Journal
MOLECULAR ECOLOGY RESOURCES
Volume 14, Issue 5, Pages 966-975Publisher
WILEY
DOI: 10.1111/1755-0998.12246
Keywords
next-generation sequencing; organellar genome; phylogenomics; tropical trees
Funding
- Agence Nationale de la Recherche (CEBA) [ANR-10-LABX-25-01]
- Agence Nationale de la Recherche (TULIP) [ANR-10-LABX-0041]
- ANR grant (METABAR)
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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 under-studied groups.
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