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.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.
