Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, United States of America.
PLoS One. 2013 Nov 28;8(11):e81853. doi: 10.1371/journal.pone.0081853. eCollection 2013.
Development and optimization of novel species-specific microsatellites, or simple sequence repeats (SSRs) remains an important step for studies in ecology, evolution, and behavior. Numerous approaches exist for identifying new SSRs that vary widely in terms of both time and cost investments. A recent approach of using paired-end Illumina sequence data in conjunction with the bioinformatics pipeline, PAL_FINDER, has the potential to substantially reduce the cost and labor investment while also improving efficiency. However, it does not appear that the approach has been widely adopted, perhaps due to concerns over its broad applicability across taxa. Therefore, to validate the utility of the approach we developed SSRs for 32 species representing 30 families, 25 orders, 11 classes, and six phyla and optimized SSRs for 13 of the species. Overall the IPE method worked extremely well and we identified 1000s of SSRs for all species (mean = 128,485), with 17% of loci being potentially amplifiable loci, and 25% of these met our most stringent criteria designed to that avoid SSRs associated with repetitive elements. Approximately 61% of screened primers yielded strong amplification of a single locus.
开发和优化新的物种特异性微卫星或简单重复序列（SSR）仍然是生态学、进化和行为研究的重要步骤。有许多方法可以识别新的 SSR，这些方法在时间和成本投入方面差异很大。最近一种使用 Illumina 双端测序数据结合生物信息学管道 PAL_FINDER 的方法，有可能在降低成本和劳动力投入的同时提高效率。然而，该方法似乎并没有被广泛采用，也许是因为人们担心它在分类学上的广泛适用性。因此，为了验证该方法的实用性，我们为代表 30 个科、25 个目、11 个纲和 6 个门的 32 个物种开发了 SSR，并为其中的 13 个物种优化了 SSR。总体而言，IPE 方法非常有效，我们为所有物种鉴定了数千个 SSR（平均值=128485），其中 17%的位点可能是可扩增的，而这些位点中有 25%符合我们为避免与重复元件相关的 SSR 而设计的最严格标准。大约 61%的筛选引物能够对单个位点进行强烈扩增。
