title: Mass production of SNP markers in a nonmodel passerine bird through RAD sequencing and contig mapping to the zebra finch genome.
abstract: 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 Réunion 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 600 000 contigs, among which at least 386 000 could be mapped to the zebra finch (Taeniopygia guttata) genome. This yielded more than 80 000 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.
authors.affiliation: Laboratoire Évolution et Diversité Biologique, UMR 5174 CNRS - Université Paul Sabatier - ENFA, 118 route de Narbonne, Bâtiment 4R1, F-31062, Toulouse Cedex 9, France. yann.x.c.bourgeois@gmail.com
authors.forename: Yann X C
authors.initials: YX
authors.lastname: Bourgeois
authors.forename: Emeline
authors.initials: E
authors.lastname: Lhuillier
authors.forename: Timothée
authors.initials: T
authors.lastname: Cézard
authors.forename: Joris A M
authors.initials: JA
authors.lastname: Bertrand
authors.forename: Boris
authors.initials: B
authors.lastname: Delahaie
authors.forename: Josselin
authors.initials: J
authors.lastname: Cornuault
authors.forename: Thomas
authors.initials: T
authors.lastname: Duval
authors.forename: Olivier
authors.initials: O
authors.lastname: Bouchez
authors.forename: Borja
authors.initials: B
authors.lastname: Milá
authors.forename: Christophe
authors.initials: C
authors.lastname: Thébaud
mesh_terms: D000818:Animals; D020451:Contig Mapping; D004262:DNA Restriction Enzymes / Q000378:metabolism; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D046109:Passeriformes / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide
chemical_list: D004262:DNA Restriction Enzymes
keywords: SNP detection; Zosterops; next-generation sequencing; passerine; pooled DNA; zebra finch genome