Multi-individual microsatellite identification: A multiple genome approach to microsatellite design (MiMi)
Multi-individual microsatellite identification: A multiple genome approach to microsatellite design (MiMi)
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DOI：
10.1111/1755-0998.13065
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发表时间：
2019-08-27
影响因子：
7.7
通讯作者：
Rowntree, Jennifer K.
中科院分区：
文献类型：
--
作者：
Fox, Graeme;Preziosi, Richard F.;Rowntree, Jennifer K.
定制的微卫星标记面板越来越便宜，对研究人员和自然资源保护主义者来说也越来越容易处理。在鸟枪基因组数据集内，微卫星发现率非常高，但需要对标记进行广泛的实验室测试以确认扩增和多态性。通过整合来自同一物种多个个体的鸟枪法下一代测序数据集，我们开发了一种新的微卫星标记优化设计方法。这种新工具使我们能够在直接比较中将合适的候选标记选择率提高58%，并促进与生产新型微卫星面板相关的成本降低约16%。我们的方法使每个微卫星位点的多序列比对，允许几个重要的质量检查进行可视化。多态性基因座可以被识别和优先化。可以避免在侧翼区域含有片段长度改变突变的位点，这可能使关于微卫星变异的进化模型的假设失效。可以检测并避免含有点突变的引发区域，从而有助于降低由遗传隔离引起的样品位点标记特异性和无效等位基因发生的可能性。我们证明了这种新方法在两个物种中的实用性：棘皮动物和鸟类。我们的方法对最大限度地减少基因分型错误和降低与开发新的标记物面板相关的成本做出了有价值的贡献。执行我们的多个体微卫星识别（MiMi）方法的Python脚本可以从GitHub（）免费获得。
Bespoke microsatellite marker panels are increasingly affordable and tractable to researchers and conservationists. The rate of microsatellite discovery is very high within a shotgun genomic data set, but extensive laboratory testing of markers is required for confirmation of amplification and polymorphism. By incorporating shotgun next-generation sequencing data sets from multiple individuals of the same species, we have developed a new method for the optimal design of microsatellite markers. This new tool allows us to increase the rate at which suitable candidate markers are selected by 58% in direct comparisons and facilitate an estimated 16% reduction in costs associated with producing a novel microsatellite panel. Our method enables the visualisation of each microsatellite locus in a multiple sequence alignment allowing several important quality checks to be made. Polymorphic loci can be identified and prioritised. Loci containing fragment-length-altering mutations in the flanking regions, which may invalidate assumptions regarding the model of evolution underlying variation at the microsatellite, can be avoided. Priming regions containing point mutations can be detected and avoided, helping to reduce sample-site-marker specificity arising from genetic isolation, and the likelihood of null alleles occurring. We demonstrate the utility of this new approach in two species: an echinoderm and a bird. Our method makes a valuable contribution towards minimising genotyping errors and reducing costs associated with developing a novel marker panel. The Python script to perform our method of multi-individual microsatellite identification (MiMi) is freely available from GitHub ().