Zosterops_color
RAD-seq data for Zosterops borbonicus
New genomic techniques are of great interest for evolutionary biologists, as the large number of markers they make available allows to study in unprecedented detail how selection acts on genomes and drives phenotypic variability. Here we present an adaptation to the Illumina HiSeq2000 technology of restriction-site-associated DNA sequencing (RAD-seq) to produce very large numbers of SNP markers in the Réunion grey white-eye (Zosterops borbonicus), a non-model passerine bird species with no reference genome. By sequencing a set of six pools of several individuals, we were able to build around 600,000 contigs, among which at least 386,000 were single hits that could be placed at a known position on the zebra finch (Taeniopygia guttata) genome. This enabled us to detect hundreds of thousands of candidate SNPs using a single Illumina HiSeq2000 sequencing lane. At least 60% of these markers could be placed unambiguously at a known position on the zebra finch genome. This illustrates the very high potential of using information from paired-end RAD sequencing of pools to build large contigs and identifying SNPs in non-model passerine bird species, at a relatively low cost.
New genomic techniques are of great interest for evolutionary biologists, as the large number of markers they make available allows to study in unprecedented detail how selection acts on genomes and drives phenotypic variability. Here we present an adaptation to the Illumina HiSeq2000 technology of restriction-site-associated DNA sequencing (RAD-seq) to produce very large numbers of SNP markers in the Réunion grey white-eye (Zosterops borbonicus), a non-model passerine bird species with no reference genome. By sequencing a set of six pools of several individuals, we were able to build around 600,000 contigs, among which at least 386,000 were single hits that could be placed at a known position on the zebra finch (Taeniopygia guttata) genome. This enabled us to detect hundreds of thousands of candidate SNPs using a single Illumina HiSeq2000 sequencing lane. At least 60% of these markers could be placed unambiguously at a known position on the zebra finch genome. This illustrates the very high potential of using information from paired-end RAD sequencing of pools to build large contigs and identifying SNPs in non-model passerine bird species, at a relatively low cost.