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Published online before print November 8, 2000, 10.1101/gr.GR-1471R
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Vol. 10, Issue 11, 1690-1696, November 2000

REPORTS
Single Nucleotide Polymorphisms in Wild Isolates of Caenorhabditis elegans

Romke Koch,1 Henri G.A.M. van Luenen,2 Marieke van der Horst,1 Karen L. Thijssen,1 and Ronald H.A. Plasterk1,3

1 The Hubrecht Laboratory, Centre for Biomedical Genetics, 3584 CT Utrecht, Netherlands; 2 The Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands

Caenorhabditis elegans (isolate N2 from Bristol, UK) is the first animal of which the complete genome sequence was available. We sampled genomic DNA of natural isolates of C. elegans from four different locations (Australia, Germany, California, and Wisconsin) and found single nucleotide polymorphisms (SNPs) by comparing with the Bristol strain. SNPs are under-represented in coding regions, and many were found to be third base silent codon mutations. We tested 19 additional natural isolates for the presence and distribution of SNPs originally found in one of the four strains. Most SNPs are present in isolates from around the globe and thus are older than the latest contact between these strains. An exception is formed by an isolate from an island (Hawaii) that contains many unique SNPs, absent in the tested isolates from the rest of the world. It has been noticed previously that conserved genes (as defined by homology to genes in Saccharomyces cerevisiae) cluster in the chromosome centers. We found that the SNP frequency outside these regions is 4.5 times higher, supporting the notion of a higher rate of evolution of genes on the chromosome arms.

3 Corresponding author.

10:1690-1696 ©2000 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/00 $5.00
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