Data from: Rapid microsatellite isolation from a butterfly by de novo transcriptome sequencing: performance and a comparison with AFLP-derived distances

BACKGROUND: The isolation of microsatellite markers remains laborious and expensive. For some taxa, such as Lepidoptera, development of microsatellite markers has been particularly difficult, as many markers appear to be located in repetitive DNA and have nearly identical flanking regions. We attempted to circumvent this problem by bioinformatic mining of microsatellite sequences from a de novo-sequenced transcriptome of a butterfly (Euphydryas editha). PRINCIPAL FINDINGS: By searching the assembled sequence data for perfect microsatellite repeats we found 10 polymorphic loci. Although, like many expressed sequence tag-derived microsatellites, our markers show strong deviations from Hardy-Weinberg equilibrium in many populations, and, in some cases, a high incidence of null alleles, we show that they nonetheless provide measures of population differentiation consistent with those obtained by amplified fragment length polymorphism analysis. Estimates of pairwise population differentiation between 23 populations were concordant between microsatellite-derived data and AFLP analysis of the same samples (r = 0.71, p<0.00001, 425 individuals from 23 populations). SIGNIFICANCE: De novo transcriptional sequencing appears to be a rapid and cost-effective tool for developing microsatellite markers for difficult genomes.

背景：微卫星标记（microsatellite markers）的分离始终繁琐且成本高昂。对于鳞翅目（Lepidoptera）等类群而言，微卫星标记的开发难度尤甚，因为多数标记似乎位于重复DNA区域内，且侧翼区域（flanking regions）几乎完全一致。我们尝试通过对伊迪丝蛱蝶（Euphydryas editha）的从头测序转录组（de novo-sequenced transcriptome）进行生物信息学挖掘（bioinformatic mining），以规避这一难题。
主要发现：通过对组装后的序列数据进行完美型微卫星重复序列检索，我们共获得10个多态性位点（polymorphic loci）。尽管与诸多表达序列标签衍生的微卫星类似，本研究开发的标记在多个种群中均显著偏离哈迪-温伯格平衡（Hardy-Weinberg equilibrium），且部分种群中存在较高比例的无效等位基因（null alleles），但研究结果表明，这些标记仍可用于种群分化（population differentiation）的评估，其结果与扩增片段长度多态性（amplified fragment length polymorphism, AFLP）分析所得结果一致。针对23个种群的两两种群分化值评估显示，微卫星标记来源数据与同一样本的AFLP分析结果高度一致（相关系数r=0.71，p<0.00001，样本覆盖23个种群的425个个体）。
意义：从头转录组测序（de novo transcriptional sequencing）似乎是一种快速且经济高效的工具，可用于为难以开发标记的基因组开发微卫星标记。