<?xml version="1.0" encoding="utf-8"?>
<TEI xmlns="http://www.tei-c.org/ns/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:hal="http://hal.archives-ouvertes.fr/" xmlns:gml="http://www.opengis.net/gml/3.3/" xmlns:gmlce="http://www.opengis.net/gml/3.3/ce" version="1.1" xsi:schemaLocation="http://www.tei-c.org/ns/1.0 http://api.archives-ouvertes.fr/documents/aofr-sword.xsd">
  <teiHeader>
    <fileDesc>
      <titleStmt>
        <title>HAL TEI export of hal-03239739</title>
      </titleStmt>
      <publicationStmt>
        <distributor>CCSD</distributor>
        <availability status="restricted">
          <licence target="https://creativecommons.org/publicdomain/zero/1.0/">CC0 1.0 - Universal</licence>
        </availability>
        <date when="2026-05-26T15:32:30+02:00"/>
      </publicationStmt>
      <sourceDesc>
        <p part="N">HAL API Platform</p>
      </sourceDesc>
    </fileDesc>
  </teiHeader>
  <text>
    <body>
      <listBibl>
        <biblFull>
          <titleStmt>
            <title xml:lang="en">Sequencing, de novo assembly and annotation of the genome of the scleractinian coral, Pocillopora acuta</title>
            <author role="aut">
              <persName>
                <forename type="first">Jeremie</forename>
                <surname>Vidal-Dupiol</surname>
              </persName>
              <email type="md5">ccd7d126edfbaad899f04dd28760d9a1</email>
              <email type="domain">ifremer.fr</email>
              <idno type="idhal" notation="string">jeremie-vidal-dupiol</idno>
              <idno type="idhal" notation="numeric">747176</idno>
              <idno type="halauthorid" notation="string">53791-747176</idno>
              <idno type="RESEARCHERID">http://www.researcherid.com/rid/https://publons.com/researcher/2843367/jeremie-vidal-dupiol/</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-0577-2953</idno>
              <idno type="IDREF">https://www.idref.fr/199462380</idno>
              <affiliation ref="#struct-1100741"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Cristian</forename>
                <surname>Chaparro</surname>
              </persName>
              <email type="md5">57c6d7c7a71199140a2e4544dab55967</email>
              <email type="domain">univ-perp.fr</email>
              <idno type="idhal" notation="string">cristian-chaparro</idno>
              <idno type="idhal" notation="numeric">172039</idno>
              <idno type="halauthorid" notation="string">4864-172039</idno>
              <idno type="RESEARCHERID">http://www.researcherid.com/rid/D-1427-2015</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-5162-349X</idno>
              <idno type="IDREF">https://www.idref.fr/253122988</idno>
              <idno type="RESEARCHERID">http://www.researcherid.com/rid/http://www.researcherid.com/rid/D-1427-2015</idno>
              <affiliation ref="#struct-1100741"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Marine</forename>
                <surname>Pratlong</surname>
              </persName>
              <email type="md5">06ae8abae8271bb1f1114d7837e422c9</email>
              <email type="domain">gmail.fr</email>
              <idno type="idhal" notation="numeric">773613</idno>
              <idno type="halauthorid" notation="string">901089-773613</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-3406-9829</idno>
              <affiliation ref="#struct-188653"/>
              <affiliation ref="#struct-1223753"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Pierre</forename>
                <surname>Pontarotti</surname>
              </persName>
              <email type="md5">6f160881a5764960b1b3f5fece07d785</email>
              <email type="domain">univ-amu.fr</email>
              <idno type="idhal" notation="string">pontarotti</idno>
              <idno type="idhal" notation="numeric">741162</idno>
              <idno type="halauthorid" notation="string">18192-741162</idno>
              <idno type="ORCID">https://orcid.org/0000-0001-7202-3648</idno>
              <idno type="IDREF">https://www.idref.fr/14869196X</idno>
              <affiliation ref="#struct-1223753"/>
              <affiliation ref="#struct-441569"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Christoph</forename>
                <surname>Grunau</surname>
              </persName>
              <email type="md5">fa3ff922a470ba225fa71c81d69f5360</email>
              <email type="domain">univ-perp.fr</email>
              <idno type="idhal" notation="string">christoph-grunau</idno>
              <idno type="idhal" notation="numeric">171567</idno>
              <idno type="halauthorid" notation="string">5082-171567</idno>
              <idno type="RESEARCHERID">http://www.researcherid.com/rid/A-6989-2010</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-2161-412X</idno>
              <idno type="IDREF">https://www.idref.fr/17660832X</idno>
              <idno type="RESEARCHERID">http://www.researcherid.com/rid/http://www.researcherid.com/rid/A-6989-2010</idno>
              <affiliation ref="#struct-1100741"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Guillaume</forename>
                <surname>Mitta</surname>
              </persName>
              <email type="md5">d442d2596ac0ec3defc3d68838edf6a2</email>
              <email type="domain">univ-perp.fr</email>
              <idno type="idhal" notation="numeric">757161</idno>
              <idno type="halauthorid" notation="string">226494-757161</idno>
              <idno type="ORCID">https://orcid.org/0000-0003-1188-1467</idno>
              <idno type="IDREF">https://www.idref.fr/11522081X</idno>
              <idno type="VIAF">https://viaf.org/viaf/216264161</idno>
              <idno type="ISNI">http://isni.org/isni/000000014026659X</idno>
              <affiliation ref="#struct-1100741"/>
            </author>
            <editor role="depositor">
              <persName>
                <forename>Anne</forename>
                <surname>Modat</surname>
              </persName>
              <email type="md5">aa4801e7909c9ac5fccd1a6a3ca461ff</email>
              <email type="domain">umontpellier.fr</email>
            </editor>
          </titleStmt>
          <editionStmt>
            <edition n="v1" type="current">
              <date type="whenSubmitted">2021-05-27 16:14:17</date>
              <date type="whenModified">2026-03-11 03:06:47</date>
              <date type="whenReleased">2021-05-28 14:14:39</date>
              <date type="whenProduced">2021-05-27</date>
              <date type="whenEndEmbargoed">2021-05-27</date>
              <ref type="file" target="https://hal.science/hal-03239739v1/document">
                <date notBefore="2021-05-27"/>
              </ref>
              <ref type="file" subtype="author" n="1" target="https://hal.science/hal-03239739v1/file/Vidal-2020-Biorxiv-sequencing-manuscrit.pdf" id="file-3239739-2843992">
                <date notBefore="2021-05-27"/>
              </ref>
              <ref type="externalLink" target="https://www.biorxiv.org/content/biorxiv/early/2020/04/19/698688.full.pdf"/>
            </edition>
            <respStmt>
              <resp>contributor</resp>
              <name key="104000">
                <persName>
                  <forename>Anne</forename>
                  <surname>Modat</surname>
                </persName>
                <email type="md5">aa4801e7909c9ac5fccd1a6a3ca461ff</email>
                <email type="domain">umontpellier.fr</email>
              </name>
            </respStmt>
          </editionStmt>
          <publicationStmt>
            <distributor>CCSD</distributor>
            <idno type="halId">hal-03239739</idno>
            <idno type="halUri">https://hal.science/hal-03239739</idno>
            <idno type="halBibtex">vidaldupiol:hal-03239739</idno>
            <idno type="halRefHtml">2021</idno>
            <idno type="halRef">2021</idno>
            <availability status="restricted">
              <licence target="https://about.hal.science/hal-authorisation-v1/">HAL Authorization<ref corresp="#file-3239739-2843992"/></licence>
            </availability>
          </publicationStmt>
          <seriesStmt>
            <idno type="stamp" n="IRD">IRD - Institut de recherche pour le développement</idno>
            <idno type="stamp" n="UNIV-AVIGNON">Université d'Avignon</idno>
            <idno type="stamp" n="CNRS">CNRS - Centre national de la recherche scientifique</idno>
            <idno type="stamp" n="UNIV-AMU">Aix Marseille Université</idno>
            <idno type="stamp" n="UNIV-PERP">Université Perpignan Via Domitia</idno>
            <idno type="stamp" n="IFREMER">IFREMER : Institut français de recherche pour l'exploitation de la mer</idno>
            <idno type="stamp" n="IMBE" corresp="OSU-INSTITUT-PYTHEAS">Institut méditerranéen de biodiversité et d'écologie marine et continentale</idno>
            <idno type="stamp" n="OSU-INSTITUT-PYTHEAS">OSU INSTITUT PYTHEAS</idno>
            <idno type="stamp" n="GIP-BE">GIP Bretagne Environnement</idno>
            <idno type="stamp" n="UNIV-MONTPELLIER">Université de Montpellier</idno>
            <idno type="stamp" n="IHPE" corresp="UNIV-MONTPELLIER">Interactions hôtes-pathologies-environnement</idno>
            <idno type="stamp" n="IHPE-2MAP">Mécanismes Moléculaires d'Adaptation et de Plasticité</idno>
            <idno type="stamp" n="IHPE-MIA">Micro-évolution des Interactions dans l'Anthropocène</idno>
            <idno type="stamp" n="UM-2015-2021" corresp="UNIV-MONTPELLIER">Université de Montpellier (2015-2021)</idno>
            <idno type="stamp" n="UM-EPE" corresp="UNIV-MONTPELLIER">Université de Montpellier - EPE</idno>
            <idno type="stamp" n="TEST3-HALCNRS">TEST3-HALCNRS</idno>
            <idno type="stamp" n="TEST4-HALCNRS">collection test</idno>
            <idno type="stamp" n="TEST5-HALCNRS">collection test 5</idno>
            <idno type="stamp" n="INEE-CNRS">Institut écologie et environnement du CNRS</idno>
            <idno type="stamp" n="ORIGINES">Institut Origines, des planètes à la vie</idno>
          </seriesStmt>
          <notesStmt/>
          <sourceDesc>
            <biblStruct>
              <analytic>
                <title xml:lang="en">Sequencing, de novo assembly and annotation of the genome of the scleractinian coral, Pocillopora acuta</title>
                <author role="aut">
                  <persName>
                    <forename type="first">Jeremie</forename>
                    <surname>Vidal-Dupiol</surname>
                  </persName>
                  <email type="md5">ccd7d126edfbaad899f04dd28760d9a1</email>
                  <email type="domain">ifremer.fr</email>
                  <idno type="idhal" notation="string">jeremie-vidal-dupiol</idno>
                  <idno type="idhal" notation="numeric">747176</idno>
                  <idno type="halauthorid" notation="string">53791-747176</idno>
                  <idno type="RESEARCHERID">http://www.researcherid.com/rid/https://publons.com/researcher/2843367/jeremie-vidal-dupiol/</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-0577-2953</idno>
                  <idno type="IDREF">https://www.idref.fr/199462380</idno>
                  <affiliation ref="#struct-1100741"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Cristian</forename>
                    <surname>Chaparro</surname>
                  </persName>
                  <email type="md5">57c6d7c7a71199140a2e4544dab55967</email>
                  <email type="domain">univ-perp.fr</email>
                  <idno type="idhal" notation="string">cristian-chaparro</idno>
                  <idno type="idhal" notation="numeric">172039</idno>
                  <idno type="halauthorid" notation="string">4864-172039</idno>
                  <idno type="RESEARCHERID">http://www.researcherid.com/rid/D-1427-2015</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-5162-349X</idno>
                  <idno type="IDREF">https://www.idref.fr/253122988</idno>
                  <idno type="RESEARCHERID">http://www.researcherid.com/rid/http://www.researcherid.com/rid/D-1427-2015</idno>
                  <affiliation ref="#struct-1100741"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Marine</forename>
                    <surname>Pratlong</surname>
                  </persName>
                  <email type="md5">06ae8abae8271bb1f1114d7837e422c9</email>
                  <email type="domain">gmail.fr</email>
                  <idno type="idhal" notation="numeric">773613</idno>
                  <idno type="halauthorid" notation="string">901089-773613</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-3406-9829</idno>
                  <affiliation ref="#struct-188653"/>
                  <affiliation ref="#struct-1223753"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Pierre</forename>
                    <surname>Pontarotti</surname>
                  </persName>
                  <email type="md5">6f160881a5764960b1b3f5fece07d785</email>
                  <email type="domain">univ-amu.fr</email>
                  <idno type="idhal" notation="string">pontarotti</idno>
                  <idno type="idhal" notation="numeric">741162</idno>
                  <idno type="halauthorid" notation="string">18192-741162</idno>
                  <idno type="ORCID">https://orcid.org/0000-0001-7202-3648</idno>
                  <idno type="IDREF">https://www.idref.fr/14869196X</idno>
                  <affiliation ref="#struct-1223753"/>
                  <affiliation ref="#struct-441569"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Christoph</forename>
                    <surname>Grunau</surname>
                  </persName>
                  <email type="md5">fa3ff922a470ba225fa71c81d69f5360</email>
                  <email type="domain">univ-perp.fr</email>
                  <idno type="idhal" notation="string">christoph-grunau</idno>
                  <idno type="idhal" notation="numeric">171567</idno>
                  <idno type="halauthorid" notation="string">5082-171567</idno>
                  <idno type="RESEARCHERID">http://www.researcherid.com/rid/A-6989-2010</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-2161-412X</idno>
                  <idno type="IDREF">https://www.idref.fr/17660832X</idno>
                  <idno type="RESEARCHERID">http://www.researcherid.com/rid/http://www.researcherid.com/rid/A-6989-2010</idno>
                  <affiliation ref="#struct-1100741"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Guillaume</forename>
                    <surname>Mitta</surname>
                  </persName>
                  <email type="md5">d442d2596ac0ec3defc3d68838edf6a2</email>
                  <email type="domain">univ-perp.fr</email>
                  <idno type="idhal" notation="numeric">757161</idno>
                  <idno type="halauthorid" notation="string">226494-757161</idno>
                  <idno type="ORCID">https://orcid.org/0000-0003-1188-1467</idno>
                  <idno type="IDREF">https://www.idref.fr/11522081X</idno>
                  <idno type="VIAF">https://viaf.org/viaf/216264161</idno>
                  <idno type="ISNI">http://isni.org/isni/000000014026659X</idno>
                  <affiliation ref="#struct-1100741"/>
                </author>
              </analytic>
              <monogr>
                <imprint/>
              </monogr>
              <idno type="biorxiv">698688</idno>
              <idno type="doi">10.1101/698688</idno>
            </biblStruct>
          </sourceDesc>
          <profileDesc>
            <langUsage>
              <language ident="en">English</language>
            </langUsage>
            <textClass>
              <classCode scheme="halDomain" n="sdv.bid.evo">Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]</classCode>
              <classCode scheme="halTypology" n="UNDEFINED">Preprints, Working Papers, ...</classCode>
              <classCode scheme="halOldTypology" n="UNDEFINED">Preprints, Working Papers, ...</classCode>
              <classCode scheme="halTreeTypology" n="UNDEFINED">Preprints, Working Papers, ...</classCode>
            </textClass>
            <abstract xml:lang="en">
              <p>Coral reefs are the most divers marine ecosystem. However, under the pressure of global changes and anthropogenic disturbances corals and coral reefs are declining worldwide. In order to better predict and understand the future of these organisms all the tools of modern biology are needed today. However, many NGS based approaches are not feasible in corals because of the lack of reference genomes. Therefore we have sequenced, de novo assembled, and annotated, the draft genome of one of the most studied coral species, Pocillopora acuta (ex damicornis ). The sequencing strategy was based on four libraries with complementary insert size and sequencing depth (180pb, 100x; 3Kb, 25x; 8kb, 12x and 20 kb, 12x). The de novo assembly was performed with Platanus (352 Mb; 25,553 scaffolds; N50 171,375 bp). 36,140 genes were annotated by RNA-seq data and 64,558 by AUGUSTUS (Hidden-Markov model). Gene functions were predicted through Blast and orthology based approaches. This new genomic resource will enable the development of a large array of genome wide studies but also shows that the de novo assembly of a coral genome is now technically feasible and economically realistic.</p>
            </abstract>
          </profileDesc>
        </biblFull>
      </listBibl>
    </body>
    <back>
      <listOrg type="structures">
        <org type="laboratory" xml:id="struct-1100741" status="VALID">
          <idno type="IdRef">189954582</idno>
          <idno type="ISNI">0000000403840099</idno>
          <idno type="RNSR">200711909U</idno>
          <idno type="ROR">https://ror.org/00zn13224</idno>
          <orgName>Interactions Hôtes-Pathogènes-Environnements</orgName>
          <orgName type="acronym">IHPE</orgName>
          <date type="start">2015-01-01</date>
          <desc>
            <address>
              <addrLine>Université de Perpignan Via Domitia Bâtiment R 52 Avenue Paul Alduy 66860 Perpignan cedex (Languedoc-Roussillon)</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://ihpe.univ-perp.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-101475" type="direct"/>
            <relation active="#struct-300022" type="direct"/>
            <relation name="UMR5244" active="#struct-441569" type="direct"/>
            <relation active="#struct-1100589" type="direct"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-188653" status="VALID">
          <idno type="IdRef">179775251</idno>
          <idno type="ISNI">0000000406002381</idno>
          <idno type="RNSR">201220339K</idno>
          <idno type="ROR">https://ror.org/0409c3995</idno>
          <orgName>Institut méditerranéen de biodiversité et d'écologie marine et continentale</orgName>
          <orgName type="acronym">IMBE</orgName>
          <date type="start">2012-01-01</date>
          <desc>
            <address>
              <addrLine>Aix Marseille Université, Campus Etoile, Faculté St-Jérôme case 421 Av. . escadrille Normandie-Niemen 13397 MARSEILLE CEDEX 20</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.imbe.fr/</ref>
          </desc>
          <listRelation>
            <relation name="UMR7263" active="#struct-195507" type="direct"/>
            <relation name="UMR7263" active="#struct-198056" type="direct"/>
            <relation name="UMR7263" active="#struct-302715" type="direct"/>
            <relation name="UMR7263" active="#struct-441569" type="direct"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-1223753" status="OLD">
          <idno type="RNSR">201822835X</idno>
          <orgName>Microbes Evolution Phylogénie et Infections</orgName>
          <orgName type="acronym">MEPHI</orgName>
          <date type="start">2019-01-01</date>
          <date type="end">2023-12-31</date>
          <desc>
            <address>
              <addrLine>IHU Méditerranée Infection, 19-21 boulevard Jean Moulin 13005 Marseille</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://mephi.eu/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-67872" type="direct"/>
            <relation active="#struct-198056" type="direct"/>
          </listRelation>
        </org>
        <org type="regroupinstitution" xml:id="struct-441569" status="VALID">
          <idno type="IdRef">02636817X</idno>
          <idno type="ISNI">0000000122597504</idno>
          <idno type="ROR">https://ror.org/02feahw73</idno>
          <orgName>Centre National de la Recherche Scientifique</orgName>
          <orgName type="acronym">CNRS</orgName>
          <date type="start">1939-10-19</date>
          <desc>
            <address>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.cnrs.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-101475" status="VALID">
          <idno type="ROR">https://ror.org/03am2jy38</idno>
          <orgName>Université de Perpignan Via Domitia</orgName>
          <orgName type="acronym">UPVD</orgName>
          <desc>
            <address>
              <addrLine>52 avenue Paul Alduy - 66860 Perpignan Cedex 9</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.univ-perp.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-300022" status="VALID">
          <idno type="IdRef">027783073</idno>
          <idno type="ISNI">0000000121634107</idno>
          <idno type="ROR">https://ror.org/044jxhp58</idno>
          <orgName>Institut Français de Recherche pour l'Exploitation de la Mer</orgName>
          <orgName type="acronym">IFREMER</orgName>
          <date type="start">1984-01-01</date>
          <desc>
            <address>
              <country key="FR"/>
            </address>
            <ref type="url">https://wwz.ifremer.fr/</ref>
          </desc>
        </org>
        <org type="regroupinstitution" xml:id="struct-1100589" status="VALID">
          <idno type="ROR">https://ror.org/051escj72</idno>
          <orgName>Université de Montpellier</orgName>
          <orgName type="acronym">UM</orgName>
          <date type="start">2022-01-01</date>
          <desc>
            <address>
              <addrLine>163 rue Auguste Broussonnet - 34090 Montpellier</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.umontpellier.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-195507" status="VALID">
          <idno type="ROR">https://ror.org/00mfpxb84</idno>
          <orgName>Avignon Université</orgName>
          <orgName type="acronym">AU</orgName>
          <desc>
            <address>
              <addrLine>74 rue Louis Pasteur - 84 029 Avignon cedex 1</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.univ-avignon.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-198056" status="VALID">
          <idno type="IdRef">15863621X</idno>
          <idno type="ISNI">0000 0001 2176 4817</idno>
          <idno type="ROR">https://ror.org/035xkbk20</idno>
          <orgName>Aix Marseille Université</orgName>
          <orgName type="acronym">AMU</orgName>
          <date type="start">2012-01-01</date>
          <desc>
            <address>
              <addrLine>Aix-Marseille UniversitéJardins du Pharo58 Boulevard Charles Livon13284 Marseille cedex 7</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.univ-amu.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-302715" status="VALID">
          <orgName>Institut de recherche pour le développement [IRD] : UMR237</orgName>
          <desc>
            <address>
              <country key="FR"/>
            </address>
          </desc>
        </org>
        <org type="institution" xml:id="struct-67872" status="VALID">
          <idno type="IdRef">050165224</idno>
          <idno type="ROR">https://ror.org/05q3vnk25</idno>
          <orgName>Institut de Recherche pour le Développement</orgName>
          <orgName type="acronym">IRD</orgName>
          <desc>
            <address>
              <addrLine>SiègeLe Sextant 44, bd de DunkerqueCS 9000913572 Marseille cedex 02</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.ird.fr/</ref>
          </desc>
        </org>
      </listOrg>
    </back>
  </text>
</TEI>