Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies
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.
id |
dig-cirad-fr-574305 |
---|---|
record_format |
koha |
spelling |
dig-cirad-fr-5743052024-01-28T22:17:37Z http://agritrop.cirad.fr/574305/ http://agritrop.cirad.fr/574305/ Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies. Mariac Cédric, Scarcelli Nora, Pouzadou Juliette, Barnaud Adeline, Billot Claire, Faye Adama, Kougbeadjo Ayite, Maillol Vincent, Martin Guillaume, Sabot François, Santoni Sylvain, Vigouroux Yves, Couvreur Thomas. 2014. Molecular Ecology Resources, 14 (6) : 1103-1113.https://doi.org/10.1111/1755-0998.12258 <https://doi.org/10.1111/1755-0998.12258> Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies Mariac, Cédric Scarcelli, Nora Pouzadou, Juliette Barnaud, Adeline Billot, Claire Faye, Adama Kougbeadjo, Ayite Maillol, Vincent Martin, Guillaume Sabot, François Santoni, Sylvain Vigouroux, Yves Couvreur, Thomas eng 2014 Molecular Ecology Resources F30 - Génétique et amélioration des plantes génie génétique sonde nucléique hybridation PCR chloroplaste génome collection de matériel génétique phylogénie Oryza glaberrima Digitaria exilis Cenchrus americanus Dioscorea Dioscorea rotundata http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_35729 http://aims.fao.org/aos/agrovoc/c_3706 http://aims.fao.org/aos/agrovoc/c_34079 http://aims.fao.org/aos/agrovoc/c_9824 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_36739 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_5436 http://aims.fao.org/aos/agrovoc/c_2280 http://aims.fao.org/aos/agrovoc/c_13199 http://aims.fao.org/aos/agrovoc/c_2288 http://aims.fao.org/aos/agrovoc/c_2298 Cameroun http://aims.fao.org/aos/agrovoc/c_1229 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/574305/1/document_574305.pdf application/pdf Cirad license info:eu-repo/semantics/restrictedAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1111/1755-0998.12258 10.1111/1755-0998.12258 info:eu-repo/semantics/altIdentifier/doi/10.1111/1755-0998.12258 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1111/1755-0998.12258 |
institution |
CIRAD FR |
collection |
DSpace |
country |
Francia |
countrycode |
FR |
component |
Bibliográfico |
access |
En linea |
databasecode |
dig-cirad-fr |
tag |
biblioteca |
region |
Europa del Oeste |
libraryname |
Biblioteca del CIRAD Francia |
language |
eng |
topic |
F30 - Génétique et amélioration des plantes génie génétique sonde nucléique hybridation PCR chloroplaste génome collection de matériel génétique phylogénie Oryza glaberrima Digitaria exilis Cenchrus americanus Dioscorea Dioscorea rotundata http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_35729 http://aims.fao.org/aos/agrovoc/c_3706 http://aims.fao.org/aos/agrovoc/c_34079 http://aims.fao.org/aos/agrovoc/c_9824 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_36739 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_5436 http://aims.fao.org/aos/agrovoc/c_2280 http://aims.fao.org/aos/agrovoc/c_13199 http://aims.fao.org/aos/agrovoc/c_2288 http://aims.fao.org/aos/agrovoc/c_2298 http://aims.fao.org/aos/agrovoc/c_1229 F30 - Génétique et amélioration des plantes génie génétique sonde nucléique hybridation PCR chloroplaste génome collection de matériel génétique phylogénie Oryza glaberrima Digitaria exilis Cenchrus americanus Dioscorea Dioscorea rotundata http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_35729 http://aims.fao.org/aos/agrovoc/c_3706 http://aims.fao.org/aos/agrovoc/c_34079 http://aims.fao.org/aos/agrovoc/c_9824 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_36739 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_5436 http://aims.fao.org/aos/agrovoc/c_2280 http://aims.fao.org/aos/agrovoc/c_13199 http://aims.fao.org/aos/agrovoc/c_2288 http://aims.fao.org/aos/agrovoc/c_2298 http://aims.fao.org/aos/agrovoc/c_1229 |
spellingShingle |
F30 - Génétique et amélioration des plantes génie génétique sonde nucléique hybridation PCR chloroplaste génome collection de matériel génétique phylogénie Oryza glaberrima Digitaria exilis Cenchrus americanus Dioscorea Dioscorea rotundata http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_35729 http://aims.fao.org/aos/agrovoc/c_3706 http://aims.fao.org/aos/agrovoc/c_34079 http://aims.fao.org/aos/agrovoc/c_9824 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_36739 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_5436 http://aims.fao.org/aos/agrovoc/c_2280 http://aims.fao.org/aos/agrovoc/c_13199 http://aims.fao.org/aos/agrovoc/c_2288 http://aims.fao.org/aos/agrovoc/c_2298 http://aims.fao.org/aos/agrovoc/c_1229 F30 - Génétique et amélioration des plantes génie génétique sonde nucléique hybridation PCR chloroplaste génome collection de matériel génétique phylogénie Oryza glaberrima Digitaria exilis Cenchrus americanus Dioscorea Dioscorea rotundata http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_35729 http://aims.fao.org/aos/agrovoc/c_3706 http://aims.fao.org/aos/agrovoc/c_34079 http://aims.fao.org/aos/agrovoc/c_9824 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_36739 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_5436 http://aims.fao.org/aos/agrovoc/c_2280 http://aims.fao.org/aos/agrovoc/c_13199 http://aims.fao.org/aos/agrovoc/c_2288 http://aims.fao.org/aos/agrovoc/c_2298 http://aims.fao.org/aos/agrovoc/c_1229 Mariac, Cédric Scarcelli, Nora Pouzadou, Juliette Barnaud, Adeline Billot, Claire Faye, Adama Kougbeadjo, Ayite Maillol, Vincent Martin, Guillaume Sabot, François Santoni, Sylvain Vigouroux, Yves Couvreur, Thomas Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies |
description |
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. |
format |
article |
topic_facet |
F30 - Génétique et amélioration des plantes génie génétique sonde nucléique hybridation PCR chloroplaste génome collection de matériel génétique phylogénie Oryza glaberrima Digitaria exilis Cenchrus americanus Dioscorea Dioscorea rotundata http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_35729 http://aims.fao.org/aos/agrovoc/c_3706 http://aims.fao.org/aos/agrovoc/c_34079 http://aims.fao.org/aos/agrovoc/c_9824 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_36739 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_5436 http://aims.fao.org/aos/agrovoc/c_2280 http://aims.fao.org/aos/agrovoc/c_13199 http://aims.fao.org/aos/agrovoc/c_2288 http://aims.fao.org/aos/agrovoc/c_2298 http://aims.fao.org/aos/agrovoc/c_1229 |
author |
Mariac, Cédric Scarcelli, Nora Pouzadou, Juliette Barnaud, Adeline Billot, Claire Faye, Adama Kougbeadjo, Ayite Maillol, Vincent Martin, Guillaume Sabot, François Santoni, Sylvain Vigouroux, Yves Couvreur, Thomas |
author_facet |
Mariac, Cédric Scarcelli, Nora Pouzadou, Juliette Barnaud, Adeline Billot, Claire Faye, Adama Kougbeadjo, Ayite Maillol, Vincent Martin, Guillaume Sabot, François Santoni, Sylvain Vigouroux, Yves Couvreur, Thomas |
author_sort |
Mariac, Cédric |
title |
Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies |
title_short |
Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies |
title_full |
Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies |
title_fullStr |
Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies |
title_full_unstemmed |
Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies |
title_sort |
cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies |
url |
http://agritrop.cirad.fr/574305/ http://agritrop.cirad.fr/574305/1/document_574305.pdf |
work_keys_str_mv |
AT mariaccedric costeffectiveenrichmenthybridizationcaptureofchloroplastgenomesatdeepmultiplexinglevelsforpopulationgeneticsandphylogeographystudies AT scarcellinora costeffectiveenrichmenthybridizationcaptureofchloroplastgenomesatdeepmultiplexinglevelsforpopulationgeneticsandphylogeographystudies AT pouzadoujuliette costeffectiveenrichmenthybridizationcaptureofchloroplastgenomesatdeepmultiplexinglevelsforpopulationgeneticsandphylogeographystudies AT barnaudadeline costeffectiveenrichmenthybridizationcaptureofchloroplastgenomesatdeepmultiplexinglevelsforpopulationgeneticsandphylogeographystudies AT billotclaire costeffectiveenrichmenthybridizationcaptureofchloroplastgenomesatdeepmultiplexinglevelsforpopulationgeneticsandphylogeographystudies AT fayeadama costeffectiveenrichmenthybridizationcaptureofchloroplastgenomesatdeepmultiplexinglevelsforpopulationgeneticsandphylogeographystudies AT kougbeadjoayite costeffectiveenrichmenthybridizationcaptureofchloroplastgenomesatdeepmultiplexinglevelsforpopulationgeneticsandphylogeographystudies AT maillolvincent costeffectiveenrichmenthybridizationcaptureofchloroplastgenomesatdeepmultiplexinglevelsforpopulationgeneticsandphylogeographystudies AT martinguillaume costeffectiveenrichmenthybridizationcaptureofchloroplastgenomesatdeepmultiplexinglevelsforpopulationgeneticsandphylogeographystudies AT sabotfrancois costeffectiveenrichmenthybridizationcaptureofchloroplastgenomesatdeepmultiplexinglevelsforpopulationgeneticsandphylogeographystudies AT santonisylvain costeffectiveenrichmenthybridizationcaptureofchloroplastgenomesatdeepmultiplexinglevelsforpopulationgeneticsandphylogeographystudies AT vigourouxyves costeffectiveenrichmenthybridizationcaptureofchloroplastgenomesatdeepmultiplexinglevelsforpopulationgeneticsandphylogeographystudies AT couvreurthomas costeffectiveenrichmenthybridizationcaptureofchloroplastgenomesatdeepmultiplexinglevelsforpopulationgeneticsandphylogeographystudies |
_version_ |
1792498709086339072 |