miRNA Repertoires of Demosponges Stylissa carteri and Xestospongia testudinaria
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{"title"=>"miRNA repertoires of demosponges Stylissa carteri and Xestospongia testudinaria", "type"=>"journal", "authors"=>[{"first_name"=>"Yi Jin", "last_name"=>"Liew", "scopus_author_id"=>"55892374300"}, {"first_name"=>"Taewoo", "last_name"=>"Ryu", "scopus_author_id"=>"16508181500"}, {"first_name"=>"Manuel", "last_name"=>"Aranda", "scopus_author_id"=>"7005278191"}, {"first_name"=>"Timothy", "last_name"=>"Ravasi", "scopus_author_id"=>"6603069555"}], "year"=>2016, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"608920733", "scopus"=>"2-s2.0-84960533478", "isbn"=>"1932-6203 (Electronic) 1932-6203 (Linking)", "pmid"=>"26871907", "sgr"=>"84960533478", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0149080"}, "id"=>"11d6d327-c012-354e-97ef-a2ba63a6cfd5", "abstract"=>"MicroRNAs (miRNAs) are small regulatory RNAs that are involved in many biological process in eukaryotes. They play a crucial role in modulating genetic expression of their targets, which makes them integral components of transcriptional regulatory networks. As sponges (phylum Porifera) are commonly considered the most basal metazoan, the in-depth capture of miRNAs from these organisms provides additional clues to the evolution of miRNA families in metazoans. Here, we identified the core proteins involved in the biogenesis of miRNAs, and obtained evidence for bona fide miRNA sequences for two marine sponges Stylissa carteri and Xestospongia testudinaria (11 and 19 respectively). Our analysis identified several miRNAs that are conserved amongst demosponges, and revealed that all of the novel miRNAs identified in these two species are specific to the class Demospongiae.", "link"=>"http://www.mendeley.com/research/mirna-repertoires-demosponges-stylissa-carteri-xestospongia-testudinaria", "reader_count"=>10, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>4, "Student > Bachelor"=>1, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>4, "Student > Bachelor"=>1, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>5, "Chemistry"=>2}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>5}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Norway"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/3981385", "https://ndownloader.figshare.com/files/3981577", "https://ndownloader.figshare.com/files/3981568", "https://ndownloader.figshare.com/files/3981550", "https://ndownloader.figshare.com/files/3981520", "https://ndownloader.figshare.com/files/3981502", "https://ndownloader.figshare.com/files/3981493", "https://ndownloader.figshare.com/files/3981463", "https://ndownloader.figshare.com/files/3981442", "https://ndownloader.figshare.com/files/3981430", "https://ndownloader.figshare.com/files/3981409", "https://ndownloader.figshare.com/files/3981391", "https://ndownloader.figshare.com/files/3981589"], "description"=>"<div><p>MicroRNAs (miRNAs) are small regulatory RNAs that are involved in many biological process in eukaryotes. They play a crucial role in modulating genetic expression of their targets, which makes them integral components of transcriptional regulatory networks. As sponges (phylum Porifera) are commonly considered the most basal metazoan, the in-depth capture of miRNAs from these organisms provides additional clues to the evolution of miRNA families in metazoans. Here, we identified the core proteins involved in the biogenesis of miRNAs, and obtained evidence for <i>bona fide</i> miRNA sequences for two marine sponges <i>Stylissa carteri</i> and <i>Xestospongia testudinaria</i> (11 and 19 respectively). Our analysis identified several miRNAs that are conserved amongst demosponges, and revealed that all of the novel miRNAs identified in these two species are specific to the class Demospongiae.</p></div>", "links"=>[], "tags"=>["Demosponges Stylissa carteri", "phylum Porifera", "miRNA sequences", "basal metazoan", "marine sponges Stylissa carteri", "integral components", "miRNA families", "Xestospongia testudinaria MicroRNAs", "core proteins", "novel miRNAs", "miRNA Repertoires", "class Demospongiae"], "article_id"=>2343328, "categories"=>["Biochemistry", "Physical Sciences not elsewhere classified", "Cell Biology", "Genetics", "Molecular Biology", "Evolutionary Biology", "Ecology", "Biological Sciences not elsewhere classified", "Infectious Diseases", "Plant Biology", "Computational Biology"], "users"=>["Yi Jin Liew", "Taewoo Ryu", "Manuel Aranda", "Timothy Ravasi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0149080.s001", "https://dx.doi.org/10.1371/journal.pone.0149080.s012", "https://dx.doi.org/10.1371/journal.pone.0149080.s011", "https://dx.doi.org/10.1371/journal.pone.0149080.s010", "https://dx.doi.org/10.1371/journal.pone.0149080.s009", "https://dx.doi.org/10.1371/journal.pone.0149080.s008", "https://dx.doi.org/10.1371/journal.pone.0149080.s007", "https://dx.doi.org/10.1371/journal.pone.0149080.s006", "https://dx.doi.org/10.1371/journal.pone.0149080.s005", "https://dx.doi.org/10.1371/journal.pone.0149080.s004", "https://dx.doi.org/10.1371/journal.pone.0149080.s003", "https://dx.doi.org/10.1371/journal.pone.0149080.s002", "https://dx.doi.org/10.1371/journal.pone.0149080.s013"], "stats"=>{"downloads"=>8, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/miRNA_Repertoires_of_Demosponges_i_Stylissa_carteri_i_and_i_Xestospongia_testudinaria_i_/2343328", "title"=>"miRNA Repertoires of Demosponges <i>Stylissa carteri</i> and <i>Xestospongia testudinaria</i>", "pos_in_sequence"=>1, "defined_type"=>4, "published_date"=>"2016-02-12 07:56:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/3981760"], "description"=>"<p>The statistics of reads used for the miRNA identification.</p>", "links"=>[], "tags"=>["Demosponges Stylissa carteri", "phylum Porifera", "miRNA sequences", "basal metazoan", "marine sponges Stylissa carteri", "integral components", "miRNA families", "Xestospongia testudinaria MicroRNAs", "core proteins", "novel miRNAs", "miRNA Repertoires", "class Demospongiae"], "article_id"=>2343541, "categories"=>["Biochemistry", "Physical Sciences not elsewhere classified", "Cell Biology", "Genetics", "Molecular Biology", "Evolutionary Biology", "Ecology", "Biological Sciences not elsewhere classified", "Infectious Diseases", "Plant Biology", "Computational Biology"], "users"=>["Yi Jin Liew", "Taewoo Ryu", "Manuel Aranda", "Timothy Ravasi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0149080.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_statistics_of_reads_used_for_the_miRNA_identification_/2343541", "title"=>"The statistics of reads used for the miRNA identification.", "pos_in_sequence"=>4, "defined_type"=>3, "published_date"=>"2016-02-12 07:56:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/3981871"], "description"=>"<p>miRNAs in bold are the mature miRNA, while the unbolded ones are star sequences.</p>", "links"=>[], "tags"=>["Demosponges Stylissa carteri", "phylum Porifera", "miRNA sequences", "basal metazoan", "marine sponges Stylissa carteri", "integral components", "miRNA families", "Xestospongia testudinaria MicroRNAs", "core proteins", "novel miRNAs", "miRNA Repertoires", "class Demospongiae"], "article_id"=>2343607, "categories"=>["Biochemistry", "Physical Sciences not elsewhere classified", "Cell Biology", "Genetics", "Molecular Biology", "Evolutionary Biology", "Ecology", "Biological Sciences not elsewhere classified", "Infectious Diseases", "Plant Biology", "Computational Biology"], "users"=>["Yi Jin Liew", "Taewoo Ryu", "Manuel Aranda", "Timothy Ravasi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0149080.t003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Number_of_reads_present_in_i_S_i_i_carteri_i_and_i_X_i_i_testudinaria_i_that_matches_known_sequences_in_i_A_i_i_queenslandica_i_/2343607", "title"=>"Number of reads present in <i>S</i>. <i>carteri</i> and <i>X</i>. <i>testudinaria</i> that matches known sequences in <i>A</i>. <i>queenslandica</i>.", "pos_in_sequence"=>6, "defined_type"=>3, "published_date"=>"2016-02-12 07:56:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/3981820"], "description"=>"<p>Abbreviations used are ‘aqu’: <i>A</i>. <i>queenslandica</i>; ‘sca’: <i>S</i>. <i>carteri</i>; ‘xte’: <i>X</i>. <i>testudinaria</i>.</p>", "links"=>[], "tags"=>["Demosponges Stylissa carteri", "phylum Porifera", "miRNA sequences", "basal metazoan", "marine sponges Stylissa carteri", "integral components", "miRNA families", "Xestospongia testudinaria MicroRNAs", "core proteins", "novel miRNAs", "miRNA Repertoires", "class Demospongiae"], "article_id"=>2343580, "categories"=>["Biochemistry", "Physical Sciences not elsewhere classified", "Cell Biology", "Genetics", "Molecular Biology", "Evolutionary Biology", "Ecology", "Biological Sciences not elsewhere classified", "Infectious Diseases", "Plant Biology", "Computational Biology"], "users"=>["Yi Jin Liew", "Taewoo Ryu", "Manuel Aranda", "Timothy Ravasi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0149080.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/List_of_11_i_bona_fide_i_miRNAs_in_i_S_i_i_carteri_i_and_19_in_i_X_i_i_testudinaria_i_/2343580", "title"=>"List of 11 <i>bona fide</i> miRNAs in <i>S</i>. <i>carteri</i> and 19 in <i>X</i>. <i>testudinaria</i>.", "pos_in_sequence"=>5, "defined_type"=>3, "published_date"=>"2016-02-12 07:56:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/3981643"], "description"=>"<p>Trees were constructed for (A) Argonaute, (B) Piwi, (C) Dicer, (D) Drosha, (E) Pasha, and (F) HEN1. (A), (D), and (F) were constructed using the LG+G amino acid substitution model, while (B), (C), and (E) were constructed using the LG+I+G model. Bootstrap support values are indicated above the branches. Species abbreviations: Ath, <i>Arabidopsis thaliana</i>; Aqu, <i>Amphimedon queenslandica</i>; Cel, <i>Caenorhabditis elegans</i>; Dme, <i>Drosophila melanogaster</i>; Efl, <i>Ephydatia fluviatilis</i>; Hsa, <i>Homo sapiens</i>; Hvu, <i>Hydra vulgaris</i>; Nve, <i>Nematostella vectensis</i>; Sca, <i>S</i>. <i>carteri</i>; Spi, <i>Stylophora pistillata</i>; Spu, <i>Strongylocentrotus purpuratus</i>; and Xte, <i>X</i>. <i>testudinaria</i>. <i>A</i>. <i>thaliana</i> sequences were selected as the outgroup when available. For Piwi, Drosha, and Pasha (whose protein families are not found in plants), sponge sequences were chosen as the outgroup, as they phylogenetically form the most basal clade in the tree.</p>", "links"=>[], "tags"=>["Demosponges Stylissa carteri", "phylum Porifera", "miRNA sequences", "basal metazoan", "marine sponges Stylissa carteri", "integral components", "miRNA families", "Xestospongia testudinaria MicroRNAs", "core proteins", "novel miRNAs", "miRNA Repertoires", "class Demospongiae"], "article_id"=>2343484, "categories"=>["Biochemistry", "Physical Sciences not elsewhere classified", "Cell Biology", "Genetics", "Molecular Biology", "Evolutionary Biology", "Ecology", "Biological Sciences not elsewhere classified", "Infectious Diseases", "Plant Biology", "Computational Biology"], "users"=>["Yi Jin Liew", "Taewoo Ryu", "Manuel Aranda", "Timothy Ravasi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0149080.g001", "stats"=>{"downloads"=>1, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Maximum_likelihood_phylogenies_of_the_core_proteins_involved_in_small_RNA_biogenesis_/2343484", "title"=>"Maximum-likelihood phylogenies of the core proteins involved in small RNA biogenesis.", "pos_in_sequence"=>2, "defined_type"=>1, "published_date"=>"2016-02-12 07:56:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/3981688"], "description"=>"<p>Homologues of (A) aqu-miR-2015, (B) aqu-miR-2016, (C) aqu-miR-2017, (D) aqu-miR-2018, (E) aqu-miR-2019, (F) aqu-miR-2020, and (G) aqu-miR-2021 were identified in <i>S</i>. <i>carteri</i> and <i>X</i>. <i>testudinaria</i>. The miRNA sequences from the 5’ and 3’ arms are presented on the left and right, respectively. The bolded name denotes the arm that had more reads mapped to it (i.e., the mature arm for that miRNA). Bases are coloured to enable visualisation of the conservation level, as follows: dark blue, > 80%; blue, > 60%; light blue, > 40%; uncoloured, ≤ 40%). The abbreviations are as described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0149080#pone.0149080.g001\" target=\"_blank\">Fig 1</a>.</p>", "links"=>[], "tags"=>["Demosponges Stylissa carteri", "phylum Porifera", "miRNA sequences", "basal metazoan", "marine sponges Stylissa carteri", "integral components", "miRNA families", "Xestospongia testudinaria MicroRNAs", "core proteins", "novel miRNAs", "miRNA Repertoires", "class Demospongiae"], "article_id"=>2343502, "categories"=>["Biochemistry", "Physical Sciences not elsewhere classified", "Cell Biology", "Genetics", "Molecular Biology", "Evolutionary Biology", "Ecology", "Biological Sciences not elsewhere classified", "Infectious Diseases", "Plant Biology", "Computational Biology"], "users"=>["Yi Jin Liew", "Taewoo Ryu", "Manuel Aranda", "Timothy Ravasi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0149080.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Alignments_of_predicted_i_S_i_i_carteri_i_and_i_X_i_i_testudinaria_i_miRNAs_against_known_i_A_i_i_queenslandica_i_miRNAs_/2343502", "title"=>"Alignments of predicted <i>S</i>. <i>carteri</i> and <i>X</i>. <i>testudinaria</i> miRNAs against known <i>A</i>. <i>queenslandica</i> miRNAs.", "pos_in_sequence"=>3, "defined_type"=>1, "published_date"=>"2016-02-12 07:56:29"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2016-01-01T00:00:00Z", "end_date"=>"2016-12-31T00:00:00Z", "subject_areas"=>[]}
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