<?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-00306595</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="2026-04-30T21:01:15+02:00"/>
      </publicationStmt>
      <sourceDesc>
        <p part="N">HAL API Platform</p>
      </sourceDesc>
    </fileDesc>
  </teiHeader>
  <text>
    <body>
      <listBibl>
        <biblFull>
          <titleStmt>
            <title xml:lang="en">Evolution of gene order in the genomes of two related yeast species</title>
            <author role="crp">
              <persName>
                <forename type="first">Gilles</forename>
                <surname>Fischer</surname>
              </persName>
              <email type="md5">824473d59798a6a904bf902dbca34bb2</email>
              <email type="domain">sorbonne-universite.fr</email>
              <idno type="idhal" notation="string">gilles-fischer</idno>
              <idno type="idhal" notation="numeric">740227</idno>
              <idno type="halauthorid" notation="string">23674-740227</idno>
              <idno type="ORCID">https://orcid.org/0000-0001-5732-2682</idno>
              <idno type="GOOGLE SCHOLAR">https://scholar.google.com/citations?user=0v9nlVMAAAAJ&amp;hl=fr</idno>
              <idno type="IDREF">https://www.idref.fr/139512624</idno>
              <affiliation ref="#struct-24267"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Cécile</forename>
                <surname>Neuvéglise</surname>
              </persName>
              <email type="md5">9f1aac4a82fab27a21a21503ffa631b0</email>
              <email type="domain">inrae.fr</email>
              <idno type="idhal" notation="string">cecile-neuveglise</idno>
              <idno type="idhal" notation="numeric">183393</idno>
              <idno type="halauthorid" notation="string">3191-183393</idno>
              <idno type="ORCID">https://orcid.org/0000-0001-5017-7830</idno>
              <idno type="IDREF">https://www.idref.fr/185868169</idno>
              <idno type="VIAF">https://viaf.org/viaf/316670881</idno>
              <affiliation ref="#struct-52300"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Pascal</forename>
                <surname>Durrens</surname>
              </persName>
              <email type="md5">a0a2273567930587107d598bd8dcc762</email>
              <email type="domain">labri.fr</email>
              <idno type="idhal" notation="string">pascal-durrens</idno>
              <idno type="idhal" notation="numeric">3548</idno>
              <idno type="halauthorid" notation="string">3190-3548</idno>
              <idno type="IDREF">https://www.idref.fr/225317915</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-3948-7106</idno>
              <affiliation ref="#struct-588"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Claude</forename>
                <surname>Gaillardin</surname>
              </persName>
              <idno type="halauthorid">171455-0</idno>
              <affiliation ref="#struct-52300"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Bernard</forename>
                <surname>Dujon</surname>
              </persName>
              <email type="md5">27d75daef3d6b61b227d139ff4a8a4ba</email>
              <email type="domain">pasteur.fr</email>
              <idno type="idhal" notation="numeric">946635</idno>
              <idno type="halauthorid" notation="string">171413-946635</idno>
              <affiliation ref="#struct-24267"/>
            </author>
            <editor role="depositor">
              <persName>
                <forename>Pascal</forename>
                <surname>Durrens</surname>
              </persName>
              <email type="md5">a0a2273567930587107d598bd8dcc762</email>
              <email type="domain">labri.fr</email>
            </editor>
            <funder>This work was supported by the CNRS as part of the network GDR 2354 Ge´nolevures II. We thank our colleagues from the Ge´nolevures  network and especially J.L. Souciet. We also thank B. Llorente for critical reading of the article as well as our colleagues from the Unite´ de Ge´ne´tique Mole´culaire des Levures for fruitful discussions. B.D. is a member of the Institut Universitaire de France.The publication costs of this article were defrayed in partby payment of page charges. This article must therefore behereby marked “advertisement” in accordance with 18 USCsection 1734 solely to indicate this fac</funder>
          </titleStmt>
          <editionStmt>
            <edition n="v1" type="current">
              <date type="whenSubmitted">2008-07-28 10:58:19</date>
              <date type="whenModified">2025-10-23 12:57:34</date>
              <date type="whenReleased">2008-07-28 10:59:38</date>
              <date type="whenProduced">2001</date>
              <ref type="externalLink" target="https://genome.cshlp.org/content/11/12/2009.full.pdf"/>
              <fs>
                <f name="inra_etatDocument_local" notation="numeric">
                  <numeric>0</numeric>
                </f>
                <f name="inra_etatDocument_local" notation="string" n="0">
                  <string>inra_etatDocument_local_0</string>
                </f>
                <f name="inra_publicVise_local" notation="string" n="SC">
                  <string>inra_publicVise_local_SC</string>
                </f>
              </fs>
            </edition>
            <respStmt>
              <resp>contributor</resp>
              <name key="132019">
                <persName>
                  <forename>Pascal</forename>
                  <surname>Durrens</surname>
                </persName>
                <email type="md5">a0a2273567930587107d598bd8dcc762</email>
                <email type="domain">labri.fr</email>
              </name>
            </respStmt>
          </editionStmt>
          <publicationStmt>
            <distributor>CCSD</distributor>
            <idno type="halId">hal-00306595</idno>
            <idno type="halUri">https://hal.science/hal-00306595</idno>
            <idno type="halBibtex">fischer:hal-00306595</idno>
            <idno type="halRefHtml">&lt;i&gt;Genome Research&lt;/i&gt;, 2001, 11, pp.2009-2019. &lt;a target="_blank" href="https://dx.doi.org/10.1101/gr.212701"&gt;&amp;#x27E8;10.1101/gr.212701&amp;#x27E9;&lt;/a&gt;</idno>
            <idno type="halRef">Genome Research, 2001, 11, pp.2009-2019. &amp;#x27E8;10.1101/gr.212701&amp;#x27E9;</idno>
            <availability status="restricted"/>
          </publicationStmt>
          <seriesStmt>
            <idno type="stamp" n="PASTEUR">Institut Pasteur</idno>
            <idno type="stamp" n="UPMC" corresp="SORBONNE-UNIVERSITE">Université Pierre et Marie Curie</idno>
            <idno type="stamp" n="CNRS">CNRS - Centre national de la recherche scientifique</idno>
            <idno type="stamp" n="INRA">INRA - Institut national de la recherche agronomique</idno>
            <idno type="stamp" n="LABRI-MABIOVIS" corresp="LABRI">Modèles et algorithmes pour la bioinformatique et la visualisation d'informations</idno>
            <idno type="stamp" n="AGREENIUM">Archive ouverte en agrobiosciences</idno>
            <idno type="stamp" n="SORBONNE-UNIVERSITE">Sorbonne Université</idno>
            <idno type="stamp" n="INRAE">Institut National de Recherche en Agriculture, Alimentation et Environnement</idno>
            <idno type="stamp" n="SU-TI">Sorbonne Université - Texte Intégral</idno>
            <idno type="stamp" n="ALLIANCE-SU"> Alliance Sorbonne Université</idno>
            <idno type="stamp" n="UMR5095">Institut de Biochimie et Génétique Cellulaires</idno>
            <idno type="stamp" n="UNIVERSITE-BORDEAUX">Université de Bordeaux</idno>
          </seriesStmt>
          <notesStmt>
            <note type="audience" n="1">Not set</note>
            <note type="popular" n="0">No</note>
            <note type="peer" n="1">Yes</note>
          </notesStmt>
          <sourceDesc>
            <biblStruct>
              <analytic>
                <title xml:lang="en">Evolution of gene order in the genomes of two related yeast species</title>
                <author role="crp">
                  <persName>
                    <forename type="first">Gilles</forename>
                    <surname>Fischer</surname>
                  </persName>
                  <email type="md5">824473d59798a6a904bf902dbca34bb2</email>
                  <email type="domain">sorbonne-universite.fr</email>
                  <idno type="idhal" notation="string">gilles-fischer</idno>
                  <idno type="idhal" notation="numeric">740227</idno>
                  <idno type="halauthorid" notation="string">23674-740227</idno>
                  <idno type="ORCID">https://orcid.org/0000-0001-5732-2682</idno>
                  <idno type="GOOGLE SCHOLAR">https://scholar.google.com/citations?user=0v9nlVMAAAAJ&amp;hl=fr</idno>
                  <idno type="IDREF">https://www.idref.fr/139512624</idno>
                  <affiliation ref="#struct-24267"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Cécile</forename>
                    <surname>Neuvéglise</surname>
                  </persName>
                  <email type="md5">9f1aac4a82fab27a21a21503ffa631b0</email>
                  <email type="domain">inrae.fr</email>
                  <idno type="idhal" notation="string">cecile-neuveglise</idno>
                  <idno type="idhal" notation="numeric">183393</idno>
                  <idno type="halauthorid" notation="string">3191-183393</idno>
                  <idno type="ORCID">https://orcid.org/0000-0001-5017-7830</idno>
                  <idno type="IDREF">https://www.idref.fr/185868169</idno>
                  <idno type="VIAF">https://viaf.org/viaf/316670881</idno>
                  <affiliation ref="#struct-52300"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Pascal</forename>
                    <surname>Durrens</surname>
                  </persName>
                  <email type="md5">a0a2273567930587107d598bd8dcc762</email>
                  <email type="domain">labri.fr</email>
                  <idno type="idhal" notation="string">pascal-durrens</idno>
                  <idno type="idhal" notation="numeric">3548</idno>
                  <idno type="halauthorid" notation="string">3190-3548</idno>
                  <idno type="IDREF">https://www.idref.fr/225317915</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-3948-7106</idno>
                  <affiliation ref="#struct-588"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Claude</forename>
                    <surname>Gaillardin</surname>
                  </persName>
                  <idno type="halauthorid">171455-0</idno>
                  <affiliation ref="#struct-52300"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Bernard</forename>
                    <surname>Dujon</surname>
                  </persName>
                  <email type="md5">27d75daef3d6b61b227d139ff4a8a4ba</email>
                  <email type="domain">pasteur.fr</email>
                  <idno type="idhal" notation="numeric">946635</idno>
                  <idno type="halauthorid" notation="string">171413-946635</idno>
                  <affiliation ref="#struct-24267"/>
                </author>
              </analytic>
              <monogr>
                <idno type="halJournalId" status="VALID">4985</idno>
                <idno type="issn">1088-9051</idno>
                <idno type="eissn">1549-5469</idno>
                <title level="j">Genome Research</title>
                <imprint>
                  <publisher>Cold Spring Harbor Laboratory Press</publisher>
                  <biblScope unit="volume">11</biblScope>
                  <biblScope unit="pp">2009-2019</biblScope>
                  <date type="datePub">2001</date>
                </imprint>
              </monogr>
              <idno type="doi">10.1101/gr.212701</idno>
              <idno type="pubmed">11731490</idno>
            </biblStruct>
          </sourceDesc>
          <profileDesc>
            <langUsage>
              <language ident="en">English</language>
            </langUsage>
            <textClass>
              <classCode scheme="halDomain" n="sdv">Life Sciences [q-bio]</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>Changes in gene order between the genomes of two related yeast species, Saccharomyces cerevisiae and Saccharomyces bayanus var. uvarum were studied. From the dataset of a previous low coverage sequencing of the S. bayanus var.uvarum genome, 35 different synteny breakpoints between neighboring genes and two cases of local gene inversion were characterized in detail. The number and the type of the chromosomal rearrangements that have lead to these differences were identified. We show that evolution of gene order in the genomes of these two yeast species is driven mainly by gene duplication onto different chromosomes followed by differential loss of the repeated copies. In addition, local gene inversions also would result from a mechanism of gene duplication, but in an inverted orientation, followed by loss of the original copy. The identification of traces of anciently duplicated genes, called relics, show that the loss of duplicates is more frequently caused by the accumulation of numerous mutations in one of the two copies than by DNA deletion. Surprisingly, gross chromosomal rearrangements such as translocations have only a minor effect on gene order reshuffling as they account for &amp;lt;10% of the synteny breakpoints.</p>
            </abstract>
          </profileDesc>
        </biblFull>
      </listBibl>
    </body>
    <back>
      <listOrg type="structures">
        <org type="laboratory" xml:id="struct-24267" status="OLD">
          <orgName>Génétique Moléculaire des Levures</orgName>
          <desc>
            <address>
              <addrLine>25-28 rue du Docteur Roux 75724 PARIS Cedex 15</addrLine>
              <country key="FR"/>
            </address>
          </desc>
          <listRelation>
            <relation active="#struct-93591" type="direct"/>
            <relation active="#struct-300027" type="direct"/>
            <relation name="URA2171" active="#struct-441569" type="direct"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-52300" status="OLD">
          <orgName>Laboratoire de génétique moléculaire et cellulaire</orgName>
          <date type="start">1973-01-01</date>
          <date type="end">2002-12-31</date>
          <desc>
            <address>
              <addrLine>78850 Thiverval-Grignon</addrLine>
              <country key="FR"/>
            </address>
          </desc>
          <listRelation>
            <relation name="UMR0216" active="#struct-92114" type="direct"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-588" status="VALID">
          <idno type="IdRef">185481035</idno>
          <idno type="ISNI">0000000417952841</idno>
          <idno type="RNSR">199911781P</idno>
          <idno type="ROR">https://ror.org/048xwe611</idno>
          <orgName>Institut de biochimie et génétique cellulaires</orgName>
          <orgName type="acronym">IBGC</orgName>
          <date type="start">1994-01-01</date>
          <desc>
            <address>
              <addrLine>1 Rue Camille Saint-Saens 33077 BORDEAUX CEDEX</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.ibgc.cnrs.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-259761" type="direct"/>
            <relation name="UMR5095 / UPR9026" active="#struct-441569" type="direct"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-93591" status="OLD">
          <idno type="ROR">https://ror.org/02en5vm52</idno>
          <orgName>Université Pierre et Marie Curie - Paris 6</orgName>
          <orgName type="acronym">UPMC</orgName>
          <date type="end">2017-12-31</date>
          <desc>
            <address>
              <addrLine>4 place Jussieu - 75005 Paris</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.upmc.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-300027" status="VALID">
          <idno type="IdRef">027936643</idno>
          <idno type="ISNI">0000 0001 2353 6535</idno>
          <idno type="ROR">https://ror.org/0495fxg12</idno>
          <orgName>Institut Pasteur [Paris]</orgName>
          <orgName type="acronym">IP</orgName>
          <date type="start">1887-06-04</date>
          <desc>
            <address>
              <addrLine>25-28, rue du docteur Roux, 75724 Paris cedex 15</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.pasteur.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-92114" status="OLD">
          <idno type="ROR">https://ror.org/01x3gbx83</idno>
          <orgName>Institut National de la Recherche Agronomique</orgName>
          <orgName type="acronym">INRA</orgName>
          <date type="start">1946-05-18</date>
          <date type="end">2019-12-31</date>
          <desc>
            <address>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.inra.fr</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-259761" status="VALID">
          <idno type="IdRef">175206562</idno>
          <idno type="ROR">https://ror.org/057qpr032</idno>
          <orgName>Université de Bordeaux</orgName>
          <orgName type="acronym">UB</orgName>
          <desc>
            <address>
              <addrLine>35, place Pey Berland - 33076 Bordeaux</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.u-bordeaux.fr/</ref>
          </desc>
        </org>
      </listOrg>
    </back>
  </text>
</TEI>