Genomic Sequence of a Mutant Strain of Caenorhabditis elegans with an Altered Recombination Pattern

Background: The original sequencing and annotation of the Caenorhabditis elegans genome along with recentadvances in sequencing technology provide an exceptional opportunity for the genomic analysis of wild-type andmutant strains. Using the Illumina Genome Analyzer, we sequenced the entire genome of Rec-1, a strain that altersthe distribution of meiotic crossovers without changing the overall frequency. Rec-1 was derived fromethylmethane 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 thedistribution of meiotic recombination events.Results: Using Illumina sequencing and MAQ software, 83% of the base pair sequence reads were aligned to thereference genome available at Wormbase, providing a 21-fold coverage of the genome. Using the softwareprograms MAQ and Slider, we observed 1124 base pair differences between Rec-1 and the reference genome inWormbase (WS190), and 441 between the mutagenized Rec-1 (BC313) and the wild-type N2 strain (VC2010). Themost frequent base-substitution was G:C to A:T, 141 for the entire genome most of which were on chromosomes Ior X, 55 and 31 respectively. With this data removed, no obvious pattern in the distribution of the base differencesalong the chromosomes was apparent. No major chromosomal rearrangements were observed, but additionalinsertions of transposable elements were detected. There are 11 extra copies of Tc1, and 8 of Tc2 in the Rec-1genome, 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 affectingcoding 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 recombinationevent with no other significant phenotypic consequences. In this study, we observed no evidence of a mutatoreffect at the nucleotide level attributable to the Rec-1 mutation.