Abstract
BackgroundGenome wide analysis of variation within a species can reveal the evolution of fundamental biological processes such as mutation, recombination, and natural selection. We compare genome wide sequence differences between two independent isolates of the nematode Caenorhabditis elegans (CB4856 and CB4858) and the reference genome (N2).ResultsThe base substitution pattern when comparing N2 against CB4858 reveals a transition over transversion bias (1.32:1) that is not present in CB4856. In CB4856, there is a significant bias in the direction of base substitution. The frequency of A or T bases in N2 that are G or C bases in CB4856 outnumber the opposite frequencies for transitions as well as transversions. These differences were not observed in the N2/CB4858 comparison. Similarly, we observed a strong bias for deletions over insertions in CB4856 (1.44: 1) that is not present in CB4858. In both CB4856 and CB4858, there is a significant correlation between SNP rate and recombination rate on the autosomes but not on the X chromosome. Furthermore, we identified numerous significant hotspots of variation in the CB4856-N2 comparison.In both CB4856 and CB4858, based on a measure of the strength of selection (ka/ks), all the chromosomes are under negative selection and in CB4856, there is no difference in the strength of natural selection in either the autosomes versus X or between any of the chromosomes. By contrast, in CB4858, ka/ks values are smaller in the autosomes than in the X chromosome. In addition, in CB4858, ka/ks values differ between chromosomes.ConclusionsThe clear bias of deletions over insertions in CB4856 suggests that either the CB4856 genome is becoming smaller or the N2 genome is getting larger. We hypothesize the hotspots found represent alleles that are shared between CB4856 and CB4858 but not N2. Because the ka/ks ratio in the X chromosome is higher than the autosomes on average in CB4858, purifying selection is reduced on the X chromosome.
Highlights
Genome wide analysis of variation within a species can reveal the evolution of fundamental biological processes such as mutation, recombination, and natural selection
Overview of single-nucleotide polymorphism (SNP) variation We identified a total of 13360 putative SNPs in our analysis of the CB4856 genome compared to N2
A recent genome wide comparison of N2 and the strain CB4858 [11] revealed a much lower genome wide SNP level (5.89 × 10-4 SNPs per base) and those differences were dominated by base substitutions
Summary
Genome wide analysis of variation within a species can reveal the evolution of fundamental biological processes such as mutation, recombination, and natural selection. N2 (from Bristol, England) is the most commonly used lab strain It is the strain for which the genome sequence has been completely determined. They have been cultured in the lab In their C. elegans population genomics study, Rockman and Kruglyak [12] distinguished 41 haplotypes among 125 wild isolates in their genotype data from 1460 N2-CB4856 SNPs. In their C. elegans population genomics study, Rockman and Kruglyak [12] distinguished 41 haplotypes among 125 wild isolates in their genotype data from 1460 N2-CB4856 SNPs They indicated that CB4858 shares haplotype 20 with strains from other localities, including AB2-4, from Adelaide, Australia, and CB4855, from Palo Alto, California. The genotypic similarity among CB4858, CB4855, and AB2-4 suggests they may share an ancestor in a laboratory
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