Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family. (2nd April 2014)

• Record Type: Journal Article
• Authors: Malé, Pierre‐Jean G.; Bardon, Léa; Besnard, Guillaume; Coissac, Eric; Delsuc, Frédéric; Engel, Julien; Lhuillier, Emeline; Scotti‐Saintagne, Caroline; Tinaut, Alexandra; Chave, Jérôme
• Is Part Of: Molecular ecology resources. Volume 14:Number 5(2014:Sep.)
• Page Start: 966
• Page End: 975
• Publication Date: 2014-04-02
• Subjects: Molecular ecology -- Periodicals; 572.8
• DOI: 10.1111/1755-0998.12246
• Languages: English
• ISSNs: 1755-098X

Abstract

<abstract abstract-type="main" id="men12246-abs-0001"> <title>Abstract</title> <p>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.</p> </abstract>