A massively parallel strategy for STR marker development, capture, and genotyping

• DOI: 10.1101/063727
• Publication Date: 2016-07-14T08:24:30Z
• Authors: Logan Kistler; Stephen M. Johnson; Mitchell T. Irwin; Edward E. Louis; Aakrosh Ratan; George H. Perry
• Keywords: Massive parallel sequencing; STR multiplex system

Abstract Short tandem repeat (STRs or microsatellites) variants, are highly polymorphic markers that facilitate powerful, high-precision population genetic analyses. STRs especially valuable in conservation and ecological research, yielding detailed information on structure short-term demographic flux. However, STR marker development analysis by conventional PCR-based methods imposes a workflow bottleneck is suboptimal for noninvasive sampling strategies such as fecal DNA recovery. While massively parallel sequencing has not previously been leveraged scalable, efficient recovery, here we present pipeline developing directly from high-throughput shotgun data without requiring reference genome assembly, methodological approach recovery of enriched loci. We first employed our to design capture panel 5,000 loci test group diademed sifakas ( Propithecus diadema , n=3), endangered Malagasy rainforest lemurs, report extremely targeted loci—97.3-99.6% characterized with ≥10x non-redundant coverage. Second, tested strategy P. preparation, robust initial results suggestions future implementations. In addition targets, this also generates large, genome-wide single nucleotide polymorphism (SNP) panels regions flanking the Our method provides cost-effective scalable solution rapid large SNP datasets any species need genome, can be used even DNA, which more easily acquired studies. Data Deposition Raw available under Study Accession numbers SRP073167 (genomic Oberon Tatiana) SRP076225 (targeted re-sequencing data) NCBI Sequence Read Archive. BaitSTR software at Github (core programs: https://github.com/aakrosh/BaitSTR ; BaitSTR_type.pl companion script genotyping block manipulation: https://github.com/lkistler/BaitSTR_type ).