Résumé
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 understudied
groups.