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，以下简称1KP，包含1000余个已组装的植物转录组）为在植物生命树中开发微卫星位点提供了海量资源。本研究基于该计划的转录组数据开发微卫星位点，并对其应用效能进行了验证。
方法与结果：本研究借助软件包与自定义脚本，在1KP的转录组数据中鉴定微卫星位点。我们评估了这些位点的跨分类群扩增潜力，并与基因组DNA来源的分子标记对比，分析了位点是否偏向外显子区域。本研究从1334个植物转录组中共鉴定出超570万个简单序列重复（simple sequence repeat，以下简称SSR）位点。其中18%的位点与开放阅读框（open reading frame，以下简称ORF）存在显著重叠，电子PCR实验显示超半数位点可在同种分类群中成功扩增。相较于基因组SSR，转录组来源的SSR定位到翻译区域的概率约为其三倍。
结论：我们认为，即便在基因组学时代，微卫星依然具有重要应用价值——它们仍是高效且高性价比的分子标记。本研究提供的位点将为相关科研人员提供宝贵的研究资源。