Data from: A new resource for the development of SSR markers: millions of loci from a thousand plant transcriptomes

Premise of the study: The One Thousand Plant Transcriptomes Project (1KP, 1000+ assembled plant transcriptomes) provides an enormous resource for developing microsatellite loci across the plant tree of life. We developed loci from these transcriptomes and tested their utility. Methods and Results: Using software packages and custom scripts, we identified microsatellite loci in 1KP transcriptomes. We assessed the potential for cross-amplification and whether loci were biased toward exons, as compared to markers derived from genomic DNA. We characterized over 5.7 million simple sequence repeat (SSR) loci from 1334 plant transcriptomes. Eighteen percent of loci substantially overlapped with open reading frames (ORFs), and electronic PCR revealed that over half the loci would amplify successfully in conspecific taxa. Transcriptomic SSRs were approximately three times more likely to map to translated regions than genomic SSRs. Conclusions: We believe microsatellites still have a place in the genomic age—they remain effective and cost-efficient markers. The loci presented here are a valuable resource for researchers.

研究背景：千种植物转录组计划（One Thousand Plant Transcriptomes Project，简称1KP）包含1000余个已组装的植物转录组，为在植物生命之树范围内开发微卫星位点提供了极为丰富的研究资源。本研究基于该转录组数据集开发相关位点，并对其应用潜力进行了验证。
方法与结果：本研究借助各类软件包与自定义脚本，在1KP转录组中鉴定出微卫星位点。我们评估了位点的跨物种扩增潜力，并相较于基因组DNA来源的分子标记，分析了该类位点是否更倾向于富集在外显子区域。本研究对1334个植物转录组中的570余万个简单序列重复（simple sequence repeat，SSR）位点进行了注释分析，其中18%的位点与开放阅读框（open reading frames，ORFs）存在显著重叠；电子PCR实验结果显示，超过半数的位点可在同种类群中成功扩增。转录组来源的SSR位点定位到翻译区域的概率约为基因组来源SSR位点的三倍。
结论：我们认为，在组学时代微卫星仍具备应用价值——其仍是高效且经济的分子标记。本研究开发的上述位点可为广大科研人员提供宝贵的研究资源。