Mass production of SNP markers in a nonmodel passerine bird through RAD sequencing and contig mapping to the zebra finch genome
Mass production of SNP markers in a nonmodel passerine bird through RAD sequencing and contig mapping to the zebra finch genome
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DOI：
10.1111/1755-0998.12137
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发表时间：
2013-09-01
影响因子：
7.7
通讯作者：
Thebaud, Christophe
中科院分区：
文献类型：
--
作者：
Bourgeois, Yann X. C.;Lhuillier, Emeline;Thebaud, Christophe
在此，我们展示了限制性位点相关 DNA 测序 (RAD-seq) 与 Illumina HiSeq2000 技术的结合，我们使用该技术在留尼旺灰绣眼鸟 (Zosterops borbonicus)（一种没有参考基因组的非模式雀形目鸟类）中以低成本生产大量 SNP 标记。我们使用单个测序泳道对一组 6 个池（每组 18-25 个个体）进行了测序。这使我们能够构建大约 600000 个重叠群，其中至少 386000 个可以映射到斑胸草雀 (Taeniopygia guttata) 基因组。这产生了超过 80000 个 SNP，这些 SNP 可以明确定位并均匀分布在基因组中。因此，我们的方法很好地说明了混合 DNA 样本的双端 RAD 测序与斑胸草雀基因组的比较组装相结合的巨大潜力，可以构建大型重叠群，并以一种非常高效且经济高效的方式表征非模式雀形目鸟类中大量信息丰富的 SNP。
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.