Data from: Molecular Inversion Probes for targeted resequencing in non-model organisms

Applications that require resequencing of hundreds or thousands of predefined genomic regions in numerous samples are common in studies of non-model organisms. However few approaches at the scale intermediate between multiplex PCR and sequence capture methods are available. Here we explored the utility of Molecular Inversion Probes (MIPs) for the medium-scale targeted resequencing in a non-model system. Markers targeting 112 bp of exonic sequence were designed from transcriptome of Lissotriton newts. We assessed performance of 248 MIP markers in a sample of 85 individuals. Among the 234 (94.4%) successfully amplified markers 80% had median coverage within one order of magnitude, indicating relatively uniform performance; coverage uniformity across individuals was also high. In the analysis of polymorphism and segregation within family, 77% of 248 tested MIPs were confirmed as single copy Mendelian markers. Genotyping concordance assessed using replicate samples exceeded 99%. MIP markers for targeted resequencing have a number of advantages: high specificity, high multiplexing level, low sample requirement, straightforward laboratory protocol, no need for preparation of genomic libraries and no ascertainment bias. We conclude that MIP markers provide an effective solution for resequencing targets of tens or hundreds of kb in any organism and in a large number of samples.

在非模式生物研究领域，针对大量样本中的数百乃至数千个预设基因组区域开展重测序的应用场景十分普遍。然而，目前介于多重PCR与序列捕获技术之间的中等规模靶向重测序方案却较为匮乏。本研究以非模式生物体系为对象，探究了分子倒置探针（Molecular Inversion Probes, MIPs）应用于中等规模靶向重测序的潜力。我们从真螈属（Lissotriton）蝾螈的转录组中，设计了靶向112 bp外显子序列的标记位点。我们针对85个个体组成的样本队列，评估了248个MIP标记位点的扩增性能。在成功扩增的234个标记位点（占总位点的94.4%）中，80%的位点覆盖度中位数处于一个数量级范围内，表明其扩增性能相对均匀；不同个体间的覆盖度均匀性同样优异。通过家系内多态性与分离模式分析，248个被测MIP位点中有77%被证实为单拷贝孟德尔式遗传标记。利用重复样本开展的基因分型一致性评估结果显示，一致性率超过99%。用于靶向重测序的MIP标记位点具备多项显著优势：特异性强、多重化水平高、样本需求量低、实验室操作流程简便，无需构建基因组文库，且不存在检出偏倚（ascertainment bias）。综上，MIP标记位点可为任意物种的大量样本中数十乃至数百kb的重测序靶区域提供高效可行的解决方案。