TY  - JOUR
AU  - Malé, P.-J.G.
AU  - Bardon, L.
AU  - Besnard, G.
AU  - Coissac, E.
AU  - Delsuc, F.
AU  - Engel, J.
AU  - Lhuillier, E.
AU  - Scotti-Saintagne, C.
AU  - Tinaut, A.
AU  - Chave, J.
PY  - 2014//
TI  - Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family
T2  - Mol. Ecol. Resour.
JO  - Molecular Ecology Resources
SP  - 966
EP  - 975
VL  - 14
IS  - 5
PB  - Blackwell Publishing Ltd
KW  - Next-generation sequencing
KW  - Organellar genome
KW  - Phylogenomics
KW  - Tropical trees
N2  - 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.
SN  - 17550998 (Issn)
UR  - http://www.scopus.com/inward/record.url?eid=2-s2.0-84905966537&partnerID=40&md5=ac30f0f3b88f3a8a1607bdd52719ce08
N1  - 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
ID  - Male_etal2014
ER  -