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Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies

التفاصيل البيبلوغرافية
العنوان: Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies
المؤلفون: 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
المصدر: Molecular Ecology Resources
سنة النشر: 2014
المجموعة: CIRAD: Agritrop (Centre de coopération internationale en recherche agronomique pour le développement)
مصطلحات موضوعية: 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_15974Test, http://aims.fao.org/aos/agrovoc/c_35729Test, http://aims.fao.org/aos/agrovoc/c_3706Test, http://aims.fao.org/aos/agrovoc/c_34079Test, http://aims.fao.org/aos/agrovoc/c_9824Test, http://aims.fao.org/aos/agrovoc/c_3224Test, http://aims.fao.org/aos/agrovoc/c_36739Test, http://aims.fao.org/aos/agrovoc/c_13325Test, http://aims.fao.org/aos/agrovoc/c_5436Test, http://aims.fao.org/aos/agrovoc/c_2280Test, http://aims.fao.org/aos/agrovoc/c_13199Test, http://aims.fao.org/aos/agrovoc/c_2288Test, http://aims.fao.org/aos/agrovoc/c_2298Test, http://aims.fao.org/aos/agrovoc/c_1229Test
جغرافية الموضوع: Cameroun
الوصف: 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.
نوع الوثيقة: article in journal/newspaper
وصف الملف: application/pdf
اللغة: English
العلاقة: http://agritrop.cirad.fr/574305Test/; 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/10.1111/1755-0998.12258Test; http://agritrop.cirad.fr/574305/1/document_574305.pdfTest
DOI: 10.1111/1755-0998.12258
الإتاحة: https://doi.org/10.1111/1755-0998.12258Test
http://agritrop.cirad.fr/574305Test/
http://agritrop.cirad.fr/574305/1/document_574305.pdfTest
حقوق: Cirad license ; info:eu-repo/semantics/restrictedAccess ; https://agritrop.cirad.fr/mention_legale.htmlTest
رقم الانضمام: edsbas.BDE44E7B
قاعدة البيانات: BASE
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