Genetic changes associated with laboratory domestication of the nematode C. elegans

Defining the mutational landscape when individuals of a species grow separately and diverge over many generations can provide insights into trait evolution. A specific example of this involves studying changes associated with domestication where different lines of the same wild stock have been cultivated independently in different standard environments. Whole genome sequence comparison of such lines permits estimation of mutation rates, inference of genes’ ancestral states and ancestry of existing strains, and correction of sequencing errors in genome databases. Here we study domestication of the C. elegans Bristol strain as a model, and report the genome sequence of LSJ1 (Bristol), a sibling of the standard C. elegans reference wild type N2 (Bristol). The LSJ1 and N2 lines were cultivated separately for an estimated 20 years, from shortly after the Bristol strain was isolated until worm freezing methods were developed in 1970. We find that during this time they have accumulated 1208 genetic differences. We also describe phenotypic differences between N2 and LSJ1 in the rate at which embryos develop, the rate of production of eggs, the maturity of eggs at laying, and feeding behavior, all the result of post-isolation changes. We infer the ancestral alleles in the original Bristol isolate and correct 2038 likely sequencing errors in the original N2 reference genome sequence. Many of these corrections modify genome annotation. Our study not only provides a starting point to further investigate genotype-phenotype association but also provides insights into the process of selection as a result of laboratory domestication.