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Open Access Research article

Genomic sequence of a mutant strain of Caenorhabditis elegans with an altered recombination pattern

Ann M Rose1*, Nigel J O'Neil1, Mikhail Bilenky2, Yaron S Butterfield2, Nawar Malhis2, Stephane Flibotte2, Martin R Jones1, Marco Marra2, David L Baillie3 and Steven JM Jones2

Author Affiliations

1 Department of Medical Genetics, University of British Columbia, 419 - 2125 East Mall, Vancouver, BC, V6T 1Z4, Canada

2 Genome Sciences Centre, British Columbia Cancer Research Centre, 600 West 10th Avenue, Vancouver, BC, V5Z 4E6, Canada

3 Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada

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BMC Genomics 2010, 11:131  doi:10.1186/1471-2164-11-131

Published: 23 February 2010

Abstract

Background

The original sequencing and annotation of the Caenorhabditis elegans genome along with recent advances in sequencing technology provide an exceptional opportunity for the genomic analysis of wild-type and mutant strains. Using the Illumina Genome Analyzer, we sequenced the entire genome of Rec-1, a strain that alters the distribution of meiotic crossovers without changing the overall frequency. Rec-1 was derived from ethylmethane sulfonate (EMS)-treated strains, one of which had a high level of transposable element mobility. Sequencing of this strain provides an opportunity to examine the consequences on the genome of altering the distribution of meiotic recombination events.

Results

Using Illumina sequencing and MAQ software, 83% of the base pair sequence reads were aligned to the reference genome available at Wormbase, providing a 21-fold coverage of the genome. Using the software programs MAQ and Slider, we observed 1124 base pair differences between Rec-1 and the reference genome in Wormbase (WS190), and 441 between the mutagenized Rec-1 (BC313) and the wild-type N2 strain (VC2010). The most frequent base-substitution was G:C to A:T, 141 for the entire genome most of which were on chromosomes I or X, 55 and 31 respectively. With this data removed, no obvious pattern in the distribution of the base differences along the chromosomes was apparent. No major chromosomal rearrangements were observed, but additional insertions of transposable elements were detected. There are 11 extra copies of Tc1, and 8 of Tc2 in the Rec-1 genome, most likely the remains of past high-hopper activity in a progenitor strain.

Conclusion

Our analysis of high-throughput sequencing was able to detect regions of direct repeat sequences, deletions, insertions of transposable elements, and base pair differences. A subset of sequence alterations affecting coding regions were confirmed by an independent approach using oligo array comparative genome hybridization. The major phenotype of the Rec-1 strain is an alteration in the preferred position of the meiotic recombination event with no other significant phenotypic consequences. In this study, we observed no evidence of a mutator effect at the nucleotide level attributable to the Rec-1 mutation.