Data from: Remarkably divergent regions punctuate the genome assembly of the Caenorhabditis elegans Hawaiian strain CB4856

The Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most
divergent from the canonical laboratory strain N2 and has been widely used
in developmental, population and evolutionary studies. To enhance the
utility of the strain, we have generated a draft sequence of the CB4856
genome, exploiting a variety of resources and strategies. The CB4856
genome when compared against the N2 reference has 327,050 single
nucleotide variants (SNVs) and 79,529 insertion-deletion events (indels)
that result in a total of 3.3 megabasepairs (Mb) of N2 sequence missing
from CB4856 and 1.4 Mb of sequence present in CB4856 not present in N2. As
previously reported, the density of SNVs varies along the chromosomes,
with the arms of chromosomes showing greater average variation than the
centers. In addition, we find 61 regions totaling 2.8 Mb, distributed
across all six chromosomes, that have a greatly elevated SNV density,
ranging from 2% to 16% SNVs. A survey of other wild isolates show that the
two alternative haplotypes for each region are widely distributed,
suggesting they have been maintained by balancing selection over long
evolutionary times. These divergent regions contain an abundance of genes
from large rapidly evolving families encoding F-box, MATH, BATH,
seven-transmembrane G-coupled receptors, and nuclear hormone receptors
suggesting that they provide selective advantages in natural environments.
The draft sequence makes available a comprehensive catalog of sequence
differences between the CB4856 and N2 strains that will facilitate the
molecular dissection of their phenotypic differences. Our work also
emphasizes the importance of going beyond simple alignment of reads to a
reference genome when assessing differences between genomes.