Abstract
Mapping-by-sequencing has become a standard method to map and identify phenotype-causing mutations in model species. Here, we show that a fragmented draft assembly is sufficient to perform mapping-by-sequencing in nonmodel species. We generated a draft assembly and annotation of the genome of the free-living nematode Oscheius tipulae, a distant relative of the model Caenorhabditis elegans We used this draft to identify the likely causative mutations at the O. tipulae cov-3 locus, which affect vulval development. The cov-3 locus encodes the O. tipulae ortholog of C. elegans mig-13, and we further show that Cel-mig-13 mutants also have an unsuspected vulval-development phenotype. In a virtuous circle, we were able to use the linkage information collected during mutant mapping to improve the genome assembly. These results showcase the promise of genome-enabled forward genetics in nonmodel species.
Highlights
Mapping-by-sequencing has become a standard method to map and identify phenotype-causing mutations in model species
Besides its mode of reproduction and easy culture, O. tipulae has been chosen for several reasons: the two-step, anchor-cell induction of vulval-precursor-cell fates and its simple vulval cell lineage (Félix and Sternberg 1997), its easy isolation from various regions of the world (Baïlle et al 2008), and its phylogenetic position compared to C. elegans as an outgroup to Caenorhabditis species but an ingroup to P. pacificus (Blaxter et al 1998)
Inspired by the versatile and robust pipelines of mapping-by-sequencing routinely used for C. elegans (Minevich et al 2012), we generated a genome assembly for O. tipulae and here test mapping-by-sequencing in this species
Summary
Mapping-by-sequencing has become a standard method to map and identify phenotype-causing mutations in model species. We generated a draft assembly and annotation of the genome of the free-living nematode Oscheius tipulae, a distant relative of the model Caenorhabditis elegans. We used this draft to identify the likely causative mutations at the O. tipulae cov-3 locus, which affect vulval development. Genetic mapping information is required because a mutagenized strain and its nonmutagenized reference will have many spurious fixed differences: nonphenotype-causing mutations due to mutagenesis, or de novo spontaneous mutations fixed by drift in each strain Technical noise, such as sequencing or mapping errors, can contribute to observed variation. Sequencing bulk-segregant F2 populations and mapping allele frequencies on a reference genome is key to identifying the phenotype-causing mutation. Inspired by the versatile and robust pipelines of mapping-by-sequencing routinely used for C. elegans (Minevich et al 2012), we generated a genome assembly for O. tipulae and here test mapping-by-sequencing in this species
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