Publications des scientifiques de l'IRD

Mariac Cédric, Scarcelli Nora, Pouzadou J., Barnaud Adeline, Billot C., Faye A., Kougbeadjo A., Maillol V., Martin G., Sabot François, Santoni S., Vigouroux Yves, Couvreur Thomas. (2014). Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies. Molecular Ecology Resources, 14 (6), p. 1103-1113. ISSN 1755-098X.

Titre du document
Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies
Année de publication
2014
Type de document
Article référencé dans le Web of Science WOS:000343805400002
Auteurs
Mariac Cédric, Scarcelli Nora, Pouzadou J., Barnaud Adeline, Billot C., Faye A., Kougbeadjo A., Maillol V., Martin G., Sabot François, Santoni S., Vigouroux Yves, Couvreur Thomas
Source
Molecular Ecology Resources, 2014, 14 (6), p. 1103-1113 ISSN 1755-098X
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.
Plan de classement
Sciences fondamentales / Techniques d'analyse et de recherche [020] ; Sciences du monde végétal [076]
Localisation
Fonds IRD [F B010062644]
Identifiant IRD
fdi:010062644
Contact