title: Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family.
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.
authors.affiliation: UMR 5174 Laboratoire Évolution & Diversité Biologique, CNRS, Université Paul Sabatier, ENFA, 118 route de Narbonne, F-31062, Toulouse, France; Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada.
authors.forename: Pierre-Jean G
authors.initials: PJ
authors.lastname: Malé
authors.forename: Léa
authors.initials: L
authors.lastname: Bardon
authors.forename: Guillaume
authors.initials: G
authors.lastname: Besnard
authors.forename: Eric
authors.initials: E
authors.lastname: Coissac
authors.forename: Frédéric
authors.initials: F
authors.lastname: Delsuc
authors.forename: Julien
authors.initials: J
authors.lastname: Engel
authors.forename: Emeline
authors.initials: E
authors.lastname: Lhuillier
authors.forename: Caroline
authors.initials: C
authors.lastname: Scotti-Saintagne
authors.forename: Alexandra
authors.initials: A
authors.lastname: Tinaut
authors.forename: Jérôme
authors.initials: J
authors.lastname: Chave
mesh_terms: D045469:Chrysobalanaceae / Q000145:classification* / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D018742:DNA, Chloroplast / Q000737:chemistry / Q000235:genetics; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D018745:Genome, Plant; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D018742:DNA, Chloroplast; D004272:DNA, Mitochondrial; D018744:DNA, Plant
keywords: next-generation sequencing; organellar genome; phylogenomics; tropical trees