Rapid microsatellite isolation from a butterfly by de novo transcriptome sequencing: performance and a comparison with AFLP-derived distances.
Rapid microsatellite isolation from a butterfly by de novo transcriptome sequencing: performance and a comparison with AFLP-derived distances.
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DOI：
10.1371/journal.pone.0011212
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发表时间：
2010-06-18
期刊：
影响因子：
3.7
通讯作者：
Parmesan C
中科院分区：
文献类型：
--
作者：
Mikheyev AS;Vo T;Wee B;Singer MC;Parmesan C
微卫星标记的分离仍然是费力和昂贵的。对于一些分类群，如鳞翅目，微卫星标记的发展一直是特别困难的，因为许多标记似乎位于重复DNA中，并具有几乎相同的侧翼区。我们试图绕过这个问题的生物信息学挖掘的微卫星序列的从头测序转录组的蝴蝶（Euphydryas editha）。通过对组装的序列数据进行微卫星重复序列的搜索，我们发现了10个多态位点。虽然，像许多表达序列标签衍生的微卫星，我们的标记显示出强烈的偏差，在许多人群中的Hardy-Weinberg平衡，在某些情况下，无效等位基因的发生率很高，我们表明，他们仍然提供了人口分化的措施与扩增片段长度多态性分析所获得的一致。23个群体间成对群体分化的估计值在微卫星数据和相同样品的AFLP分析之间是一致的（r = 0.71，p<0.00001，来自23个群体的425个个体）。 从头转录测序似乎是一个快速和成本效益高的工具，为困难的基因组开发微卫星标记。
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). 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). De novo transcriptional sequencing appears to be a rapid and cost-effective tool for developing microsatellite markers for difficult genomes.
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