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Author Malé, P.-J.G.; Bardon, L.; Besnard, G.; Coissac, E.; Delsuc, F.; Engel, J.; Lhuillier, E.; Scotti-Saintagne, C.; Tinaut, A.; Chave, J.
Title Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family Type Journal Article
Year 2014 Publication Molecular Ecology Resources Abbreviated Journal Mol. Ecol. Resour.
Volume 14 Issue 5 Pages 966-975
Keywords Next-generation sequencing; Organellar genome; Phylogenomics; Tropical trees
Abstract 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 1000×, 450× and 120× 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. © 2014 John Wiley & Sons Ltd.
Address GeT-PlaGe, Genotoul, INRA Auzeville, Castanet-Tolosan, F-31326, France
Corporate Author Thesis
Publisher Blackwell Publishing Ltd Place of Publication Editor
Language Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 17550998 (Issn) ISBN Medium
Area Expedition Conference (up)
Notes Export Date: 1 September 2014; Correspondence Address: Malé, P.-J.G.; UMR 5174 Laboratoire Évolution and Diversité Biologique, CNRS, Université Paul Sabatier, ENFA, 118 route de Narbonne, Toulouse, F-31062, France; email: pjg.male@gmail.com Approved no
Call Number EcoFoG @ webmaster @ Serial 559
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