Worm Breeder's Gazette 15(5): 17 (February 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.
The Netherlands Cancer Institute, Division of Molecular Biology, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
The previous WBG described that Single Nucleotide
Polymorphisms (SNP) between the RC301 strain and the canonical
genome sequence of Bristol N2 were detected after directed PCR
amplification of intergenic regions and subsequent sequencing
(Jakubowski and Kornfeld, WBG 15#4, p 16) or restriction digestions
(Schaefer et al., WBG 15#4, p 17). Jakubowski and Kornfeld found
on average one SNP per 1.4 kbp.
We sampled the genome of C. elegans for SNPs,
taking a different approach. We shotgun cloned fragments of around
1.5 kbp of genomic DNA, sequenced these, then compared them to
the Bristol N2 genome sequence, to ask: does the clone map to
a unique sequence, and -if so- do we recognise polymorphisms?
We performed this analysis for 4 natural isolates, 2 from the
USA, one from Germany, and one from Australia. We found the following:
|strain||isolated in||bp sequenced||SNPs||SNP/bp|
The SNPs found thus far seem to be spread over the
genome (4 SNPs on chromosome I, 4 on II, 5 on III, 1 on IV, 2
on V and 4 on X). Our current numbers are too low to investigate
whether indeed SNPs are more common in non-coding regions.
For the first few SNPs, we asked whether the sequences
in the other natural isolates resembled that of Bristol N2, or
that of the SNP. As expected, we found that several SNPs initially
detected in one strain were also found in some but not in all
other isolates. One example: a T in the Australian AB1, is a G
in Bristol N2, and we found it to be like AB1 in the Californian
CB4857 strain and the German RC301 strain, while the TR403 strain
from Wisconsin resembled the Bristol N2 strain. Thus different
patches of the genome have different common ancestors.
We are now scaling up this approach, with the goal
to find in the order of 500 SNPs spread over the genome. We will
then probe these positions in the other 3 strains (and possibly
some more natural isolates), to try and generate a world-wide
SNP map of the species. This should allow one to make statements
such as: the strain from California has the centre of chromosome
III in common with the Australian strain, but the left arm in
common with the German strain.
The SNPs will be added to ACeDB, and can be used
as markers on the genetic map. They can be recognised by PCR followed
by sequencing, but we also found that the SNPs we looked at could
be visualised by SSCP analysis.