Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska Cesta 25, 10000 Zagreb, Croatia.
Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000 Zagreb, Croatia.
Int J Mol Sci. 2024 Mar 9;25(6):3169. doi: 10.3390/ijms25063169.
Simple sequence repeats (SSRs) have become one of the most popular molecular markers and are used in numerous fields, including conservation genetics, population genetic studies, and genetic mapping. Advances in next-generation sequencing technology and the growing amount of genomic data are driving the development of bioinformatics tools for SSR marker design. These tools work with different combinations of input data, which can be raw reads or assemblies, and with one or more input datasets. We present here a new strategy and implementation of a simple standalone pipeline that utilizes more than one assembly for the in silico design of PCR primers for microsatellite loci in more than one species. Primers are tested in silico to determine if they are polymorphic, eliminating the need to test time-consuming cross-species amplification in the laboratory. The end result is a set of markers that are in silico polymorphic in all analyzed species and have great potential for the identification of interspecies hybrids. The efficiency of the tool is demonstrated using two examples at different taxonomic levels and with different numbers of input assemblies to generate promising, high-quality SSR markers.
简单序列重复（SSR）已成为最受欢迎的分子标记之一，广泛应用于保护遗传学、群体遗传学研究和遗传图谱构建等领域。下一代测序技术的进步和基因组数据的不断增加，推动了用于 SSR 标记设计的生物信息学工具的发展。这些工具可以与不同的输入数据组合一起使用，包括原始读取或组装，以及一个或多个输入数据集。我们在此提出了一种新的策略和简单的独立管道的实现方法，该方法利用多个组装来对多个物种中的微卫星位点进行 PCR 引物的计算机设计。通过计算机测试来确定引物是否多态性，从而无需在实验室中进行耗时的跨物种扩增测试。最终结果是一组在所有分析物种中都具有计算机多态性的标记，这些标记非常有潜力用于鉴定种间杂种。该工具的效率通过在不同的分类学水平和使用不同数量的输入组装来生成有前途的高质量 SSR 标记的两个示例得到了证明。
