Isolation of microsatellites from unknown genomes using known genomes as enrichment templates
Isolation of microsatellites from unknown genomes using known genomes as enrichment templates
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DOI：
10.4319/lom.2008.6.412
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发表时间：
2008-09-01
影响因子：
2.7
通讯作者：
Held, Christoph
中科院分区：
文献类型：
--
作者：
Leese, Florian;Mayer, Christoph;Held, Christoph
这项研究分析了从很大程度上未知的目标基因组中分离微卫星的方法的性能。该报告基因组方案 (RGP) 利用远缘相关生物体基因组中天然存在的重复基序作为杂交探针。事实证明，RGP 在八种海洋目标物种（包括甲藻、硅藻和六种节肢动物）的所有 13 次富集反应中都非常成功，平均产生 85.5% 的阳性菌落。 RGP 自然地筛选报告基因组中出现的所有重复类型，因此比通常仅测试少量短基序的标准方案偏差更小。在这项研究中，使用小家鼠、果蝇和智人的基因组作为报告基因组，获得了 133 种不同的二至六核苷酸重复类型。 RGP 的成功并不取决于报告基因组中的总体微卫星密度，而是随着目标基因组和报告基因组之间的遗传距离而增加，因为与保守的非重复区域的杂交不太频繁。报告基因组中重复类型的相对丰度对目标文库中重复类型的频率有显着影响。总而言之，RGP 极大地简化了从未知基因组中分离微卫星的过程，并使微卫星标记对广泛的研究更具吸引力。
This study analyzes the performance of a method to isolate microsatellites from largely unknown target genomes. This reporter genome protocol (RGP) utilizes naturally occurring repeat motifs in genomes of distantly related organisms as hybridization probes. The RGP proved very successful in all 13 enrichment reactions from eight marine target species (comprising a dinoflagellate, a diatom, and six arthropod species), yielding on average 85.5% positive colonies. The RGP naturally screens for all repeat types occurring in the reporter genomes and is therefore less biased than standard protocols that typically test few, short motifs only. Using the genomes of Mus musculus, Drosophila melanogaster, and Homo sapiens as reporter genomes in this study, 133 different di- to hexanucleotide repeat types were obtained. Success of the RGP did not depend on overall microsatellite density in the reporter genome but increased with genetic distance between target and reporter genomes because hybridization to conserved nonrepeat regions is less frequent. Relative abundance of repeat types in the reporter genome had a significant effect on repeat type frequencies in the target library. Altogether, the RGP greatly simplifies the isolation of microsatellites from unknown genomes and makes microsatellite markers more attractive for a wide range of studies.