PhenoMIP: High-Throughput Phenotyping of Diverse Caenorhabditis elegans Populations via Molecular Inversion Probes
| Autor: | Gabriella Belmarez, Calvin Mok, Mark L. Edgley, Robert H. Waterston, Donald G. Moerman |
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| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
molecular inversion probes
Mutant ved/biology.organism_classification_rank.species Population Computational biology Biology QH426-470 03 medical and health sciences competitive fitness assay 0302 clinical medicine Genetics Model organism education quantitative fitness Molecular Biology Gene Genetics (clinical) Caenorhabditis elegans 030304 developmental biology 0303 health sciences education.field_of_study Massive parallel sequencing ved/biology Strain (biology) biology.organism_classification million mutation project caenorhabditis elegans multiplex population Mutation (genetic algorithm) 030217 neurology & neurosurgery |
| Zdroj: | G3: Genes, Genomes, Genetics, Vol 10, Iss 11, Pp 3977-3990 (2020) |
| ISSN: | 2160-1836 |
| DOI: | 10.1534/g3.120.401656 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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