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Mass production of SNP markers in a nonmodel passerine bird through RAD sequencing and contig mapping to the zebra finch genome
Author(s) -
Bourgeois Yann X. C.,
Lhuillier Emeline,
Cézard Timothée,
Bertrand Joris A. M.,
Delahaie Boris,
Cornuault Josselin,
Duval Thomas,
Bouchez Olivier,
Milá Borja,
Thébaud Christophe
Publication year - 2013
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12137
Subject(s) - zebra finch , biology , passerine , contig , genome , dna sequencing , genetics , reference genome , sequence assembly , whole genome sequencing , genomics , computational biology , evolutionary biology , transcriptome , gene , zoology , gene expression , neuroscience
Here, we present an adaptation of restriction‐site‐associated DNA sequencing ( RAD ‐seq) to the I llumina H i S eq2000 technology that we used to produce SNP markers in very large quantities at low cost per unit in the R éunion grey white‐eye ( Z osterops 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 ( T aeniopygia guttata ) genome. This yielded more than 80 000 SNP s 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 SNP s in nonmodel passerine bird species in a very efficient and cost‐effective way.