcripts in a pathway that are downregulated (blue), non-responsive (yellow), upregulated (red) or not observed in the experiment (gray) relative to the control condition. Differentially expressed transcripts were determined using a p-value threshold of 5%.</p>", "links"=>[], "tags"=>["gene ontology profiles", "catesbeiana", "Xenopus laevis Tadpole Livers", "liver transcriptomes", "laevis transcriptome contigs", "throughput RNA sequencing", "baseline expression profiles change", "Thyroid Hormone", "Gene Ontology terms", "tadpole liver transcriptomes", "frog species"], "article_id"=>1467660, "categories"=>["Uncategorised"], "users"=>["Inanc Birol", "Bahar Behsaz", "S. Austin Hammond", "Erdi Kucuk", "Nik Veldhoen", "Caren C. Helbing"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130720.g004", "stats"=>{"downloads"=>3, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pathway_analysis_for_liver_transcripts_from_R_catesbeiana_CAT_and_X_laevis_LAE_/1467660", "title"=>"Pathway analysis for liver transcripts from <i>R. catesbeiana</i> (CAT) and <i>X. laevis</i> (LAE).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-29 03:39:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2154774"], "description"=>"<p>The two series in each stacked bar plot correspond to differentially expressed <i>R. catesbeiana</i> (CAT) and <i>X. laevis</i> (LAE) transcripts, with a p-value threshold of 5%.</p>", "links"=>[], "tags"=>["gene ontology profiles", "catesbeiana", "Xenopus laevis Tadpole Livers", "liver transcriptomes", "laevis transcriptome contigs", "throughput RNA sequencing", "baseline expression profiles change", "Thyroid Hormone", "Gene Ontology terms", "tadpole liver transcriptomes", "frog species"], "article_id"=>1467656, "categories"=>["Uncategorised"], "users"=>["Inanc Birol", "Bahar Behsaz", "S. Austin Hammond", "Erdi Kucuk", "Nik Veldhoen", "Caren C. Helbing"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130720.g003", "stats"=>{"downloads"=>2, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_ontology_classification_of_DESeq_selected_TH_responsive_R_catesbeiana_and_X_laevis_liver_transcripts_with_UniProtKB_AC_numbers_/1467656", "title"=>"Gene ontology classification of DESeq-selected, TH-responsive <i>R. catesbeiana</i> and <i>X. laevis</i> liver transcripts with UniProtKB AC numbers.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-29 03:39:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2154781"], "description"=>"<p>Sequences were generated using 75 bp paired end reads.</p><p>RNA-seq data and transcriptome assembly results.</p>", "links"=>[], "tags"=>["gene ontology profiles", "catesbeiana", "Xenopus laevis Tadpole Livers", "liver transcriptomes", "laevis transcriptome contigs", "throughput RNA sequencing", "baseline expression profiles change", "Thyroid Hormone", "Gene Ontology terms", "tadpole liver transcriptomes", "frog species"], "article_id"=>1467663, "categories"=>["Uncategorised"], "users"=>["Inanc Birol", "Bahar Behsaz", "S. Austin Hammond", "Erdi Kucuk", "Nik Veldhoen", "Caren C. Helbing"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130720.t001", "stats"=>{"downloads"=>3, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_RNA_seq_data_and_transcriptome_assembly_results_/1467663", "title"=>"RNA-seq data and transcriptome assembly results.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-29 03:39:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2154782"], "description"=>"<p>Three annotation approaches were taken: using BLASTn against a collection of nucleotide sequences of select amphibia, BLASTx against the non-redundant NCBI protein database, and using BLASTx against the ENSEMBL (<i>H</i>. <i>sapiens</i>) database for subsequent GO analysis.</p><p>Annotation of assembled transcriptome contigs.</p>", "links"=>[], "tags"=>["gene ontology profiles", "catesbeiana", "Xenopus laevis Tadpole Livers", "liver transcriptomes", "laevis transcriptome contigs", "throughput RNA sequencing", "baseline expression profiles change", "Thyroid Hormone", "Gene Ontology terms", "tadpole liver transcriptomes", "frog species"], "article_id"=>1467664, "categories"=>["Uncategorised"], "users"=>["Inanc Birol", "Bahar Behsaz", "S. Austin Hammond", "Erdi Kucuk", "Nik Veldhoen", "Caren C. Helbing"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130720.t002", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Annotation_of_assembled_transcriptome_contigs_/1467664", "title"=>"Annotation of assembled transcriptome contigs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-29 03:39:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2154780"], "description"=>"<p>Top 25 impacted pathways after TH treatment for <i>X. laevis</i> ranked by the highest proportion of overall observed genes. The asterisk indicates those pathways that are found in the top 25 list of <i>R. catesbeiana</i>. Plot details are as in the <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130720#pone.0130720.g004\" target=\"_blank\">Fig 4</a> legend.</p>", "links"=>[], "tags"=>["gene ontology profiles", "catesbeiana", "Xenopus laevis Tadpole Livers", "liver transcriptomes", "laevis transcriptome contigs", "throughput RNA sequencing", "baseline expression profiles change", "Thyroid Hormone", "Gene Ontology terms", "tadpole liver transcriptomes", "frog species"], "article_id"=>1467662, "categories"=>["Uncategorised"], "users"=>["Inanc Birol", "Bahar Behsaz", "S. Austin Hammond", "Erdi Kucuk", "Nik Veldhoen", "Caren C. Helbing"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130720.g005", "stats"=>{"downloads"=>2, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pathway_analysis_for_liver_transcripts_from_R_catesbeiana_CAT_and_X_laevis_LAE_/1467662", "title"=>"Pathway analysis for liver transcripts from <i>R. catesbeiana</i> (CAT) and <i>X. laevis</i> (LAE).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-29 03:39:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2154767"], "description"=>"<p>Three shades of purple designate p-values of differential expression estimates 0.05, 0.02 and 0.002, lighter colours indicating lower thresholds.</p>", "links"=>[], "tags"=>["gene ontology profiles", "catesbeiana", "Xenopus laevis Tadpole Livers", "liver transcriptomes", "laevis transcriptome contigs", "throughput RNA sequencing", "baseline expression profiles change", "Thyroid Hormone", "Gene Ontology terms", "tadpole liver transcriptomes", "frog species"], "article_id"=>1467649, "categories"=>["Uncategorised"], "users"=>["Inanc Birol", "Bahar Behsaz", "S. Austin Hammond", "Erdi Kucuk", "Nik Veldhoen", "Caren C. Helbing"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130720.g002", "stats"=>{"downloads"=>1, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differential_expression_of_assembled_transcripts_for_A_R_catesbeiana_and_B_X_laevis_/1467649", "title"=>"Differential expression of assembled transcripts for (A) <i>R. catesbeiana</i> and (B) <i>X. laevis</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-29 03:39:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2154784", "https://ndownloader.figshare.com/files/2154785", "https://ndownloader.figshare.com/files/2154786", "https://ndownloader.figshare.com/files/2154787"], "description"=>"<div><p>In this work we studied the liver transcriptomes of two frog species, the American bullfrog (<i>Rana</i> (<i>Lithobates</i>) <i>catesbeiana</i>) and the African clawed frog (<i>Xenopus laevis</i>). We used high throughput RNA sequencing (RNA-seq) data to assemble and annotate these transcriptomes, and compared how their baseline expression profiles change when tadpoles of the two species are exposed to thyroid hormone. We generated more than 1.5 billion RNA-seq reads in total for the two species under two conditions as treatment/control pairs. We <i>de novo</i> assembled these reads using Trans-ABySS to reconstruct reference transcriptomes, obtaining over 350,000 and 130,000 putative transcripts for <i>R</i>. <i>catesbeiana</i> and <i>X</i>. <i>laevis</i>, respectively. Using available genomics resources for <i>X</i>. <i>laevis</i>, we annotated over 97% of our <i>X</i>. <i>laevis</i> transcriptome contigs, demonstrating the utility and efficacy of our methodology. Leveraging this validated analysis pipeline, we also annotated the assembled <i>R</i>. <i>catesbeiana</i> transcriptome. We used the expression profiles of the annotated genes of the two species to examine the similarities and differences between the tadpole liver transcriptomes. We also compared the gene ontology terms of expressed genes to measure how the animals react to a challenge by thyroid hormone. Our study reports three main conclusions. First, <i>de novo</i> assembly of RNA-seq data is a powerful method for annotating and establishing transcriptomes of non-model organisms. Second, the liver transcriptomes of the two frog species, <i>R</i>. <i>catesbeiana</i> and <i>X</i>. <i>laevis</i>, show many common features, and the distribution of their gene ontology profiles are statistically indistinguishable. Third, although they broadly respond the same way to the presence of thyroid hormone in their environment, their receptor/signal transduction pathways display marked differences.</p></div>", "links"=>[], "tags"=>["gene ontology profiles", "catesbeiana", "Xenopus laevis Tadpole Livers", "liver transcriptomes", "laevis transcriptome contigs", "throughput RNA sequencing", "baseline expression profiles change", "Thyroid Hormone", "Gene Ontology terms", "tadpole liver transcriptomes", "frog species"], "article_id"=>1467666, "categories"=>["Uncategorised"], "users"=>["Inanc Birol", "Bahar Behsaz", "S. Austin Hammond", "Erdi Kucuk", "Nik Veldhoen", "Caren C. Helbing"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0130720.s001", "https://dx.doi.org/10.1371/journal.pone.0130720.s002", "https://dx.doi.org/10.1371/journal.pone.0130720.s003", "https://dx.doi.org/10.1371/journal.pone.0130720.s004"], "stats"=>{"downloads"=>4, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_De_novo_Transcriptome_Assemblies_of_Rana_Lithobates_catesbeiana_and_Xenopus_laevis_Tadpole_Livers_for_Comparative_Genomics_without_Reference_Genomes/1467666", "title"=>"<i>De novo</i> Transcriptome Assemblies of <i>Rana</i> (<i>Lithobates</i>) <i>catesbeiana</i> and <i>Xenopus laevis</i> Tadpole Livers for Comparative Genomics without Reference Genomes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-06-29 03:39:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2154765"], "description"=>"<p>The two series in each stacked bar plot correspond to all <i>R. catesbeiana</i> (CAT) and <i>X. laevis</i> (LAE) transcripts.</p>", "links"=>[], "tags"=>["gene ontology profiles", "catesbeiana", "Xenopus laevis Tadpole Livers", "liver transcriptomes", "laevis transcriptome contigs", "throughput RNA sequencing", "baseline expression profiles change", "Thyroid Hormone", "Gene Ontology terms", "tadpole liver transcriptomes", "frog species"], "article_id"=>1467647, "categories"=>["Uncategorised"], "users"=>["Inanc Birol", "Bahar Behsaz", "S. Austin Hammond", "Erdi Kucuk", "Nik Veldhoen", "Caren C. Helbing"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130720.g001", "stats"=>{"downloads"=>0, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_ontology_classification_of_all_reconstructed_R_catesbeiana_and_X_laevis_liver_transcripts_with_UniProtKB_AC_numbers_/1467647", "title"=>"Gene ontology classification of all reconstructed <i>R</i>. <i>catesbeiana</i> and <i>X. laevis</i> liver transcripts with UniProtKB AC numbers.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-29 03:39:18"}

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