PhenoMIP: High-Throughput Phenotyping of Diverse Caenorhabditis elegans Populations via Molecular Inversion Probes.
PhenoMIP: High-Throughput Phenotyping of Diverse Caenorhabditis elegans Populations via Molecular Inversion Probes.
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PhenoMIP：通过分子倒置探针对不同秀丽隐杆线虫种群进行高通量表型分析。
DOI：
10.1534/g3.120.401656
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发表时间：
2020-11-05
期刊：
影响因子：
--
通讯作者：
Waterston RH
中科院分区：
文献类型：
--
作者：
Mok C;Belmarez G;Edgley ML;Moerman DG;Waterston RH
无论是在实验室环境中产生还是从野生环境中分离，变异等位基因仍然是解码模式生物（如秀丽隐杆线虫）基因功能的重要资源。随着大规模并行测序的进步，多个全基因组测序（WGS）菌株集合现在可供研究界使用。例如，百万突变项目（MMP）分析了2007年N2衍生的诱变菌株。单独地，每个菌株平均有10400个单核苷酸变异，相当于1080个蛋白质编码变异。然而，这些变体的影响在很大程度上仍然是未表征的，并且查询这些菌株的表型变化的广度需要适合于快速和灵敏的高通量分析的方法。在这里，我们提出了一个汇集的竞争健身的方法，通过分子倒置探针（PhenoMIP）的测序集合的表型亚群定量。我们对217种突变株在多种食物来源上的相对适应性进行了表型分析，并将其分为五类。我们还证明了这些菌株的一个子集，他们的健身缺陷可以遗传映射。总的来说，我们的结果表明，大约80%的MMP突变株可能具有相对于实验室参考N2降低的适应性。通过WGS方法产生这种形式的分析的成本将是令人望而却步的，而以这种方式完成的PhenoMIP分析不到WGS预计成本的十分之一。我们提出了将PhenoMIP以具有成本效益的方式应用于广泛的群体选择实验的方法，这对整个社会都是有用的。
Whether generated within a lab setting or isolated from the wild, variant alleles continue to be an important resource for decoding gene function in model organisms such as Caenorhabditis elegans. With advances in massively parallel sequencing, multiple whole-genome sequenced (WGS) strain collections are now available to the research community. The Million Mutation Project (MMP) for instance, analyzed 2007 N2-derived, mutagenized strains. Individually, each strain averages ∼400 single nucleotide variants amounting to ∼80 protein-coding variants. The effects of these variants, however, remain largely uncharacterized and querying the breadth of these strains for phenotypic changes requires a method amenable to rapid and sensitive high-throughput analysis. Here we present a pooled competitive fitness approach to quantitatively phenotype subpopulations of sequenced collections via molecular inversion probes (PhenoMIP). We phenotyped the relative fitness of 217 mutant strains on multiple food sources and classified these into five categories. We also demonstrate on a subset of these strains, that their fitness defects can be genetically mapped. Overall, our results suggest that approximately 80% of MMP mutant strains may have a decreased fitness relative to the lab reference, N2. The costs of generating this form of analysis through WGS methods would be prohibitive while PhenoMIP analysis in this manner is accomplished at less than one-tenth of projected WGS costs. We propose methods for applying PhenoMIP to a broad range of population selection experiments in a cost-efficient manner that would be useful to the community at large.
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