Comparative Transcriptome Analyses Indicate Molecular Homology of Zebrafish Swimbladder and Mammalian Lung
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{"title"=>"Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and mammalian lung", "type"=>"journal", "authors"=>[{"first_name"=>"Weiling", "last_name"=>"Zheng", "scopus_author_id"=>"35094877000"}, {"first_name"=>"Zhengyuan", "last_name"=>"Wang", "scopus_author_id"=>"50362085800"}, {"first_name"=>"John E.", "last_name"=>"Collins", "scopus_author_id"=>"35371959700"}, {"first_name"=>"Robert M.", "last_name"=>"Andrews", "scopus_author_id"=>"9332878300"}, {"first_name"=>"Derek", "last_name"=>"Stemple", "scopus_author_id"=>"7003286759"}, {"first_name"=>"Zhiyuan", "last_name"=>"Gong", "scopus_author_id"=>"7201947961"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-80052048466", "doi"=>"10.1371/journal.pone.0024019", "pui"=>"362415038", "issn"=>"19326203", "pmid"=>"21887364", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "sgr"=>"80052048466"}, "id"=>"04e39798-e6e8-37fb-a2f3-133436b2a3cc", "abstract"=>"The fish swimbladder is a unique organ in vertebrate evolution and it functions for regulating buoyancy in most teleost species. It has long been postulated as a homolog of the tetrapod lung, but the molecular evidence is scarce. In order to understand the molecular function of swimbladder as well as its relationship with lungs in tetrapods, transcriptomic analyses of zebrafish swimbladder were carried out by RNA-seq. Gene ontology classification showed that genes in cytoskeleton and endoplasmic reticulum were enriched in the swimbladder. Further analyses depicted gene sets and pathways closely related to cytoskeleton constitution and regulation, cell adhesion, and extracellular matrix. Several prominent transcription factor genes in the swimbladder including hoxc4a, hoxc6a, hoxc8a and foxf1 were identified and their expressions in developing swimbladder during embryogenesis were confirmed. By comparison of enriched transcripts in the swimbladder with those in human and mouse lungs, we established the resemblance of transcriptome of the zebrafish swimbladder and mammalian lungs. Based on the transcriptomic data of zebrafish swimbladder, the predominant functions of swimbladder are in its epithelial and muscular tissues. Our comparative analyses also provide molecular evidence of the relatedness of the fish swimbladder and mammalian lung.", "link"=>"http://www.mendeley.com/research/comparative-transcriptome-analyses-indicate-molecular-homology-zebrafish-swimbladder-mammalian-lung", "reader_count"=>78, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>7, "Student > Doctoral Student"=>3, "Researcher"=>20, "Student > Ph. D. Student"=>24, "Student > Postgraduate"=>1, "Student > Master"=>10, "Other"=>1, "Student > Bachelor"=>6, "Lecturer > Senior Lecturer"=>2, "Professor"=>3, "Unspecified"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>7, "Student > Doctoral Student"=>3, "Researcher"=>20, "Student > Ph. D. Student"=>24, "Student > Postgraduate"=>1, "Student > Master"=>10, "Other"=>1, "Student > Bachelor"=>6, "Lecturer > Senior Lecturer"=>2, "Professor"=>3, "Unspecified"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>3, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>13, "Agricultural and Biological Sciences"=>52, "Medicine and Dentistry"=>3, "Neuroscience"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>2, "Immunology and Microbiology"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Neuroscience"=>{"Neuroscience"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>52}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>13}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>2}}, "reader_count_by_country"=>{"Austria"=>1, "Sweden"=>1, "United States"=>3, "United Kingdom"=>3}, "group_count"=>5}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/374169", "https://ndownloader.figshare.com/files/374200", "https://ndownloader.figshare.com/files/374243", "https://ndownloader.figshare.com/files/374254", "https://ndownloader.figshare.com/files/374286", "https://ndownloader.figshare.com/files/374319", "https://ndownloader.figshare.com/files/374353"], "description"=>"<div><p>The fish swimbladder is a unique organ in vertebrate evolution and it functions for regulating buoyancy in most teleost species. It has long been postulated as a homolog of the tetrapod lung, but the molecular evidence is scarce. In order to understand the molecular function of swimbladder as well as its relationship with lungs in tetrapods, transcriptomic analyses of zebrafish swimbladder were carried out by RNA-seq. Gene ontology classification showed that genes in cytoskeleton and endoplasmic reticulum were enriched in the swimbladder. Further analyses depicted gene sets and pathways closely related to cytoskeleton constitution and regulation, cell adhesion, and extracellular matrix. Several prominent transcription factor genes in the swimbladder including <em>hoxc4a</em>, <em>hoxc6a</em>, <em>hoxc8a</em> and <em>foxf1</em> were identified and their expressions in developing swimbladder during embryogenesis were confirmed. By comparison of enriched transcripts in the swimbladder with those in human and mouse lungs, we established the resemblance of transcriptome of the zebrafish swimbladder and mammalian lungs. Based on the transcriptomic data of zebrafish swimbladder, the predominant functions of swimbladder are in its epithelial and muscular tissues. Our comparative analyses also provide molecular evidence of the relatedness of the fish swimbladder and mammalian lung.</p> </div>", "links"=>[], "tags"=>["comparative", "transcriptome", "analyses", "molecular", "homology", "zebrafish", "swimbladder", "mammalian"], "article_id"=>133883, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Weiling Zheng", "Zhengyuan Wang", "John E. Collins", "Robert M. Andrews", "Derek Stemple", "Zhiyuan Gong"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0024019.s001", "https://dx.doi.org/10.1371/journal.pone.0024019.s002", "https://dx.doi.org/10.1371/journal.pone.0024019.s003", "https://dx.doi.org/10.1371/journal.pone.0024019.s004", "https://dx.doi.org/10.1371/journal.pone.0024019.s005", "https://dx.doi.org/10.1371/journal.pone.0024019.s006", "https://dx.doi.org/10.1371/journal.pone.0024019.s007"], "stats"=>{"downloads"=>32, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Comparative_Transcriptome_Analyses_Indicate_Molecular_Homology_of_Zebrafish_Swimbladder_and_Mammalian_Lung/133883", "title"=>"Comparative Transcriptome Analyses Indicate Molecular Homology of Zebrafish Swimbladder and Mammalian Lung", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-08-26 01:04:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/741303"], "description"=>"<p>Gene ontology classification and energy distribution are based on GO Slim classification of molecular functions. Genes without gene ontology information constitute 40% of the total swimbladder transcriptome and they were not included in the pie chart.</p>", "links"=>[], "tags"=>["ontology", "classification", "swimbladder"], "article_id"=>411674, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Weiling Zheng", "Zhengyuan Wang", "John E. Collins", "Robert M. Andrews", "Derek Stemple", "Zhiyuan Gong"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024019.g004", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_ontology_classification_a_and_energy_distribution_b_of_the_swimbladder_transcriptome_/411674", "title"=>"Gene ontology classification (a) and energy distribution (b) of the swimbladder transcriptome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-08-26 00:27:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/741228"], "description"=>"<p>Slim classifications of the total ZGC database entries and swimbladder transcriptome are represented by blue and red bars, respectively. Astrid is used to label significantly enriched categories in the swimbladder (FDR<0.01).</p>", "links"=>[], "tags"=>["ontology", "slim", "classification", "swimbladder", "transcriptome", "molecular", "cellular"], "article_id"=>411592, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Weiling Zheng", "Zhengyuan Wang", "John E. Collins", "Robert M. Andrews", "Derek Stemple", "Zhiyuan Gong"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024019.g003", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_ontology_slim_classification_for_the_entire_swimbladder_transcriptome_under_Biological_process_Molecular_function_and_Cellular_component_classifications_/411592", "title"=>"Gene ontology slim classification for the entire swimbladder transcriptome under Biological process, Molecular function and Cellular component classifications.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-08-26 00:26:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/741643"], "description"=>"<p>Top 50 enriched Unigenes in the swimbladder with annotation.</p>", "links"=>[], "tags"=>["50", "enriched", "unigenes", "swimbladder"], "article_id"=>412014, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Weiling Zheng", "Zhengyuan Wang", "John E. Collins", "Robert M. Andrews", "Derek Stemple", "Zhiyuan Gong"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024019.t001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Top_50_enriched_Unigenes_in_the_swimbladder_with_annotation_/412014", "title"=>"Top 50 enriched Unigenes in the swimbladder with annotation.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-08-26 00:33:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/741159"], "description"=>"<p>The relative expression level of the genes selected was shown in log<sub>2</sub> fold change as compared with a housekeeping gene, <i>ef1a</i> (10680.1 RKPM).</p>", "links"=>[], "tags"=>["validation", "rna-seq"], "article_id"=>411531, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Weiling Zheng", "Zhengyuan Wang", "John E. Collins", "Robert M. Andrews", "Derek Stemple", "Zhiyuan Gong"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024019.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Real_time_validation_of_RNA_seq_data_/411531", "title"=>"Real-time validation of RNA-seq data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-08-26 00:25:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/741690"], "description"=>"<p>*NA, P value not available because the transcripts were detected only in the swimbladder.ummary of sequencing results.f Gene Ontology terms in the swimbladder enriched gene list.</p>", "links"=>[], "tags"=>["20", "enriched", "transcription", "factors"], "article_id"=>412059, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Weiling Zheng", "Zhengyuan Wang", "John E. Collins", "Robert M. Andrews", "Derek Stemple", "Zhiyuan Gong"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024019.t002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Top_20_enriched_transcription_factors_in_the_swimbladder_/412059", "title"=>"Top 20 enriched transcription factors in the swimbladder.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-08-26 00:34:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/741557"], "description"=>"<p>Each intersection of the two zebrafish and human or mouse tissues was split into two cells. Upper cell shows NES, and lower cell shows the corresponding FDR. **: very significant (p<0.001), *: significant (p<0.05).</p>", "links"=>[], "tags"=>["zebrafish", "transcriptome", "tissues"], "article_id"=>411931, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Weiling Zheng", "Zhengyuan Wang", "John E. Collins", "Robert M. Andrews", "Derek Stemple", "Zhiyuan Gong"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024019.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_zebrafish_and_human_a_or_mouse_b_transcriptome_tissues_by_GSEA_/411931", "title"=>"Comparison of zebrafish and human (a) or mouse (b) transcriptome tissues by GSEA.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-08-26 00:32:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/741403"], "description"=>"<p>Expression of <i>hoxc4a</i> in the swimbladder at 36 hpf (<b>a</b>), 60 hpf (<b>e</b>) and 72 hpf (<b>i, m</b>). (<b>b, f, j, n</b>) Expression of <i>hoxc6a</i> in the swimbladder at 36 hpf (<b>b</b>), 60 hpf (<b>f</b>) and 72 hpf (<b>j, n</b>). (<b>c, g, k, o</b>) Expression of <i>hoxc8a</i> in the swimbladder at 36 hpf (<b>c</b>), 60 hpf (<b>g</b>) and 72 hpf (<b>k, o</b>). (<b>d, h, l, p</b>) Expression of foxf1 in the swimbladder at 36 hpf (<b>d</b>), 60 hpf (<b>h</b>), and 72 hpf (<b>l, p</b>). Panels (<b>a–l</b>) are lateral view of embryos after whole mount in situ hybridization and panels (<b>m–p</b>) are cross-sections of in situ hybridized embryos. Swimbladder is indicated by red dashed-line circles or red arrows. Numbers are used to mark the position of somite 1–4.</p>", "links"=>[], "tags"=>["zebrafish"], "article_id"=>411777, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Weiling Zheng", "Zhengyuan Wang", "John E. Collins", "Robert M. Andrews", "Derek Stemple", "Zhiyuan Gong"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024019.g005", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_of_hoxc4a_hoxc6a_and_hoxc8a_in_developing_zebrafish_swimbladder_a_e_i_m_/411777", "title"=>"Expression of <i>hoxc4a</i>, <i>hoxc6a</i> and <i>hoxc8a</i> in developing zebrafish swimbladder. (a, e, i, m).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-08-26 00:29:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/741108"], "description"=>"<p>Categories of transcript abundance were assigned by setting the lower limit of the count number that includes the transcript as a category member. The percentages of total transcript counts and number of different transcript entries per category are plotted on a logarithmic scale (base 10).</p>", "links"=>[], "tags"=>["transcript", "entries", "counts", "abundance"], "article_id"=>411474, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Weiling Zheng", "Zhengyuan Wang", "John E. Collins", "Robert M. Andrews", "Derek Stemple", "Zhiyuan Gong"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024019.g001", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_transcript_entries_and_total_transcript_counts_over_different_tag_abundance_categories_/411474", "title"=>"Distribution of transcript entries and total transcript counts over different tag abundance categories.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-08-26 00:24:34"}

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