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

Rose AM, O'Neil NJ, Bilenky M, Butterfield YS, Malhis N, Flibotte S, Jones MR, Marra M, Baillie DL, Jones SJ - BMC Genomics (2010)

Bottom Line: With this data removed, no obvious pattern in the distribution of the base differences along the chromosomes was apparent.A subset of sequence alterations affecting coding regions were confirmed by an independent approach using oligo array comparative genome hybridization.In this study, we observed no evidence of a mutator effect at the nucleotide level attributable to the Rec-1 mutation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada. ann.rose@ubc.ca

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.

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Comparision of the Genetic and Physical Maps of chromosome I. The top line shows the wild-type (N2) genetic map of autosome I of C. elegans using genetic distances measured by Zetka and Rose, 1995. Line 2 is the position of the gene markers on the physical map as annotated in WormBase http://www.wormbase.org. The bottom line is the position of markers in the Rec-1 mutant (data taken from Zetka and Rose, 1995).
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Figure 1: Comparision of the Genetic and Physical Maps of chromosome I. The top line shows the wild-type (N2) genetic map of autosome I of C. elegans using genetic distances measured by Zetka and Rose, 1995. Line 2 is the position of the gene markers on the physical map as annotated in WormBase http://www.wormbase.org. The bottom line is the position of markers in the Rec-1 mutant (data taken from Zetka and Rose, 1995).

Mentions: The recombinational suppression of the gene clusters is eliminated in the mutant Rec-1 [10], resulting in increased crossing over in the autosomal central regions and a compensatory decrease in the arms [9]. The consequence is an altered distribution of meiotic exchange events while retaining the same overall number. In Rec-1, the genetic recombination map resembles more closely the physical length of the chromosome than it does the wild-type pattern of crossovers. The phenotype was originally identified as a recessive mutation in a strain heterozygous for morphological markers in the central cluster of chromosome I, dpy-5(e61) unc-15(e73) +/+ +unc-13(e51). A three-fold increase in crossing over was observed in the central region of the autosomes [10]. The visible markers were eventually eliminated by recombination resulting in a wild-type appearing strain, BC313, for which the major phenotype is an altered distribution of recombination, affecting both exchange of flanking markers and apparent intragenic gene conversion [11]. There are no detrimental effects on growth, progeny number or spontaneous mutation rate. Nondisjunction of the X-chromosome is elevated somewhat, but not dramatically. The rec-1(s180) mutation is inherited as a Mendelian recessive, and crossover distribution is altered for the entire genome [10], including the X-chromosome, despite the fact that it has a more uniform distribution of recombination events (V. Vijayaratum and AMR, unpublished data). The consequence of the mutation is that the recombination map in Rec-1 more closely reflects the physical map than the genetic map in wild type [9] (Figure 1).


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

Rose AM, O'Neil NJ, Bilenky M, Butterfield YS, Malhis N, Flibotte S, Jones MR, Marra M, Baillie DL, Jones SJ - BMC Genomics (2010)

Comparision of the Genetic and Physical Maps of chromosome I. The top line shows the wild-type (N2) genetic map of autosome I of C. elegans using genetic distances measured by Zetka and Rose, 1995. Line 2 is the position of the gene markers on the physical map as annotated in WormBase http://www.wormbase.org. The bottom line is the position of markers in the Rec-1 mutant (data taken from Zetka and Rose, 1995).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2837035&req=5

Figure 1: Comparision of the Genetic and Physical Maps of chromosome I. The top line shows the wild-type (N2) genetic map of autosome I of C. elegans using genetic distances measured by Zetka and Rose, 1995. Line 2 is the position of the gene markers on the physical map as annotated in WormBase http://www.wormbase.org. The bottom line is the position of markers in the Rec-1 mutant (data taken from Zetka and Rose, 1995).
Mentions: The recombinational suppression of the gene clusters is eliminated in the mutant Rec-1 [10], resulting in increased crossing over in the autosomal central regions and a compensatory decrease in the arms [9]. The consequence is an altered distribution of meiotic exchange events while retaining the same overall number. In Rec-1, the genetic recombination map resembles more closely the physical length of the chromosome than it does the wild-type pattern of crossovers. The phenotype was originally identified as a recessive mutation in a strain heterozygous for morphological markers in the central cluster of chromosome I, dpy-5(e61) unc-15(e73) +/+ +unc-13(e51). A three-fold increase in crossing over was observed in the central region of the autosomes [10]. The visible markers were eventually eliminated by recombination resulting in a wild-type appearing strain, BC313, for which the major phenotype is an altered distribution of recombination, affecting both exchange of flanking markers and apparent intragenic gene conversion [11]. There are no detrimental effects on growth, progeny number or spontaneous mutation rate. Nondisjunction of the X-chromosome is elevated somewhat, but not dramatically. The rec-1(s180) mutation is inherited as a Mendelian recessive, and crossover distribution is altered for the entire genome [10], including the X-chromosome, despite the fact that it has a more uniform distribution of recombination events (V. Vijayaratum and AMR, unpublished data). The consequence of the mutation is that the recombination map in Rec-1 more closely reflects the physical map than the genetic map in wild type [9] (Figure 1).

Bottom Line: With this data removed, no obvious pattern in the distribution of the base differences along the chromosomes was apparent.A subset of sequence alterations affecting coding regions were confirmed by an independent approach using oligo array comparative genome hybridization.In this study, we observed no evidence of a mutator effect at the nucleotide level attributable to the Rec-1 mutation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada. ann.rose@ubc.ca

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.

Show MeSH
Related in: MedlinePlus