A massively parallel strategy for STR marker development, capture, and genotyping
Short tandem repeat (STR, or microsatellite) variants are highly polymorphic markers that facilitate powerful, high-precision population genetic analyses. STRs are especially valuable in conservation and ecological genetic research, yielding detailed information on population structure and short-term demographic fluctuations. However, STR marker development and analysis by conventional PCR-based methods imposes a workflow bottleneck and is suboptimal for non-invasive sampling strategies such as fecal DNA recovery. While 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 requiring a reference genome assembly, and a methodological approach for highly parallel recovery of enriched STR loci. We first employed our approach to design and capture a panel of 5,000 STR loci 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 coverage. Second, we tested our STR capture strategy on a P. diadema fecal DNA preparation, and report robust initial results and methodological suggestions for future implementations. In addition to STR targets, this approach also generates large, genome-wide single nucleotide polymorphism (SNP) panels from regions flanking the STR loci. Our method provides a cost-effective and highly scalable solution for rapid recovery of large STR and SNP datasets in any species without need for a reference genome, and can be used even with suboptimal DNA, which is more easily acquired in conservation and ecological genetic studies.
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