MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
Int J Mol Sci. 2019 Jul 16;20(14):3497. doi: 10.3390/ijms20143497.
Simple sequence repeats (SSRs) are known as microsatellites, and consist of tandem 1-6-base motifs. They have become one of the most popular molecular markers, and are widely used in molecular ecology, conservation biology, molecular breeding, and many other fields. Previously reported methods identify monomorphic and polymorphic SSRs and determine the polymorphic SSRs via experimental validation, which is potentially time-consuming and costly. Herein, we present a new strategy named insertion/deletion (INDEL) SSR (IDSSR) to identify polymorphic SSRs by integrating SSRs with nucleotide insertions/deletions (INDEL) solely based on a single genome sequence and the sequenced pair-end reads. These INDEL indexes and polymorphic SSRs were identified, as well as the number of repeats, repeat motifs, chromosome location, annealing temperature, and primer sequences, enabling future experimental approaches to determine the correctness and polymorphism. Experimental validation with the giant panda demonstrated that our method has high reliability and stability. The efficient SSR pipeline would help researchers obtain high-quality genetic markers for plants and animals of interest, save labor, and reduce costly marker-screening experiments. IDSSR is freely available at https://github.com/Allsummerking/IDSSR.
简单序列重复（SSR）也被称为微卫星，由串联的 1-6 碱基基序组成。它们已成为最受欢迎的分子标记之一，广泛应用于分子生态学、保护生物学、分子育种和许多其他领域。以前报道的方法可以识别单态和多态 SSR，并通过实验验证来确定多态 SSR，这可能既耗时又昂贵。在这里，我们提出了一种新的策略，称为插入/缺失（INDEL）SSR（IDSSR），通过仅基于单个基因组序列和测序的双端读取，将 SSR 与核苷酸插入/缺失（INDEL）整合，以识别多态 SSR。这些 INDEL 指标和多态 SSR 被识别出来，包括重复次数、重复基序、染色体位置、退火温度和引物序列，这使得未来的实验方法能够确定其正确性和多态性。用大熊猫进行的实验验证表明，我们的方法具有很高的可靠性和稳定性。高效的 SSR 流水线将有助于研究人员获得感兴趣的动植物的高质量遗传标记，节省劳动力，减少昂贵的标记筛选实验。IDSSR 可在 https://github.com/Allsummerking/IDSSR 上免费获取。
