C. elegans mutant identification with a one-step whole-genome-sequencing and SNP mapping strategy.
C. elegans mutant identification with a one-step whole-genome-sequencing and SNP mapping strategy.
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DOI：
10.1371/journal.pone.0015435
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发表时间：
2010-11-08
期刊：
影响因子：
3.7
通讯作者：
Hobert O
中科院分区：
文献类型：
--
作者：
Doitsidou M;Poole RJ;Sarin S;Bigelow H;Hobert O
全基因组测序(WGS)正在成为一种快速且经济有效的方法来定位突变遗传模型系统中的分子损伤，如秀丽线虫。由于诱变菌株含有显著的突变负荷，通常仍有必要将突变映射到染色体区间，以阐明WGS鉴定的哪一种序列变体是导致表型的序列变体。我们在这里描述了我们在建立和测试一项简单战略方面的经验，该战略将基于SNP的快速测绘步骤纳入WGS程序。在该策略中，从遗传筛选中检索到的突变株与多态线虫品系杂交，从该杂交中选择单个F2代作为突变表型，将这些F2代动物的后代汇集在一起，然后进行全基因组测序。在导致表型的序列变体的区域中，多态SNP标记的密度降低，因此能够在WGS数据中识别它。作为原则的证明，我们使用这一策略来识别产生过量多巴胺能神经元的突变株中的分子损伤。我们发现分子损伤位于Pax-6/无眼直系同源基因VAB-3。这里描述的策略将进一步减少突变分离和分子损伤鉴定之间的时间。
Whole-genome sequencing (WGS) is becoming a fast and cost-effective method to pinpoint molecular lesions in mutagenized genetic model systems, such as Caenorhabditis elegans. As mutagenized strains contain a significant mutational load, it is often still necessary to map mutations to a chromosomal interval to elucidate which of the WGS-identified sequence variants is the phenotype-causing one. We describe here our experience in setting up and testing a simple strategy that incorporates a rapid SNP-based mapping step into the WGS procedure. In this strategy, a mutant retrieved from a genetic screen is crossed with a polymorphic C. elegans strain, individual F2 progeny from this cross is selected for the mutant phenotype, the progeny of these F2 animals are pooled and then whole-genome-sequenced. The density of polymorphic SNP markers is decreased in the region of the phenotype-causing sequence variant and therefore enables its identification in the WGS data. As a proof of principle, we use this strategy to identify the molecular lesion in a mutant strain that produces an excess of dopaminergic neurons. We find that the molecular lesion resides in the Pax-6/Eyeless ortholog vab-3. The strategy described here will further reduce the time between mutant isolation and identification of the molecular lesion.
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影响因子：
3.3
作者：
Sarin, Sumeet;Bertrand, Vincent;Hobert, Oliver
通讯作者：
Hobert, Oliver
影响因子：
48
作者：
Doitsidou, Maria;Flames, Nuria;Lee, Albert C.;Boyanov, Alexander;Hobert, Oliver
通讯作者：
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影响因子：
3.3
作者：
Zuryn, Steven;Le Gras, Stephanie;Jarriault, Sophie
通讯作者：
Jarriault, Sophie
影响因子：
48
作者：
Sarin, Sumeet;Prabhu, Snehit;O'Meara, M. Maggie;Pe'er, Itsik;Hobert, Oliver
通讯作者：
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影响因子：
4.4
作者：
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通讯作者：
Jorgensen, EM