Résumé
Biodiversity, phylogeography and population genetic studies will be
revolutionized by access to large datasets thanks to next generation
sequencing methods. In this study, we develop an easy and cost-effective
protocol for in-solution enrichment hybridization capture of complete
chloroplast genomes applicable at deep multiplexed levels. The protocol
uses cheap in-house species-specific probes developed via long range PCR
of the entire chloroplast. Barcoded libraries are constructed and
in-solution enrichment of the chloroplasts is done using the probes. This
protocol was tested and validated on six economically important West
African crop species, namely African rice, pearl millet, three African yam
species and fonio. For pearl millet, we also demonstrate the effectiveness
of this protocol to retrieve 95% of the sequence of the whole chloroplast
on 95 multiplexed individuals in a single MiSeq run at a success rate of
95%. This new protocol allows whole chloroplast genomes to be retrieved at
a modest cost and will allow unprecedented resolution for closely related
species in phylogeography studies using plastomes.