Dryad
Published March 4, 2014 | Version v1
Dataset Open

Data from: Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family

Authors/Creators

  • 1. University of Toronto
  • 2. Paul Sabatier University
  • 3. Joseph Fourier University
  • 4. University of Montpellier
  • 5. AgroParisTech
  • 6. Département de Génétique Animale

Description

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.

Notes

script_chloro
UNIX script used for plastid reconstruction. The following tools must be installed: VELVET, PLAST, COPE, OBITOOLS
script_plastid.txt
alignments
Plastid DNA, mitochondrial DNA and nuclear ribosomic regions alignments, including the complete sequences or the non-intronic transcribed sequences only. Alignments were performed using MAFFT and cleaned using Gblocks. Files are in fasta format.
trees
Trees obtained with plastid DNA, mitochondrial DNA and nuclear ribosomic regions alignments, including the complete sequences or the non-intronic transcribed sequences only, using RAxML and MrBayes. Files are in NEXUS format.
chrysobalanaceae_phylogenomic_trees(1).rar

Files

script_plastid.txt

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Additional details

Related works

Is cited by
10.1111/1755-0998.12246 (DOI)