Kistler Logan, Johnson Stephen M, Irwin Mitchell T, Louis Edward E, Ratan Aakrosh, Perry George H
Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.
Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA 16802, USA.
Nucleic Acids Res. 2017 Sep 6;45(15):e142. doi: 10.1093/nar/gkx574.
Short tandem repeat (STR) variants are highly polymorphic markers that facilitate powerful population genetic analyses. STRs are especially valuable in conservation and ecological genetic research, yielding detailed information on population structure and short-term demographic fluctuations. Massively parallel sequencing has not previously been leveraged for scalable, efficient STR recovery. Here, we present a pipeline for developing STR markers directly from high-throughput shotgun sequencing data without a reference genome, and an approach for highly parallel target STR recovery. We employed our approach to capture a panel of 5000 STRs from a test group of diademed sifakas (Propithecus diadema, n = 3), endangered Malagasy rainforest lemurs, and we report extremely efficient recovery of targeted loci-97.3-99.6% of STRs characterized with ≥10x non-redundant sequence coverage. We then tested our STR capture strategy on P. diadema fecal DNA, and report robust initial results and suggestions for future implementations. In addition to STR targets, this approach also generates large, genome-wide single nucleotide polymorphism (SNP) panels from flanking regions. Our method provides a cost-effective and scalable solution for rapid recovery of large STR and SNP datasets in any species without needing a reference genome, and can be used even with suboptimal DNA more easily acquired in conservation and ecological studies.
短串联重复序列（STR）变异体是高度多态性的标记，有助于进行强大的群体遗传学分析。STR在保护和生态遗传学研究中特别有价值，能提供有关种群结构和短期种群动态波动的详细信息。此前，大规模平行测序尚未用于可扩展、高效的STR回收。在此，我们提出了一种无需参考基因组即可直接从高通量鸟枪法测序数据开发STR标记的流程，以及一种高度平行的目标STR回收方法。我们采用我们的方法从冕狐猴（Propithecus diadema，n = 3）的测试组中捕获了一组5000个STR，冕狐猴是马达加斯加雨林中濒危的狐猴，我们报告了目标位点的极高回收率——97.3%-99.6%的STR具有≥10倍非冗余序列覆盖。然后，我们在冕狐猴粪便DNA上测试了我们的STR捕获策略，并报告了初步的可靠结果以及对未来实施的建议。除了STR目标外，这种方法还能从侧翼区域生成大量全基因组单核苷酸多态性（SNP）面板。我们的方法提供了一种经济高效且可扩展的解决方案，无需参考基因组即可快速回收任何物种中的大型STR和SNP数据集，甚至可以用于在保护和生态研究中更容易获得的次优DNA。
