The evolution of expression divergence in wild C. elegans

To examine the ways in which gene expression varies in natural populations and its relationship to genetic divergence, we estimated allele-specific expression in the offspring of multiple wild C. elegans strains crossed with the laboratory reference strain N2. Allele-specific expression analyses are uniquely sensitively able to identify cis regulatory changes, and coupled with analyses of differential expression between parental strains and parents and offspring can determine the regulatory pattern and inheritance mode of gene expression across the genome. We chose 7 strains that represented a range of divergence from N2 and spanned the species tree to cross with N2: EG4348; DL238; CB4856 (the classical ‘Hawaiian’ strain); ECA722; QX1211; and ECA701 and XZ1516 (two extremely diverged strains). This study sheds light on the relationship of genetic and expression divergence, the global patterns of inheritance and regulatory mode of genes in C. elegans, and the factors that differentiate genes with expression divergence from those with stabler expression. We performed RNA-sequencing on experimentally matched young (day 1) adult Caenorhabditis elegans from multiple natural genetic backgrounds (wild strains) and their hybrid offspring. Specifically, we RNA sequenced three replicates each of 7 wild C. elegans strains (EG4348, DL238, CB4856, ECA722, QX1211, ECA701, XZ1516), the laboratory reference strain N2, and the F1 offspring of crosses between each of the wild strain and N2.