Identification of MicroRNAs in the Coral Stylophora pistillata
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{"title"=>"Identification of microRNAs in the coral Stylophora pistillata", "type"=>"journal", "authors"=>[{"first_name"=>"Yi Jin", "last_name"=>"Liew", "scopus_author_id"=>"55892374300"}, {"first_name"=>"Manuel", "last_name"=>"Aranda", "scopus_author_id"=>"7005278191"}, {"first_name"=>"Adrian", "last_name"=>"Carr", "scopus_author_id"=>"7402236824"}, {"first_name"=>"Sebastian", "last_name"=>"Baumgarten", "scopus_author_id"=>"53864612000"}, {"first_name"=>"Didier", "last_name"=>"Zoccola", "scopus_author_id"=>"6603258913"}, {"first_name"=>"Sylvie", "last_name"=>"Tambutté", "scopus_author_id"=>"6507063305"}, {"first_name"=>"Denis", "last_name"=>"Allemand", "scopus_author_id"=>"7003604806"}, {"first_name"=>"Gos", "last_name"=>"Micklem", "scopus_author_id"=>"6602388532"}, {"first_name"=>"Christian R.", "last_name"=>"Voolstra", "scopus_author_id"=>"25224158700"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"24658574", "doi"=>"10.1371/journal.pone.0091101", "sgr"=>"84899125298", "isbn"=>"1932-6203", "scopus"=>"2-s2.0-84899125298", "issn"=>"19326203", "pui"=>"372921633"}, "id"=>"a8567494-6764-30eb-b79e-50264e721ff7", "abstract"=>"Coral reefs are major contributors to marine biodiversity. However, they are in rapid decline due to global environmental changes such as rising sea surface temperatures, ocean acidification, and pollution. Genomic and transcriptomic analyses have broadened our understanding of coral biology, but a study of the microRNA (miRNA) repertoire of corals is missing. miRNAs constitute a class of small non-coding RNAs of ∼22 nt in size that play crucial roles in development, metabolism, and stress response in plants and animals alike. In this study, we examined the coral Stylophora pistillata for the presence of miRNAs and the corresponding core protein machinery required for their processing and function. Based on small RNA sequencing, we present evidence for 31 bona fide microRNAs, 5 of which (miR-100, miR-2022, miR-2023, miR-2030, and miR-2036) are conserved in other metazoans. Homologues of Argonaute, Piwi, Dicer, Drosha, Pasha, and HEN1 were identified in the transcriptome of S. pistillata based on strong sequence conservation with known RNAi proteins, with additional support derived from phylogenetic trees. Examination of putative miRNA gene targets indicates potential roles in development, metabolism, immunity, and biomineralisation for several of the microRNAs. Here, we present first evidence of a functional RNAi machinery and five conserved miRNAs in S. pistillata, implying that miRNAs play a role in organismal biology of scleractinian corals. Analysis of predicted miRNA target genes in S. pistillata suggests potential roles of miRNAs in symbiosis and coral calcification. Given the importance of miRNAs in regulating gene expression in other metazoans, further expression analyses of small non-coding RNAs in transcriptional studies of corals should be informative about miRNA-affected processes and pathways.", "link"=>"http://www.mendeley.com/research/identification-micrornas-coral-stylophora-pistillata-1", "reader_count"=>70, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>1, "Researcher"=>14, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>24, "Student > Postgraduate"=>6, "Student > Master"=>10, "Student > Bachelor"=>5, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>1, "Researcher"=>14, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>24, "Student > Postgraduate"=>6, "Student > Master"=>10, "Student > Bachelor"=>5, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Environmental Science"=>5, "Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>51, "Medicine and Dentistry"=>1, "Arts and Humanities"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>51}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>5}, "Environmental Science"=>{"Environmental Science"=>5}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"New Zealand"=>1, "Colombia"=>1, "United States"=>3, "Luxembourg"=>1, "Brazil"=>1, "France"=>1, "Germany"=>1}, "group_count"=>2}

Scopus | Further Information

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/1430248"], "description"=>"1<p>Note: the names of the miRNAs are temporary. miRBase (the miRNA registry) only accepts submissions of new miRNAs after the manuscript has been accepted for publication.</p>", "links"=>[], "tags"=>["Biochemistry", "Nucleic acids", "rna", "cell biology", "Molecular cell biology", "Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "Comparative genomics", "Genome complexity", "Genome evolution", "ecology", "Evolutionary ecology", "Marine ecology", "genetics", "epigenetics", "RNA interference", "genomics", "Evolutionary biology", "Marine biology", "Coral reefs", "corals", "31", "mirdeep2-predicted", "mirnas"], "article_id"=>970082, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Yi Jin Liew", "Manuel Aranda", "Adrian Carr", "Sebastian Baumgarten", "Didier Zoccola", "Sylvie Tambutté", "Denis Allemand", "Gos Micklem", "Christian R. Voolstra"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091101.t002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Set_of_31_bona_fide_miRDeep2_predicted_miRNAs_in_S_pistillata_/970082", "title"=>"Set of 31 <i>bona fide</i> miRDeep2-predicted miRNAs in <i>S. pistillata</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-21 03:00:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/1430284", "https://ndownloader.figshare.com/files/1430285", "https://ndownloader.figshare.com/files/1430286", "https://ndownloader.figshare.com/files/1430287", "https://ndownloader.figshare.com/files/1430288", "https://ndownloader.figshare.com/files/1430289", "https://ndownloader.figshare.com/files/1430290", "https://ndownloader.figshare.com/files/1430291", "https://ndownloader.figshare.com/files/1430292", "https://ndownloader.figshare.com/files/1430293", "https://ndownloader.figshare.com/files/1430294", "https://ndownloader.figshare.com/files/1430295"], "description"=>"<div><p>Coral reefs are major contributors to marine biodiversity. However, they are in rapid decline due to global environmental changes such as rising sea surface temperatures, ocean acidification, and pollution. Genomic and transcriptomic analyses have broadened our understanding of coral biology, but a study of the microRNA (miRNA) repertoire of corals is missing. miRNAs constitute a class of small non-coding RNAs of ∼22 nt in size that play crucial roles in development, metabolism, and stress response in plants and animals alike. In this study, we examined the coral <i>Stylophora pistillata</i> for the presence of miRNAs and the corresponding core protein machinery required for their processing and function. Based on small RNA sequencing, we present evidence for 31 <i>bona fide</i> microRNAs, 5 of which (miR-100, miR-2022, miR-2023, miR-2030, and miR-2036) are conserved in other metazoans. Homologues of Argonaute, Piwi, Dicer, Drosha, Pasha, and HEN1 were identified in the transcriptome of <i>S. pistillata</i> based on strong sequence conservation with known RNAi proteins, with additional support derived from phylogenetic trees. Examination of putative miRNA gene targets indicates potential roles in development, metabolism, immunity, and biomineralisation for several of the microRNAs. Here, we present first evidence of a functional RNAi machinery and five conserved miRNAs in <i>S. pistillata</i>, implying that miRNAs play a role in organismal biology of scleractinian corals. Analysis of predicted miRNA target genes in <i>S. pistillata</i> suggests potential roles of miRNAs in symbiosis and coral calcification. Given the importance of miRNAs in regulating gene expression in other metazoans, further expression analyses of small non-coding RNAs in transcriptional studies of corals should be informative about miRNA-affected processes and pathways.</p></div>", "links"=>[], "tags"=>["Biochemistry", "Nucleic acids", "rna", "cell biology", "Molecular cell biology", "Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "Comparative genomics", "Genome complexity", "Genome evolution", "ecology", "Evolutionary ecology", "Marine ecology", "genetics", "epigenetics", "RNA interference", "genomics", "Evolutionary biology", "Marine biology", "Coral reefs", "corals", "micrornas", "coral"], "article_id"=>970114, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Yi Jin Liew", "Manuel Aranda", "Adrian Carr", "Sebastian Baumgarten", "Didier Zoccola", "Sylvie Tambutté", "Denis Allemand", "Gos Micklem", "Christian R. Voolstra"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0091101.s001", "https://dx.doi.org/10.1371/journal.pone.0091101.s002", "https://dx.doi.org/10.1371/journal.pone.0091101.s003", "https://dx.doi.org/10.1371/journal.pone.0091101.s004", "https://dx.doi.org/10.1371/journal.pone.0091101.s005", "https://dx.doi.org/10.1371/journal.pone.0091101.s006", "https://dx.doi.org/10.1371/journal.pone.0091101.s007", "https://dx.doi.org/10.1371/journal.pone.0091101.s008", "https://dx.doi.org/10.1371/journal.pone.0091101.s009", "https://dx.doi.org/10.1371/journal.pone.0091101.s010", "https://dx.doi.org/10.1371/journal.pone.0091101.s011", "https://dx.doi.org/10.1371/journal.pone.0091101.s012"], "stats"=>{"downloads"=>27, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Identification_of_MicroRNAs_in_the_Coral_Stylophora_pistillata_/970114", "title"=>"Identification of MicroRNAs in the Coral <i>Stylophora pistillata</i>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-03-21 03:00:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/1430250"], "description"=>"<p>Presence of RNAi proteins in <i>S. pistillata</i> in comparison to Cnidaria and other model organisms (‘+’: presence, ‘−’: absence, ‘?’: not determined).</p>", "links"=>[], "tags"=>["Biochemistry", "Nucleic acids", "rna", "cell biology", "Molecular cell biology", "Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "Comparative genomics", "Genome complexity", "Genome evolution", "ecology", "Evolutionary ecology", "Marine ecology", "genetics", "epigenetics", "RNA interference", "genomics", "Evolutionary biology", "Marine biology", "Coral reefs", "corals", "rnai", "proteins", "cnidaria", "organisms"], "article_id"=>970084, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Yi Jin Liew", "Manuel Aranda", "Adrian Carr", "Sebastian Baumgarten", "Didier Zoccola", "Sylvie Tambutté", "Denis Allemand", "Gos Micklem", "Christian R. Voolstra"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091101.t001", "stats"=>{"downloads"=>3, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Presence_of_RNAi_proteins_in_S_pistillata_in_comparison_to_Cnidaria_and_other_model_organisms__presence__absence__not_determined_/970084", "title"=>"Presence of RNAi proteins in <i>S. pistillata</i> in comparison to Cnidaria and other model organisms (‘+’: presence, ‘−’: absence, ‘?’: not determined).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-21 03:00:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/1430247"], "description"=>"<p>The mature sequences are shown on the left, while star sequences are on the right. Sequences were obtained from miRBase (version 20). The mature hma-miR-2030 aligned best with miR-2030* sequences from <i>N. vectensis</i> and <i>S. pistillata</i>. Sequences marked with a tilde (nve-miR-2022*, hma-miR-2022*, and hma-miR-2030) are miRNAs that we derived based on the alignment of the respective pre-miRNA sequences obtained from miRBase against <i>S. pistillata</i> miRNAs. Bases were coloured to provide visual indication of conservation (dark blue: >80%; blue: >60%; light blue: >40%; uncoloured otherwise). Abbreviations used are ‘dme’: <i>D. melanogaster</i>; ‘hma’: <i>H. magnipapillata</i>; ‘hsa’: <i>H. sapiens</i>; ‘nve’: <i>N. vectensis</i>; and ‘spi’: <i>S. pistillata</i>.</p>", "links"=>[], "tags"=>["Biochemistry", "Nucleic acids", "rna", "cell biology", "Molecular cell biology", "Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "Comparative genomics", "Genome complexity", "Genome evolution", "ecology", "Evolutionary ecology", "Marine ecology", "genetics", "epigenetics", "RNA interference", "genomics", "Evolutionary biology", "Marine biology", "Coral reefs", "corals", "mirnas", "members", "mir-100", "nve-"], "article_id"=>970081, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Yi Jin Liew", "Manuel Aranda", "Adrian Carr", "Sebastian Baumgarten", "Didier Zoccola", "Sylvie Tambutté", "Denis Allemand", "Gos Micklem", "Christian R. Voolstra"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091101.g003", "stats"=>{"downloads"=>4, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alignments_of_predicted_S_pistillata_miRNAs_against_A_members_of_the_miR_100_family_B_nve_and_hma_miR_2022_C_nve_miR_2023_D_nve_miR_2030_and_E_nve_miR_2036_/970081", "title"=>"Alignments of predicted <i>S. pistillata</i> miRNAs against (A) members of the miR-100 family; (B) nve- and hma-miR-2022; (C) nve-miR-2023; (D) nve-miR-2030; and (E) nve-miR-2036.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-21 03:00:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/1430245"], "description"=>"<p>(A), (C), and (D) were constructed using the amino acid substitution model LG+G, while (B), (E), and (F) were constructed using LG+I+G. Bootstrap support values are indicated above the branches. Abbreviations used in these trees are ‘Adi’: <i>Acropora digitifera</i>; ‘Ami’: <i>Acropora millepora</i>; ‘Aqu’: <i>Amphimedon queenslandica</i> (a sponge); ‘Cel’: <i>C. elegans</i>; ‘Dme’: <i>D. melanogaster</i>; ‘Hsa’: <i>H. sapiens</i>; ‘Hvu’: <i>Hydra vulgaris</i>; ‘Nve’: <i>N. vectensis</i>; and ‘Spi’: <i>S. pistillata</i>.</p>", "links"=>[], "tags"=>["Biochemistry", "Nucleic acids", "rna", "cell biology", "Molecular cell biology", "Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "Comparative genomics", "Genome complexity", "Genome evolution", "ecology", "Evolutionary ecology", "Marine ecology", "genetics", "epigenetics", "RNA interference", "genomics", "Evolutionary biology", "Marine biology", "Coral reefs", "corals", "phylogenies", "hen1"], "article_id"=>970079, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Yi Jin Liew", "Manuel Aranda", "Adrian Carr", "Sebastian Baumgarten", "Didier Zoccola", "Sylvie Tambutté", "Denis Allemand", "Gos Micklem", "Christian R. Voolstra"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091101.g001", "stats"=>{"downloads"=>4, "page_views"=>84, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maximum_likelihood_phylogenies_of_A_Argonaute_B_Piwi_C_Dicer_D_Drosha_E_Pasha_and_F_HEN1_proteins_/970079", "title"=>"Maximum-likelihood phylogenies of (A) Argonaute, (B) Piwi, (C) Dicer, (D) Drosha, (E) Pasha, and (F) HEN1 proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-21 03:00:22"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2014-01-01T00:00:00Z", "end_date"=>"2014-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Earth sciences/Marine and aquatic sciences", "average_usage"=>[343]}]}
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