• Login
    View Item 
    •   Home
    • Research
    • Articles
    • View Item
    •   Home
    • Research
    • Articles
    • View Item
    JavaScript is disabled for your browser. Some features of this site may not work without it.

    Browse

    All of KAUSTCommunitiesIssue DateSubmit DateThis CollectionIssue DateSubmit Date

    My Account

    Login

    Quick Links

    Open Access PolicyORCID LibguidePlumX LibguideSubmit an Item

    Statistics

    Display statistics

    Identification of microRNAs in the coral Stylophora pistillata.

    • CSV
    • RefMan
    • EndNote
    • BibTex
    • RefWorks
    Thumbnail
    Name:
    Article - PLoS ONE - Identification of microRNAs in the coral Stylophora pistillata - 2014.pdf
    Size:
    1.084Mb
    Format:
    PDF
    Description:
    Article - Full Text
    Download
    Thumbnail
    Name:
    journal.pone.0091101.s001.zip
    Size:
    15.64Mb
    Format:
    Unknown
    Description:
    Supporting Information S1 - Stylophora pistillata transcriptome (43,493 genes/loci ≥250 bp, DDBJ/EMBL/GenBank accession GARY00000000). doi:10.1371/journal.pone.0091101.s001
    Download
    Thumbnail
    Name:
    journal.pone.0091101.s002.zip
    Size:
    3.288Mb
    Format:
    Unknown
    Description:
    Supporting Information S2 - Stylophora pistillata transcriptome BLASTX and GO annotation (43,493 genes/loci ≥250 bp). doi:10.1371/journal.pone.0091101.s002
    Download
    Thumbnail
    Name:
    journal.pone.0091101.s003.docx
    Size:
    17.55Kb
    Format:
    Microsoft Word 2007
    Description:
    Supporting Information S3 - Candidate RNAi proteins in Stylophora pistillata. doi:10.1371/journal.pone.0091101.s003
    Download
    Thumbnail
    Name:
    journal.pone.0091101.s004.fa
    Size:
    51.60Kb
    Format:
    Unknown
    Description:
    Supporting Information S4 - Alignment of sequences used to construct maximum-likelihood phylogenetic trees (FASTA format). doi:10.1371/journal.pone.0091101.s004
    Download
    Thumbnail
    Name:
    journal.pone.0091101.s005.eps
    Size:
    2.730Mb
    Format:
    Postscript
    Description:
    Supporting Information S5 - Graphical alignment of the PAZ domains in Argonaute and Piwi proteins. Of note are the strong conservation of glutamate (E) at position 137 (mutants produce insoluble protein) and phenylalanine (F) at position 72 (required for RNA binding). However, the phenylalanine at position 48 in D. melanogaster AGO2 (also required for RNA binding) was not conserved at all. Key residue positions are marked with red asterisks. doi:10.1371/journal.pone.0091101.s005
    Download
    Thumbnail
    Name:
    journal.pone.0091101.s006.eps
    Size:
    3.541Mb
    Format:
    Postscript
    Description:
    Supporting Information S6 - Graphical alignment of the Piwi domains in Argonaute and Piwi proteins. The catalytic DDX triad, which contributes to the slicing activity of the ribonuclease (marked in red asterisks), is located at positions 46, 140 and 284 or positions 46, 140 and 155. This triad is present in one S. pistillata candidate, but not in two others, most likely due to the transcript sequences being incomplete. doi:10.1371/journal.pone.0091101.s006
    Download
    Thumbnail
    Name:
    journal.pone.0091101.s007.eps
    Size:
    1.822Mb
    Format:
    Postscript
    Description:
    Supporting Information S7 - Graphical alignment of the first RNase III domain in Dicer and Drosha proteins. Remarkably, all of the key acidic aspartate (D) and glutamate (E) residues, which are involved in the coordination of a divalent metal cation, are conserved across the candidate homologues and known sequences. doi:10.1371/journal.pone.0091101.s007
    Download
    Thumbnail
    Name:
    journal.pone.0091101.s008.eps
    Size:
    1.485Mb
    Format:
    Postscript
    Description:
    Supporting Information S8 - Graphical alignment of the second RNase III domain in Dicer and Drosha proteins. Similarly, most of the aspartate (D) and glutamate (E) residues involved in the coordination of a divalent metal cation are conserved - perfectly conserved for the Drosha candidate (“Locus_18820”), while the Dicer candidate (“Locus_10081”) only has the first two key residues. Both sequences however align well to known Dicer and Drosha proteins. doi:10.1371/journal.pone.0091101.s008
    Download
    Thumbnail
    Name:
    journal.pone.0091101.s009.eps
    Size:
    753.9Kb
    Format:
    Postscript
    Description:
    Supporting Information S9 - Graphical alignment of the dsRNA-binding domain in Pasha. The key alanine/alanine pair (AA, positions 21 and 22) and alanine/serine pair (AS, positions 139 and 140) involved in the binding of dsRNA are also present in the S. pistillata candidate Pasha. As Pasha is an essential cofactor of Drosha, it lends support to the positive discovery of Drosha in S. pistillata. doi:10.1371/journal.pone.0091101.s009
    Download
    Thumbnail
    Name:
    journal.pone.0091101.s010.eps
    Size:
    888.9Kb
    Format:
    Postscript
    Description:
    Supporting Information S10 - Graphical alignment of the methyltransferase domain in HEN1. The residues involved in Mg2+ coordination (positions 118, 121, 122 and 123) are well-conserved across the aligned sequences; residues associated with the cofactor AdoHcy and 3′ terminus (other positions marked by a red asterisk) are also well conserved. doi:10.1371/journal.pone.0091101.s010
    Download
    Thumbnail
    Name:
    journal.pone.0091101.s011.xlsx
    Size:
    29.38Kb
    Format:
    Microsoft Excel 2007
    Description:
    Supporting Information S11 - List of additional criteria used to select bona fide miRNAs in S. pistillata from miRDeep2 results. doi:10.1371/journal.pone.0091101.s011
    Download
    Thumbnail
    Name:
    journal.pone.0091101.s012.xlsx
    Size:
    42.76Kb
    Format:
    Microsoft Excel 2007
    Description:
    Supporting Information S12 - Enriched GO terms (P<0.01) associated with the set of 31 bona fide miRNAs identified in Stylophora pistillata. doi:10.1371/journal.pone.0091101.s012
    Download
    View more filesView fewer files
    Type
    Article
    Authors
    Liew, Yi Jin cc
    Aranda, Manuel cc
    Carr, Adrian
    Baumgarten, Sebastian cc
    Zoccola, Didier cc
    Tambutté, Sylvie
    Allemand, Denis
    Micklem, Gos
    Voolstra, Christian R. cc
    KAUST Department
    Biological and Environmental Sciences and Engineering (BESE) Division
    Marine Science Program
    Red Sea Research Center (RSRC)
    Reef Genomics Lab
    Date
    2014-03-21
    Permanent link to this record
    http://hdl.handle.net/10754/323560
    
    Metadata
    Show full item record
    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.
    Citation
    Liew YJ, Aranda M, Carr A, Baumgarten S, Zoccola D, et al. (2014) Identification of MicroRNAs in the Coral Stylophora pistillata. PLoS ONE 9: e91101. doi:10.1371/journal.pone.0091101.
    Sponsors
    This project was partially funded by bursaries from Cambridge Commonwealth Trust and Trinity Hall to YJL, and an Academic Excellence Alliance (AEA) Award (Award Number 1000000533) to CRV and GM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
    Publisher
    Public Library of Science (PLoS)
    Journal
    PLoS ONE
    DOI
    10.1371/journal.pone.0091101
    PubMed ID
    24658574
    PubMed Central ID
    PMC3962355
    Additional Links
    http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0091101
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3962355/
    ae974a485f413a2113503eed53cd6c53
    10.1371/journal.pone.0091101
    Scopus Count
    Collections
    Articles; Biological and Environmental Sciences and Engineering (BESE) Division; Red Sea Research Center (RSRC); Marine Science Program; Reef Genomics, part of the Global Ocean Genome Project

    entitlement

    Related articles

    • A microRNA regulates the response of corals to thermal stress.
    • Authors: Gajigan AP, Conaco C
    • Issue date: 2017 Jul
    • Transcriptome analysis of the scleractinian coral Stylophora pistillata.
    • Authors: Karako-Lampert S, Zoccola D, Salmon-Divon M, Katzenellenbogen M, Tambutté S, Bertucci A, Hoegh-Guldberg O, Deleury E, Allemand D, Levy O
    • Issue date: 2014
    • Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals.
    • Authors: Voolstra CR, Li Y, Liew YJ, Baumgarten S, Zoccola D, Flot JF, Tambutté S, Allemand D, Aranda M
    • Issue date: 2017 Dec 14
    • Using the Acropora digitifera genome to understand coral responses to environmental change.
    • Authors: Shinzato C, Shoguchi E, Kawashima T, Hamada M, Hisata K, Tanaka M, Fujie M, Fujiwara M, Koyanagi R, Ikuta T, Fujiyama A, Miller DJ, Satoh N
    • Issue date: 2011 Jul 24
    • Eutrophication may compromise the resilience of the Red Sea coral Stylophora pistillata to global change.
    • Authors: Hall ER, Muller EM, Goulet T, Bellworthy J, Ritchie KB, Fine M
    • Issue date: 2018 Jun
    DSpace software copyright © 2002-2021  DuraSpace
    Quick Guide | Contact Us | Send Feedback
    Open Repository is a service hosted by 
    Atmire NV
     

    Export search results

    The export option will allow you to export the current search results of the entered query to a file. Different formats are available for download. To export the items, click on the button corresponding with the preferred download format.

    By default, clicking on the export buttons will result in a download of the allowed maximum amount of items. For anonymous users the allowed maximum amount is 50 search results.

    To select a subset of the search results, click "Selective Export" button and make a selection of the items you want to export. The amount of items that can be exported at once is similarly restricted as the full export.

    After making a selection, click one of the export format buttons. The amount of items that will be exported is indicated in the bubble next to export format.