Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans

Abstract

Background: Copy number variation is an important component of genetic variation in higher eukaryotes. The extent of natural copy number variation in C. elegans is unknown outside of 2 highly divergent wild isolates and the canonical N2 Bristol strain.

Results: We have used array comparative genomic hybridization (aCGH) to detect copy number variation in the genomes of 12 natural isolates of Caenorhabditis elegans. Deletions relative to the canonical N2 strain are more common in these isolates than duplications, and indels are enriched in multigene families on the autosome arms. Among the strains in our study, the Hawaiian and Madeiran strains (CB4856 and JU258) carry the largest number of deletions, followed by the Vancouver strain (KR314). Overall we detected 510 different deletions affecting 1136 genes, or over 5% of the genes in the canonical N2 genome. The indels we identified had a median length of 2.7 kb. Since many deletions are found in multiple isolates, deletion loci were used as markers to derive an unrooted tree to estimate genetic relatedness among the strains.

Conclusion: Copy number variation is extensive in C. elegans, affecting over 5% of the genes in the genome. The deletions we have detected in natural isolates of C. elegans contribute significantly to the number of deletion alleles available to researchers. The relationships between strains are complex and different regions of the genome possess different genealogies due to recombination throughout the natural history of the species, which may not be apparent in studies utilizing smaller numbers of genetic markers.

Figure 1

Indels on the left arm of chromosome II in twelve natural isolates of C. elegans. Deletions unique to a strain are plotted in grey and deletions found in multiple strains are plotted in black. Amplified sequences present in only one strain are shown in orange and those found in multiple strains are shown in red. The actual position of amplified sequences in the genome is unknown. The position of amplifications shown here corresponds to the position of the single copy of that sequence in the N2 reference genome. Small indels are not shown to scale. The blue arrows indicate the site of a possible recombination event. KR314 shares alleles with CB4853 and CB4858 to the right of the arrows but not to the left.

Figure 2

The number of deletions in each of 12 natural isolates of C. elegans that are also present in other isolates. The numbers of other isolates that carry the same deletions are indicated by the colors in the figure legend.

Figure 3

Unrooted consensus tree for 12 natural isolates of C. elegans. The two numbers listed in parentheses next to each node are the percentage of trees among 1000 bootstrap replicates that included all strains distal from CB4856, under Camin-Sokal and Wagner parsimony, respectively. The tree should not be interpreted strictly as a phylogeny due to recombination between strains.