<?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-01730435</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="2026-05-19T20:18:55+02:00"/>
      </publicationStmt>
      <sourceDesc>
        <p part="N">HAL API Platform</p>
      </sourceDesc>
    </fileDesc>
  </teiHeader>
  <text>
    <body>
      <listBibl>
        <biblFull>
          <titleStmt>
            <title xml:lang="en">The Rhizome of Lokiarchaeota Illustrates the Mosaicity of Archaeal Genomes</title>
            <author role="aut">
              <persName>
                <forename type="first">Anthony</forename>
                <surname>Levasseur</surname>
              </persName>
              <idno type="halauthorid">190180-0</idno>
              <affiliation ref="#struct-57269"/>
              <affiliation ref="#struct-199392"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Vicky</forename>
                <surname>Merhej</surname>
              </persName>
              <email type="md5">3b8cf9b1d57fdcb06cc902571f39002e</email>
              <email type="domain">univ-amu.fr</email>
              <idno type="idhal" notation="numeric">768656</idno>
              <idno type="halauthorid" notation="string">715534-768656</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-8688-6943</idno>
              <affiliation ref="#struct-240602"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Emeline</forename>
                <surname>Baptiste</surname>
              </persName>
              <idno type="halauthorid">871806-0</idno>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Vikas</forename>
                <surname>Sharma</surname>
              </persName>
              <idno type="halauthorid">953751-0</idno>
              <affiliation ref="#struct-199392"/>
              <affiliation ref="#struct-241321"/>
            </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-241321"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Didier</forename>
                <surname>Raoult</surname>
              </persName>
              <email type="md5">c85d553eaec6674caeb7cb6e360587a7</email>
              <email type="domain">gmail.com</email>
              <idno type="idhal" notation="string">didier-raoult</idno>
              <idno type="idhal" notation="numeric">8465</idno>
              <idno type="halauthorid" notation="string">16046-8465</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-0633-5974</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-2895-5824</idno>
              <idno type="IDREF">https://www.idref.fr/035496169</idno>
              <idno type="GOOGLE SCHOLAR">https://scholar.google.fr/citations?user=n8EF_6kAAAAJ</idno>
              <idno type="VIAF">https://viaf.org/viaf/56752423</idno>
              <idno type="ISNI">http://isni.org/isni/0000000119638387</idno>
              <idno type="RESEARCHERID">http://www.researcherid.com/rid/A-8434-2008</idno>
              <idno type="RESEARCHERID">http://www.researcherid.com/rid/http://www.researcherid.com/rid/A-8434-2008</idno>
              <affiliation ref="#struct-199392"/>
            </author>
            <editor role="depositor">
              <persName>
                <forename>Isabelle</forename>
                <surname>COMBE</surname>
              </persName>
              <email type="md5">bab35ba509b8723b03542abc690b8507</email>
              <email type="domain">univ-amu.fr</email>
            </editor>
          </titleStmt>
          <editionStmt>
            <edition n="v1" type="current">
              <date type="whenSubmitted">2018-04-24 15:26:23</date>
              <date type="whenModified">2025-04-10 09:42:57</date>
              <date type="whenReleased">2018-04-26 12:54:49</date>
              <date type="whenProduced">2017-10</date>
              <date type="whenEndEmbargoed">2018-04-24</date>
              <ref type="file" target="https://hal.science/hal-01730435v1/document">
                <date notBefore="2018-04-24"/>
              </ref>
              <ref type="file" subtype="publisherPaid" n="1" target="https://hal.science/hal-01730435v1/file/LEVASSEURevx208.pdf" id="file-1775352-1805744">
                <date notBefore="2018-04-24"/>
              </ref>
              <ref type="externalLink" target="https://academic.oup.com/gbe/article-pdf/9/10/2635/22894223/evx208.pdf"/>
            </edition>
            <respStmt>
              <resp>contributor</resp>
              <name key="487267">
                <persName>
                  <forename>Isabelle</forename>
                  <surname>COMBE</surname>
                </persName>
                <email type="md5">bab35ba509b8723b03542abc690b8507</email>
                <email type="domain">univ-amu.fr</email>
              </name>
            </respStmt>
          </editionStmt>
          <publicationStmt>
            <distributor>CCSD</distributor>
            <idno type="halId">hal-01730435</idno>
            <idno type="halUri">https://hal.science/hal-01730435</idno>
            <idno type="halBibtex">levasseur:hal-01730435</idno>
            <idno type="halRefHtml">&lt;i&gt;Genome Biology and Evolution&lt;/i&gt;, 2017, 9 (10), pp.2635-2639. &lt;a target="_blank" href="https://dx.doi.org/10.1093/gbe/evx208"&gt;&amp;#x27E8;10.1093/gbe/evx208&amp;#x27E9;&lt;/a&gt;</idno>
            <idno type="halRef">Genome Biology and Evolution, 2017, 9 (10), pp.2635-2639. &amp;#x27E8;10.1093/gbe/evx208&amp;#x27E9;</idno>
            <availability status="restricted">
              <licence target="https://about.hal.science/hal-authorisation-v1/">HAL Authorization<ref corresp="#file-1775352-1805744"/></licence>
            </availability>
          </publicationStmt>
          <seriesStmt>
            <idno type="stamp" n="INSERM">INSERM - Institut national de la santé et de la recherche médicale</idno>
            <idno type="stamp" n="IRD">IRD - Institut de recherche pour le développement</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="EC-MARSEILLE">Ecole Centrale de Marseille</idno>
            <idno type="stamp" n="INSMI">CNRS-INSMI - INstitut des Sciences Mathématiques et de leurs Interactions</idno>
            <idno type="stamp" n="I2M">Institut de Mathématiques de Marseille</idno>
            <idno type="stamp" n="I2M-2014-" corresp="I2M">Institut de Mathématiques de Marseille 2014-</idno>
            <idno type="stamp" n="ORIGINES">Institut Origines, des planètes à la vie</idno>
          </seriesStmt>
          <notesStmt>
            <note type="audience" n="2">International</note>
            <note type="popular" n="0">No</note>
            <note type="peer" n="1">Yes</note>
          </notesStmt>
          <sourceDesc>
            <biblStruct>
              <analytic>
                <title xml:lang="en">The Rhizome of Lokiarchaeota Illustrates the Mosaicity of Archaeal Genomes</title>
                <author role="aut">
                  <persName>
                    <forename type="first">Anthony</forename>
                    <surname>Levasseur</surname>
                  </persName>
                  <idno type="halauthorid">190180-0</idno>
                  <affiliation ref="#struct-57269"/>
                  <affiliation ref="#struct-199392"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Vicky</forename>
                    <surname>Merhej</surname>
                  </persName>
                  <email type="md5">3b8cf9b1d57fdcb06cc902571f39002e</email>
                  <email type="domain">univ-amu.fr</email>
                  <idno type="idhal" notation="numeric">768656</idno>
                  <idno type="halauthorid" notation="string">715534-768656</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-8688-6943</idno>
                  <affiliation ref="#struct-240602"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Emeline</forename>
                    <surname>Baptiste</surname>
                  </persName>
                  <idno type="halauthorid">871806-0</idno>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Vikas</forename>
                    <surname>Sharma</surname>
                  </persName>
                  <idno type="halauthorid">953751-0</idno>
                  <affiliation ref="#struct-199392"/>
                  <affiliation ref="#struct-241321"/>
                </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-241321"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Didier</forename>
                    <surname>Raoult</surname>
                  </persName>
                  <email type="md5">c85d553eaec6674caeb7cb6e360587a7</email>
                  <email type="domain">gmail.com</email>
                  <idno type="idhal" notation="string">didier-raoult</idno>
                  <idno type="idhal" notation="numeric">8465</idno>
                  <idno type="halauthorid" notation="string">16046-8465</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-0633-5974</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-2895-5824</idno>
                  <idno type="IDREF">https://www.idref.fr/035496169</idno>
                  <idno type="GOOGLE SCHOLAR">https://scholar.google.fr/citations?user=n8EF_6kAAAAJ</idno>
                  <idno type="VIAF">https://viaf.org/viaf/56752423</idno>
                  <idno type="ISNI">http://isni.org/isni/0000000119638387</idno>
                  <idno type="RESEARCHERID">http://www.researcherid.com/rid/A-8434-2008</idno>
                  <idno type="RESEARCHERID">http://www.researcherid.com/rid/http://www.researcherid.com/rid/A-8434-2008</idno>
                  <affiliation ref="#struct-199392"/>
                </author>
              </analytic>
              <monogr>
                <idno type="halJournalId" status="VALID">104503</idno>
                <idno type="issn">1759-6653</idno>
                <idno type="eissn">1759-6653</idno>
                <title level="j">Genome Biology and Evolution</title>
                <imprint>
                  <publisher>Society for Molecular Biology and Evolution</publisher>
                  <biblScope unit="volume">9</biblScope>
                  <biblScope unit="issue">10</biblScope>
                  <biblScope unit="pp">2635-2639</biblScope>
                  <date type="datePub">2017-10</date>
                </imprint>
              </monogr>
              <idno type="doi">10.1093/gbe/evx208</idno>
            </biblStruct>
          </sourceDesc>
          <profileDesc>
            <langUsage>
              <language ident="en">English</language>
            </langUsage>
            <textClass>
              <keywords scheme="author">
                <term xml:lang="en">mosaic genomes</term>
                <term xml:lang="en">gene exchange</term>
                <term xml:lang="en">Lokiarchaeota</term>
                <term xml:lang="en">tree of life</term>
              </keywords>
              <classCode scheme="halDomain" n="sdv.mhep">Life Sciences [q-bio]/Human health and pathology</classCode>
              <classCode scheme="halTypology" n="ART">Journal articles</classCode>
              <classCode scheme="halOldTypology" n="ART">Journal articles</classCode>
              <classCode scheme="halTreeTypology" n="ART">Journal articles</classCode>
            </textClass>
            <abstract xml:lang="en">
              <p>Genome remodeling and exchange of sequences are widespread in the prokaryotic world and mosaic genomes challenge the classification of prokaryotes, which cannot be properly achieved in terms of a single gene or group of genes. Here, we studied individually the gene collection of the archaic microorganism Lokiarchaeum sp., suggested as an archaeal host close to the emergence of the eukaryotes. The network or rhizome of all Lokiarchaeum sp. genes revealed that the genomic repertoire is mainly composed of genes from archaeal (similar to 36%) and bacterial origin (similar to 28%), distantly followed by components of eukaryotic origin (similar to 2%). Thirty-three percent of genes were unique to this species (ORFans). The mosaicity of archaea was also supported by studying Methanomassiliicoccus luminyensis, an archaea from the gut, in which 67% of the genomic repertoire arised from archaea and 22% from bacteria. Our results illustrate the intricate evolutionary relationships of the archaeal genome repertoire and highlight the rhizome-like processes of evolution in archaea, their mosaicity, and chimeric origin composed of different domains of life, questioning the reality of a tree of life.</p>
            </abstract>
          </profileDesc>
        </biblFull>
      </listBibl>
    </body>
    <back>
      <listOrg type="structures">
        <org type="laboratory" xml:id="struct-57269" status="INCOMING">
          <orgName>Laboratoire de Phylogénomique</orgName>
          <desc>
            <address>
              <addrLine>Marseille</addrLine>
              <country key="FR"/>
            </address>
          </desc>
          <listRelation>
            <relation active="#struct-92823" type="direct"/>
            <relation active="#struct-307024" type="direct"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-199392" status="OLD">
          <idno type="IdRef">123037891</idno>
          <idno type="RNSR">200817431S</idno>
          <orgName>Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes</orgName>
          <orgName type="acronym">URMITE</orgName>
          <date type="start">2008-01-01</date>
          <date type="end">2017-12-31</date>
          <desc>
            <address>
              <addrLine>27 Bd Jean Moulin 13385 MARSEILLE Cedex 5</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.mediterranee-infection.com/</ref>
          </desc>
          <listRelation>
            <relation name="UMR_D198" active="#struct-67872" type="direct"/>
            <relation name="UM63" active="#struct-198056" type="direct"/>
            <relation name="U1095" active="#struct-303623" type="direct"/>
            <relation active="#struct-303759" type="direct"/>
            <relation active="#struct-302108" type="indirect"/>
            <relation name="UMR7278 / UMR6236" active="#struct-441569" type="direct"/>
          </listRelation>
        </org>
        <org type="researchteam" xml:id="struct-240602" status="OLD">
          <orgName>Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes</orgName>
          <orgName type="acronym">URMITE</orgName>
          <date type="end">3107-12-31</date>
          <desc>
            <address>
              <addrLine>Campus International de Hann - BP 1386 - CP 18524 Dakar</addrLine>
              <country key="SN"/>
            </address>
          </desc>
          <listRelation>
            <relation active="#struct-199392" type="direct"/>
            <relation name="UMR_D198" active="#struct-67872" type="indirect"/>
            <relation name="UM63" active="#struct-198056" type="indirect"/>
            <relation name="U1095" active="#struct-303623" type="indirect"/>
            <relation active="#struct-303759" type="indirect"/>
            <relation active="#struct-302108" type="indirect"/>
            <relation name="UMR7278 / UMR6236" active="#struct-441569" type="indirect"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-241321" status="VALID">
          <idno type="RNSR">201420768T</idno>
          <idno type="ROR">042h2y225</idno>
          <orgName>Institut de Mathématiques de Marseille</orgName>
          <orgName type="acronym">I2M</orgName>
          <date type="start">2014</date>
          <desc>
            <address>
              <addrLine>Centre de Mathématiques et Informatique (CMI)Technopôle Château-Gombert39, rue Frédéric Joliot Curie13453 Marseille Cedex 13</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.i2m.univ-amu.fr/</ref>
          </desc>
          <listRelation>
            <relation name="UMR7373" active="#struct-198056" type="direct"/>
            <relation name="UMR7373" active="#struct-300415" type="direct"/>
            <relation name="UMR7373" active="#struct-441569" type="direct"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-92823" status="OLD">
          <idno type="IdRef">026403781</idno>
          <orgName>Université de Provence - Aix-Marseille 1</orgName>
          <date type="end">2011-12-31</date>
          <desc>
            <address>
              <addrLine>3, place Victor Hugo - 13331 Marseille Cedex 03</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.univ-provence.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-307024" status="INCOMING">
          <orgName>EA 3781</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>
        <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-303623" status="VALID">
          <idno type="IdRef">026388278</idno>
          <idno type="ROR">https://ror.org/02vjkv261</idno>
          <orgName>Institut National de la Santé et de la Recherche Médicale</orgName>
          <orgName type="acronym">INSERM</orgName>
          <desc>
            <address>
              <addrLine>101, rue de Tolbiac, 75013 Paris</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.inserm.fr</ref>
          </desc>
        </org>
        <org type="regrouplaboratory" xml:id="struct-303759" status="OLD">
          <orgName>IFR48</orgName>
          <date type="start">1996-01-01</date>
          <date type="end">2011-12-31</date>
          <desc>
            <address>
              <country key="FR"/>
            </address>
          </desc>
          <listRelation>
            <relation active="#struct-302108" type="direct"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-302108" status="VALID">
          <idno type="IdRef">232435065</idno>
          <idno type="ISNI">000000040387060X</idno>
          <idno type="ROR">https://ror.org/00rydyx93</idno>
          <orgName>Institut des sciences biologiques - CNRS Biologie</orgName>
          <orgName type="acronym">INSB-CNRS</orgName>
          <date type="start">2009-10-01</date>
          <desc>
            <address>
              <addrLine>CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE Campus Gérard Mégie 3 rue Michel-Ange 75794 PARIS CEDEX 16 - France</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.insb.cnrs.fr/fr</ref>
          </desc>
        </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-300415" status="VALID">
          <idno type="ISNI">0000 0004 1762 2703</idno>
          <idno type="ROR">https://ror.org/040baw385</idno>
          <orgName>École Centrale de Marseille</orgName>
          <orgName type="acronym">ECM</orgName>
          <date type="start">2006-09-27</date>
          <desc>
            <address>
              <addrLine>Pôle de l'étoile - Technopole de Château-Gombert - 38 rue Frédéric Joliot-Curie - 13013 Marseille</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.centrale-marseille.fr/</ref>
          </desc>
        </org>
      </listOrg>
    </back>
  </text>
</TEI>