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

BMC Genomics
Jason MaydanDonald G Moerman

Abstract

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. 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. 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 sign...Continue Reading

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Datasets Mentioned

BETA
CB4856
GSE19440

Methods Mentioned

BETA
Gene Knockout
genotyping
identified
by
electrophoresis
PCR
PCRs
ubiquitination

Software Mentioned

LOWESS
LIAN
Phylip
MegaBLAST
R
R programming language

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