<?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-04958619</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="2026-05-16T00:41:47+02:00"/>
      </publicationStmt>
      <sourceDesc>
        <p part="N">HAL API Platform</p>
      </sourceDesc>
    </fileDesc>
  </teiHeader>
  <text>
    <body>
      <listBibl>
        <biblFull>
          <titleStmt>
            <title xml:lang="en">Search for photosynthesis-related protein sites through chloroplast phylogenomics</title>
            <author role="aut">
              <persName>
                <forename type="first">Pierre</forename>
                <surname>Gérenton</surname>
              </persName>
              <email type="md5">4ad18d4045a1604c375204fedb7925a5</email>
              <email type="domain">univ-lyon1.fr</email>
              <idno type="idhal" notation="string">pierre-gerenton</idno>
              <idno type="idhal" notation="numeric">1510701</idno>
              <idno type="halauthorid" notation="string">3423812-1510701</idno>
              <affiliation ref="#struct-10025"/>
              <affiliation ref="#struct-1096260"/>
            </author>
            <author role="ctb">
              <persName>
                <forename type="first">Philippe</forename>
                <surname>Veber</surname>
              </persName>
              <idno type="halauthorid">42004-0</idno>
              <affiliation ref="#struct-10025"/>
            </author>
            <author role="sad">
              <persName>
                <forename type="first">Vincent</forename>
                <surname>Lacroix</surname>
              </persName>
              <idno type="halauthorid">16391-0</idno>
              <affiliation ref="#struct-10025"/>
              <affiliation ref="#struct-1096260"/>
            </author>
            <author role="sad">
              <persName>
                <forename type="first">Bastien</forename>
                <surname>Boussau</surname>
              </persName>
              <idno type="halauthorid">6304-0</idno>
              <affiliation ref="#struct-10025"/>
            </author>
            <editor role="depositor">
              <persName>
                <forename>Pierre</forename>
                <surname>Gérenton</surname>
              </persName>
              <email type="md5">4ad18d4045a1604c375204fedb7925a5</email>
              <email type="domain">univ-lyon1.fr</email>
            </editor>
          </titleStmt>
          <editionStmt>
            <edition n="v1" type="current">
              <date type="whenSubmitted">2025-02-20 12:45:51</date>
              <date type="whenModified">2025-03-25 11:10:02</date>
              <date type="whenReleased">2025-02-20 14:01:33</date>
              <date type="whenProduced">2025-02-03</date>
              <date type="whenEndEmbargoed">2025-02-20</date>
              <ref type="file" target="https://hal.science/hal-04958619v1/document">
                <date notBefore="2025-02-20"/>
              </ref>
              <ref type="file" subtype="author" n="1" target="https://hal.science/hal-04958619v1/file/poster_alphy_aeim_2025_search_for_photosynthesis_related_protein_sites_through_chloroplast_phylogenomics.pdf" id="file-4958619-4299174">
                <date notBefore="2025-02-20"/>
              </ref>
            </edition>
            <respStmt>
              <resp>contributor</resp>
              <name key="1590693">
                <persName>
                  <forename>Pierre</forename>
                  <surname>Gérenton</surname>
                </persName>
                <email type="md5">4ad18d4045a1604c375204fedb7925a5</email>
                <email type="domain">univ-lyon1.fr</email>
              </name>
            </respStmt>
          </editionStmt>
          <publicationStmt>
            <distributor>CCSD</distributor>
            <idno type="halId">hal-04958619</idno>
            <idno type="halUri">https://hal.science/hal-04958619</idno>
            <idno type="halBibtex">gerenton:hal-04958619</idno>
            <idno type="halRefHtml">&lt;i&gt;ALPHY/AIEM 2025&lt;/i&gt;, Feb 2025, Villeurbanne, France. 2025</idno>
            <idno type="halRef">ALPHY/AIEM 2025, Feb 2025, Villeurbanne, France. 2025</idno>
            <availability status="restricted">
              <licence target="https://creativecommons.org/licenses/by-nc-sa/4.0/">CC BY-NC-SA 4.0 - Attribution - Non-commercial use - ShareAlike<ref corresp="#file-4958619-4299174"/></licence>
            </availability>
          </publicationStmt>
          <seriesStmt>
            <idno type="stamp" n="CNRS">CNRS - Centre national de la recherche scientifique</idno>
            <idno type="stamp" n="INRIA">INRIA - Institut National de Recherche en Informatique et en Automatique</idno>
            <idno type="stamp" n="UNIV-LYON1">Université Claude Bernard - Lyon I</idno>
            <idno type="stamp" n="GIP-BE">GIP Bretagne Environnement</idno>
            <idno type="stamp" n="INRIA2">INRIA 2</idno>
            <idno type="stamp" n="LBBE" corresp="UNIV-LYON1">Laboratoire de biométrie et biologie évolutive </idno>
            <idno type="stamp" n="UDL">UDL</idno>
            <idno type="stamp" n="UNIV-LYON">Université de Lyon</idno>
            <idno type="stamp" n="INRIA-LYS">INRIA-LYON</idno>
            <idno type="stamp" n="INEE-CNRS">Institut écologie et environnement du CNRS</idno>
          </seriesStmt>
          <notesStmt>
            <note type="audience" n="3">National</note>
            <note type="invited" n="0">No</note>
            <note type="popular" n="0">No</note>
            <note type="peer" n="0">No</note>
            <note type="proceedings" n="0">No</note>
          </notesStmt>
          <sourceDesc>
            <biblStruct>
              <analytic>
                <title xml:lang="en">Search for photosynthesis-related protein sites through chloroplast phylogenomics</title>
                <author role="aut">
                  <persName>
                    <forename type="first">Pierre</forename>
                    <surname>Gérenton</surname>
                  </persName>
                  <email type="md5">4ad18d4045a1604c375204fedb7925a5</email>
                  <email type="domain">univ-lyon1.fr</email>
                  <idno type="idhal" notation="string">pierre-gerenton</idno>
                  <idno type="idhal" notation="numeric">1510701</idno>
                  <idno type="halauthorid" notation="string">3423812-1510701</idno>
                  <affiliation ref="#struct-10025"/>
                  <affiliation ref="#struct-1096260"/>
                </author>
                <author role="ctb">
                  <persName>
                    <forename type="first">Philippe</forename>
                    <surname>Veber</surname>
                  </persName>
                  <idno type="halauthorid">42004-0</idno>
                  <affiliation ref="#struct-10025"/>
                </author>
                <author role="sad">
                  <persName>
                    <forename type="first">Vincent</forename>
                    <surname>Lacroix</surname>
                  </persName>
                  <idno type="halauthorid">16391-0</idno>
                  <affiliation ref="#struct-10025"/>
                  <affiliation ref="#struct-1096260"/>
                </author>
                <author role="sad">
                  <persName>
                    <forename type="first">Bastien</forename>
                    <surname>Boussau</surname>
                  </persName>
                  <idno type="halauthorid">6304-0</idno>
                  <affiliation ref="#struct-10025"/>
                </author>
              </analytic>
              <monogr>
                <meeting>
                  <title>ALPHY/AIEM 2025</title>
                  <date type="start">2025-02-03</date>
                  <date type="end">2025-02-05</date>
                  <settlement>Villeurbanne</settlement>
                  <country key="FR">France</country>
                </meeting>
                <respStmt>
                  <resp>conferenceOrganizer</resp>
                  <name>Guillaume Achaz</name>
                  <name>Camille Berthelot</name>
                  <name>Anouk Necsulea</name>
                  <name>Laure Ségurel</name>
                  <name>Marie Sémon</name>
                  <name>Guillaume Beslon</name>
                  <name>Simon Boitard</name>
                  <name>Vincent Castric</name>
                  <name>Damien de Vienne</name>
                  <name>Laurent Duret</name>
                  <name>Lucie Etienne</name>
                  <name>Clémentine François</name>
                  <name>Sylvain Glémin</name>
                </respStmt>
                <imprint>
                  <date type="datePub">2025-02-04</date>
                </imprint>
              </monogr>
            </biblStruct>
          </sourceDesc>
          <profileDesc>
            <langUsage>
              <language ident="en">English</language>
            </langUsage>
            <textClass>
              <keywords scheme="author">
                <term xml:lang="en">Phylogenomic</term>
                <term xml:lang="en">Phenotype</term>
                <term xml:lang="en">Photosynthesis</term>
                <term xml:lang="en">Chloroplast</term>
                <term xml:lang="en">Evolution</term>
                <term xml:lang="en">Pelican</term>
                <term xml:lang="en">C3</term>
                <term xml:lang="en">C4</term>
                <term xml:lang="en">CAM</term>
                <term xml:lang="en">Genotype</term>
                <term xml:lang="en">rcbL</term>
                <term xml:lang="en">Rubisco</term>
                <term xml:lang="en">Convergence</term>
              </keywords>
              <classCode scheme="halDomain" n="sdv.bid.evo">Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]</classCode>
              <classCode scheme="halDomain" n="sdv.bbm.gtp">Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN]</classCode>
              <classCode scheme="halDomain" n="sdv.bid.spt">Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy</classCode>
              <classCode scheme="halTypology" n="POSTER">Poster communications</classCode>
              <classCode scheme="halOldTypology" n="POSTER">Poster communications</classCode>
              <classCode scheme="halTreeTypology" n="POSTER">Poster communications</classCode>
            </textClass>
            <abstract xml:lang="en">
              <p>Since the late 90's, phylogeneticists have been interested in uncovering sites associated to phenotypes, across species.Several methods were developed to study them, including dn/ds methods or proﬁle methods. Proﬁle methods informabout the direction of the selection, and one of them -Pelican (Duchemin, 2023)-, allows us to detect proteic sites relatedto a phenotype of interest at the genome scale. In the context of my PhD, we will try to uncover genotype-phenotypeassociations in plants (Viridiplantae), a dificult kingdom to analyse because of multiple genome-wide duplications andmulticopy gene families. As a ﬁrst step, we decided to look for chloroplastic proteic sites related to the photosyntheticpathway (C3/C4/CAM), and present here our analysis and conclusion about our ﬁndings.</p>
            </abstract>
          </profileDesc>
        </biblFull>
      </listBibl>
    </body>
    <back>
      <listOrg type="structures">
        <org type="laboratory" xml:id="struct-10025" status="VALID">
          <idno type="IdRef">15069671X</idno>
          <idno type="ISNI">0000000403863493</idno>
          <idno type="RNSR">199411998X</idno>
          <idno type="ROR">https://ror.org/03skt0t88</idno>
          <orgName>Laboratoire de Biométrie et Biologie Evolutive - UMR 5558</orgName>
          <orgName type="acronym">LBBE</orgName>
          <date type="start">1995-01-01</date>
          <desc>
            <address>
              <addrLine>43 Bld du 11 Novembre 1918 69622 VILLEURBANNE CEDEX</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://lbbe.univ-lyon1.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-194495" type="direct"/>
            <relation active="#struct-301088" type="indirect"/>
            <relation active="#struct-301767" type="direct"/>
            <relation name="UMR5558" active="#struct-441569" type="direct"/>
          </listRelation>
        </org>
        <org type="researchteam" xml:id="struct-1096260" status="VALID">
          <idno type="RNSR">201521243E</idno>
          <idno type="ROR">https://ror.org/02gqj2v09</idno>
          <orgName>Equipe de recherche européenne en algorithmique et biologie formelle et expérimentale</orgName>
          <orgName type="acronym">ERABLE</orgName>
          <date type="start">2022-01-01</date>
          <date type="end">2027-06-30</date>
          <desc>
            <address>
              <addrLine>Université Claude Bernard (Lyon 1), Campus DOUA 43, Boulevard du 11 Novembre 1918 69622 Villeurbanne cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.inria.fr/equipes/erable</ref>
          </desc>
          <listRelation>
            <relation active="#struct-10025" type="direct"/>
            <relation active="#struct-194495" type="indirect"/>
            <relation active="#struct-301088" type="indirect"/>
            <relation active="#struct-301767" type="indirect"/>
            <relation name="UMR5558" active="#struct-441569" type="indirect"/>
            <relation active="#struct-1096051" type="direct"/>
            <relation active="#struct-300009" type="indirect"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-194495" status="VALID">
          <idno type="IdRef">026402823</idno>
          <idno type="ISNI">0000000121686185</idno>
          <idno type="ROR">https://ror.org/029brtt94</idno>
          <orgName>Université Claude Bernard Lyon 1</orgName>
          <orgName type="acronym">UCBL</orgName>
          <desc>
            <address>
              <addrLine>43, boulevard du 11 novembre 1918, 69622 Villeurbanne cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.univ-lyon1.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-301088" type="direct"/>
          </listRelation>
        </org>
        <org type="regroupinstitution" xml:id="struct-301088" status="VALID">
          <idno type="ROR">https://ror.org/01rk35k63</idno>
          <orgName>Université de Lyon</orgName>
          <desc>
            <address>
              <addrLine>92 rue Pasteur - CS 30122, 69361 Lyon Cedex 07</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.universite-lyon.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-301767" status="VALID">
          <idno type="ROR">https://ror.org/01c7wz417</idno>
          <orgName>VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement</orgName>
          <orgName type="acronym">VAS</orgName>
          <date type="start">2010-01-01</date>
          <desc>
            <address>
              <addrLine>Université de Lyon, VetAgro Sup, 69280 Marcy l'Etoile (campus vétérinaire); Université de Clermont, VetAgro Sup, 63370 Lempdes (campus agronomique)</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.vetagro-sup.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="laboratory" xml:id="struct-1096051" status="VALID">
          <idno type="RNSR">202224236C</idno>
          <idno type="ROR">https://ror.org/022gakr41</idno>
          <orgName>Centre Inria de Lyon</orgName>
          <desc>
            <address>
              <addrLine>Inria de Lyon / Bâtiment CEI-2 / Campus La Doua - Villeurbanne / 56, Boulevard Niels Bohr / CS 52132 / 69 603 Villeurbanne</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.inria.fr/fr/centre-inria-de-lyon</ref>
          </desc>
          <listRelation>
            <relation active="#struct-300009" type="direct"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-300009" status="VALID">
          <idno type="ROR">https://ror.org/02kvxyf05</idno>
          <orgName>Institut National de Recherche en Informatique et en Automatique</orgName>
          <orgName type="acronym">Inria</orgName>
          <desc>
            <address>
              <addrLine>Domaine de VoluceauRocquencourt - BP 10578153 Le Chesnay Cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.inria.fr/en/</ref>
          </desc>
        </org>
      </listOrg>
    </back>
  </text>
</TEI>