Mariac Cédric auteur aut IRD Scarcelli Nora auteur aut IRD Pouzadou J. auteur aut IRD Barnaud Adeline auteur aut IRD Billot C. auteur aut IRD Faye A. auteur aut IRD Kougbeadjo A. auteur aut IRD Maillol V. auteur aut IRD Martin G. auteur aut IRD Sabot François auteur aut IRD Santoni S. auteur aut IRD Vigouroux Yves auteur aut IRD Couvreur Thomas auteur aut IRD text journalArticle eng text/pdf born digital access 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. specialized DNA probes long-range PCR MiSeq next-generation sequencing plastomes whole chloroplast sequencing 076 020 14 6 1103-1113 2014 1755-098X https://www.documentation.ird.fr/hor/fdi:010062644 10.1111/1755-0998.12258 1755-098X [F B010062644] https://www.documentation.ird.fr/hor/fdi:010062644 https://www.documentation.ird.fr/intranet/publi/2014/11/010062644.pdf Accès réservé (Intranet de l'IRD) IRD - Base Horizon / Pleins textes 2014-12-05 2017-08-23 fdi:010062644 fre