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| Status |
Public on Dec 17, 2009 |
| Title |
Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Genome variation profiling by genome tiling array
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| Summary |
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.
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| Overall design |
Twelve C. elegans natural isolate samples were studied. There were no replicates or dye-swap hybridizations.
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| Contributor(s) |
Maydan JS, Lorch A, Edgley ML, Flibotte S, Moerman DG |
| Citation(s) |
20100350 |
| Submission date |
Dec 11, 2009 |
| Last update date |
Mar 21, 2012 |
| Contact name |
Stephane Flibotte |
| Organization name |
University of British Columbia
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| Department |
Faculty of Science
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| Lab |
UBC/LSI Bioinformatics Core Facility
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| Street address |
2370-6270 University Blvd.
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| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V6T 1Z3 |
| Country |
Canada |
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| Platforms (1) |
| GPL9792 |
UBC Moerman Caenorhabditis elegans WG 2006 |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA122311 |
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