title: Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies.
abstract: Biodiversity, phylogeography and population genetic studies will be revolutionized by access to large data sets 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 carried out 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.
authors.affiliation: Institut de Recherche pour le Développement, UMR DIADE, BP 64501, 34394, Montpellier, France.
authors.forename: Cédric
authors.initials: C
authors.lastname: Mariac
authors.forename: Nora
authors.initials: N
authors.lastname: Scarcelli
authors.forename: Juliette
authors.initials: J
authors.lastname: Pouzadou
authors.forename: Adeline
authors.initials: A
authors.lastname: Barnaud
authors.forename: Claire
authors.initials: C
authors.lastname: Billot
authors.forename: Adama
authors.initials: A
authors.lastname: Faye
authors.forename: Ayite
authors.initials: A
authors.lastname: Kougbeadjo
authors.forename: Vincent
authors.initials: V
authors.lastname: Maillol
authors.forename: Guillaume
authors.initials: G
authors.lastname: Martin
authors.forename: François
authors.initials: F
authors.lastname: Sabot
authors.forename: Sylvain
authors.initials: S
authors.lastname: Santoni
authors.forename: Yves
authors.initials: Y
authors.lastname: Vigouroux
authors.forename: Thomas L P
authors.initials: TL
authors.lastname: Couvreur
mesh_terms: D018742:DNA, Chloroplast / Q000235:genetics / Q000302:isolation & purification*; D005828:Genetics, Population / Q000191:economics / Q000379:methods*; D054628:Genome, Chloroplast; D059014:High-Throughput Nucleotide Sequencing / Q000191:economics / Q000379:methods*; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D058974:Phylogeography / Q000191:economics / Q000379:methods*; D017422:Sequence Analysis, DNA; D013048:Specimen Handling / Q000191:economics / Q000379:methods*
chemical_list: D018742:DNA, Chloroplast
keywords: DNA probes; MiSeq; long-range PCR; next-generation sequencing; plastomes; whole chloroplast sequencing