Mass production of SNP markers in a nonmodel passerine bird through RAD sequencing and contig mapping to the zebra finch genome
2013
Bourgeois, Yann X. C. | Lhuillier, Emeline | Cézard, Timothée | Bertrand, Joris A. M. | Delahaie, Boris | Cornuault, Josselin | Duval, Thomas | Bouchez, Olivier, O. | Mila, Borja | Thébaud, Christophe | Evolution et Diversité Biologique (EDB) ; Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3) ; Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS) | Département Génétique Animale (DEPT GA) ; Institut National de la Recherche Agronomique (INRA) | Institut National de la Recherche Agronomique (INRA) | The University of Edinburgh | Société Calédonienne d'Ornithologie | Laboratoire de Génétique Cellulaire (LGC) ; Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT) ; Institut National Polytechnique (Toulouse) (Toulouse INP) ; Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP) ; Université de Toulouse (UT)-Université de Toulouse (UT) | Museo Nacional de Ciencias Naturales [Madrid] (MNCN) ; Consejo Superior de Investigaciones Cientificas [España] = Spanish National Research Council [Spain] (CSIC) | This work was supported by Institut Français de la Biodiversité (IFB), Agence Française pour le Développement (AFD) and ANR Biodiversity Program grants to CT, the Génopole Toulouse Midi-Pyrénées, the National Geographic Society and the ‘Laboratoire d'Excellence’ TULIP (ANR-10-LABX-41).
Chantier qualité GA
اظهر المزيد [+] اقل [-]International audience
اظهر المزيد [+] اقل [-]إنجليزي. Here, we present an adaptation of restriction-site-associated DNA sequencing (RAD-seq) to the Illumina HiSeq2000 technology that we used to produce SNP markers in very large quantities at low cost per unit in the Reunion grey white-eye (Zosterops borbonicus), a nonmodel passerine bird species with no reference genome. We sequenced a set of six pools of 18-25 individuals using a single sequencing lane. This allowed us to build around 600000 contigs, among which at least 386000 could be mapped to the zebra finch (Taeniopygia guttata) genome. This yielded more than 80000 SNPs that could be mapped unambiguously and are evenly distributed across the genome. Thus, our approach provides a good illustration of the high potential of paired-end RAD sequencing of pooled DNA samples combined with comparative assembly to the zebra finch genome to build large contigs and characterize vast numbers of informative SNPs in nonmodel passerine bird species in a very efficient and cost-effective way.
اظهر المزيد [+] اقل [-]المعلومات البيبليوغرافية
تم تزويد هذا السجل من قبل Institut national de la recherche agronomique