Journal
MOLECULAR ECOLOGY RESOURCES
Volume 13, Issue 5, Pages 899-907Publisher
WILEY
DOI: 10.1111/1755-0998.12137
Keywords
next-generation sequencing; passerine; pooled DNA; SNP detection; zebra finch genome; Zosterops
Funding
- Institut Francais de la Biodiversite (IFB)
- Agence Francaise pour le Developpement (AFD)
- ANR Biodiversity Program
- Genopole Toulouse Midi-Pyrenees
- National Geographic Society
- 'Laboratoire d'Excellence' TULIP [ANR-10-LABX-41]
- MESR (Ministere de l'Enseignement Superieur et de la Recherche)
- BBSRC [BBS/E/D/20310000] Funding Source: UKRI
- MRC [MR/K001744/1] Funding Source: UKRI
- NERC [NE/H019804/1] Funding Source: UKRI
- Medical Research Council [MR/K001744/1] Funding Source: researchfish
- Natural Environment Research Council [NE/H019804/1] Funding Source: researchfish
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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.
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