Worm Breeder's Gazette 16(1): 27 (October 1, 1999)

These abstracts should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with the consent of the author.

World wide worm SNPs (II)

Romke Koch, Henri G.A.M. van Luenen, Marieke van der Horst, Karen L. Thijssen, Ronald H.A. Plasterk

The Netherlands Cancer Institute, Division of Molecular Biology, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands

In the last WBG we presented single nucleotide polymorphisms (SNPs) in natural isolates from around the world (AB1 from Australia, CB4857 from California, RC301 from Germany and TR403 from Madison) (Koch et al., WBG 15#5, p17). We now sequenced over 700 kb and found 366 polymorphisms. The majority of polymorphisms (90%) are single base point mutations, but we also found small insertions and deletions of two or more base pairs. The lowest SNP frequency was found in TR403 (1:8750 base pairs), the highest frequency was found in CB4857 (1:1445 base pairs). On average we found 1 SNP per 2000 base pairs. After checking 63 potential SNPs, we found 3 to be a sequence error in N2. Based on this we estimate the error rate for the C. elegans genome to be 1 in 42,000. SNPs are enriched on the arms of the five autosomes, which fits with the idea of more rapid evolution on the chromosome arms (C. elegans sequencing consortium, Science. 1998 Dec 11;282(5396):2012-8) .
We found 61% of the single base pair substitutions to be transitions. The nematode genome is not methylated at CpG sequences. The most common mutations in the human genome involve CpG mutations, due to deamination of the methylated C. To our surprise we found that also in C. elegans there is a  bias to involve CpG sequences in polymorphisms. Possibly there are additional ways for neighbouring nucleotides to affect mutation rates.
We extended the analysis to 6 other wild isolates: AB4 from Adelaide, Australia; CB4555 from Pasadena, California; CB4856 from Hawaii; DH424 from El Prieto Canyon and KR314 from Vancouver. Most SNPs are old. We found only 25% of the SNPs to be unique to the strain in which they were found. As can be seen in figure 1, the SNP pattern for each strain differs per chromosome. For example chromosomes II of AB1 and AB4 are different, whereas their X chromosomes are almost identical. Each isolate is a mosaic of different lineages as a result of recombination of patches of DNA between ancestral isolates.
There are regions of high and low polymorphism. The majority (80%) of sequenced clones did not have a polymorphism. If SNPs were normally distributed over the clones one would not expect to find many clones with two or more SNPs. We found clones with more than 4 SNPs. This suggested that clones are clustered in the genome. We sequenced the immediate flanks of some multi-SNP clones and found every one of these to contain one or more SNPs. We estimate the level of polymorphism between Bristol N2 and CB4857 to be 1:100 base pairs in a SNP-rich area and 15 x lower in a SNP-poor area. We determined the length of some contigous highly polymorphic SNP tracks by sequencing and found one of them to be 600 kilobase pairs long.
  We did not find any continent specific worm races, all isolates show mosaic genome patterns. An exception is formed by an isolate from an island (CB4856 from Hawaii) that in addition to shared SNPs, also contains many unique SNPs absent in the rest of the world.
We thank Amanda McMurray and Jane Rogers of The Sanger Centre and Roelof Pruntel for help in sequencing and Richard Durbin for sharing unpublished data.