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）为开发植物生命之树各分支的微卫星位点提供了海量资源。我们基于上述转录组开发了微卫星位点，并对其应用效能进行了验证。 方法与结果：借助各类软件包与自定义脚本，我们从1KP转录组中筛选出了微卫星位点。我们评估了这些位点的跨物种扩增潜力，并相较于基因组DNA来源的标记，分析了其是否偏好外显子区域。我们从1334个植物转录组中鉴定出超过570万个简单序列重复（simple sequence repeat，简称SSR）位点。其中18%的位点与开放阅读框（open reading frame，简称ORF）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定位到翻译区域的概率约为基因组SSR的三倍。 结论：我们认为，在基因组时代微卫星仍具备应用价值——它们依然是高效且经济的分子标记。本文所呈现的位点可为相关研究人员提供宝贵的研究资源。