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High-resolution array comparative genomic hybridization analysis reveals unanticipated complexity of genetic deficiencies on chromosome V in Caenorhabditis elegans

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Abstract

Genomic rearrangements are widely used in Caenorhabditis elegans research but many remain incompletely characterized at the physical level. We have used oligo-array comparative genomic analysis to assess the physical structure of 20 deficiencies and a single duplication of chromosome V. We find that while deletions internal to the chromosome appear simple in structure, terminal deletions are complex, containing duplications in addition to the deletion. Additionally, we confirm that transposon-induced deficiencies contain breakpoints that initiate at Tc1 elements. Finally, 13 of these deficiencies are known to suppress recombination far beyond the extent of the deletion. These deficiencies fall into two classes: strong and weak suppressors of adjacent recombination. Analysis of the deleted regions in these deficiencies reveals no common physical sites to explain the observed differences in recombination suppression. However, we find a strong correlation between the size of the rearranged chromosome and the severity of recombination suppression. Rearranged chromosomes that have a minor effect on recombination fall within 2% of normal chromosome size. Our observations highlight the use of array-based approaches for the analysis of rearranged genomes, revealing previously unidentified deficiency characteristics and addressing biologically relevant questions.

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Acknowledgments

This research was funded by the Canadian Space Agency and Natural Sciences and Engineering Research Council of Canada.

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Authors and Affiliations

  1. Department of Medical Genetics, Life Sciences Centre, University of British Columbia, Vancouver, BC, Canada

    Martin R. Jones, Nigel J. O’Neil & Ann M. Rose

  2. Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada

    Shu Yi Chua, Robert C. Johnsen & David L. Baillie

Authors
  1. Martin R. Jones
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  2. Shu Yi Chua
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  3. Nigel J. O’Neil
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  4. Robert C. Johnsen
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  5. Ann M. Rose
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  6. David L. Baillie
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Corresponding author

Correspondence to Martin R. Jones.

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Communicated by S. Hekimi.

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Jones, M.R., Chua, S.Y., O’Neil, N.J. et al. High-resolution array comparative genomic hybridization analysis reveals unanticipated complexity of genetic deficiencies on chromosome V in Caenorhabditis elegans . Mol Genet Genomics 282, 37–46 (2009). https://doi.org/10.1007/s00438-009-0444-8

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  • DOI: https://doi.org/10.1007/s00438-009-0444-8

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