@article{fdi:010062644,
  title = {{C}ost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies},
  author = {{M}ariac, {C}{\'e}dric and {S}carcelli, {N}ora and {P}ouzadou, {J}. and {B}arnaud, {A}deline and {B}illot, {C}. and {F}aye, {A}. and {K}ougbeadjo, {A}. and {M}aillol, {V}. and {M}artin, {G}. and {S}abot, {F}ran{\c{c}}ois and {S}antoni, {S}. and {V}igouroux, {Y}ves and {C}ouvreur, {T}homas},
  editor = {},
  language = {{ENG}},
  abstract = {{B}iodiversity, phylogeography and population genetic studies will be revolutionized by access to large data sets thanks to next-generation sequencing methods. {I}n 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. {T}he protocol uses cheap in-house species-specific probes developed via long-range {PCR} of the entire chloroplast. {B}arcoded libraries are constructed, and in-solution enrichment of the chloroplasts is carried out using the probes. {T}his protocol was tested and validated on six economically important {W}est {A}frican crop species, namely {A}frican rice, pearl millet, three {A}frican yam species and fonio. {F}or 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 {M}i{S}eq run at a success rate of 95%. {T}his 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.},
  keywords = {{DNA} probes ; long-range {PCR} ; {M}i{S}eq ; next-generation sequencing ; plastomes ; whole chloroplast sequencing},
  booktitle = {},
  journal = {{M}olecular {E}cology {R}esources},
  volume = {14},
  numero = {6},
  pages = {1103--1113},
  ISSN = {1755-098{X}},
  year = {2014},
  DOI = {10.1111/1755-0998.12258},
  URL = {https://www.documentation.ird.fr/hor/fdi:010062644},
}