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<publisher>HAL CCSD</publisher>
<title lang=en>Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family</title>
<creator>Male, Pierre-Jean G.</creator>
<creator>Bardon, Lea</creator>
<creator>Besnard, Guillaume</creator>
<creator>Coissac, Eric</creator>
<creator>Delsuc, Frederic</creator>
<creator>Engel, Julien</creator>
<creator>Lhuillier, Emeline</creator>
<creator>SCOTTI-SAINTAGNE, Caroline</creator>
<creator>Tinaut, Alexandra</creator>
<creator>Chave, Jerome</creator>
<contributor>Department of Ecology & Evolutionary Biology ; University of Toronto</contributor>
<contributor>CNRS, UMR 5174 Laboratoire Évolution & Diversité Biologique,ENFA ; Université Paul Sabatier - Toulouse 3 (UPS)</contributor>
<contributor>Laboratoire d'Ecologie Alpine (LECA) ; Université Joseph Fourier - Grenoble 1 (UJF) - Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]) - Centre National de la Recherche Scientifique (CNRS)</contributor>
<contributor>Institut des Sciences de l'Evolution [Montpellier] (ISEM) ; Université de Montpellier (UM) - Institut de recherche pour le développement [IRD] : UR226 - Centre National de la Recherche Scientifique (CNRS)</contributor>
<contributor>Ecologie des forêts de Guyane (ECOFOG) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) - Institut National de la Recherche Agronomique (INRA) - Université des Antilles et de la Guyane (UAG) - AgroParisTech - Centre National de la Recherche Scientifique (CNRS)</contributor>
<contributor>GeT PlaGe, Genotoul ; Institut National de la Recherche Agronomique (INRA)</contributor>
<contributor>UAR 1209 Département de Génétique Animale ; Institut National de la Recherche Agronomique (INRA)</contributor>
<contributor>Unité de Recherches Forestières Méditerranéennes (URFM) ; Institut National de la Recherche Agronomique (INRA)</contributor>
<contributor>Agence Nationale de la Recherche (CEBA) ANR-10-LABX-25-01 ; Agence Nationale de la Recherche (TULIP) ANR-10-LABX-0041 ; ANR grant (METABAR)</contributor>
<source>ISSN: 1755-098X</source>
<source>EISSN: 1755-0998</source>
<source>Molecular Ecology Resources</source>
<publisher>Wiley/Blackwell</publisher>
<identifier>hal-01204217</identifier>
<identifier>https://hal.archives-ouvertes.fr/hal-01204217</identifier>
<source>https://hal.archives-ouvertes.fr/hal-01204217</source>
<source>Molecular Ecology Resources, Wiley/Blackwell, 2014, 14 (5), pp.966 - 975. 〈10.1111/1755-0998.12246〉</source>
<identifier>DOI : 10.1111/1755-0998.12246</identifier>
<relation>info:eu-repo/semantics/altIdentifier/doi/10.1111/1755-0998.12246</relation>
<identifier>PRODINRA : 283530</identifier>
<language>en</language>
<subject lang=en>next-generation sequencing</subject>
<subject lang=en>organellar genome</subject>
<subject lang=en>phylogenomics</subject>
<subject lang=en>tropical trees</subject>
<subject lang=en>biased gene conversion</subject>
<subject lang=en>chloroplast genome</subject>
<subject lang=en>ribosomal dna</subject>
<subject lang=en>species identification</subject>
<subject lang=en>nucleotide-sequence</subject>
<subject lang=en>maximum-likelihood</subject>
<subject lang=en>basal angiosperm</subject>
<subject lang=en>mixed models</subject>
<subject lang=en>plant mitochondrial-dna</subject>
<subject lang=en>generation</subject>
<subject>[SDV.BV] Life Sciences [q-bio]/Vegetal Biology</subject>
<subject>[SDV.SA] Life Sciences [q-bio]/Agricultural sciences</subject>
<type>info:eu-repo/semantics/article</type>
<type>Journal articles</type>
<description lang=en>Whole genome sequencing is helping generate robust phylogenetic hypotheses for a range of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic approaches. As a case study, we performed a shallow shotgun sequencing of eight species in the tropical tree family Chrysobalanaceae to retrieve large fragments of high-copy number DNA regions and test the potential of these regions for phylogeny reconstruction. We were able to assemble the nuclear ribosomal cluster (nrDNA), the complete plastid genome (ptDNA) and a large fraction of the mitochondrial genome (mtDNA) with approximately 1000x, 450x and 120x sequencing depth respectively. The phylogenetic tree obtained with ptDNA resolved five of the seven internal nodes. In contrast, the tree obtained with mtDNA and nrDNA data were largely unresolved. This study demonstrates that genome skimming is a cost-effective approach and shows potential in plant molecular systematics within Chrysobalanaceae and other under-studied groups.</description>
<date>2014</date>
</dc>
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