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Nucleic Acids Research, 2003, Vol. 31, No. 10 2553-2560
© 2003 Oxford University Press

Limited microsynteny between the genomes of Pristionchus pacificus and Caenorhabditis elegans

Kwang-Zin Lee, Andreas Eizinger, Ramkumar Nandakumar1, Stephan C. Schuster1 and Ralf J. Sommer

Abteilung für Evolutionsbiologie and 1 Genomzentrum, Max-Planck Institut für Entwicklungsbiologie, Spemannstrasse 37, 72076 Tübingen, Germany

Andreas Eizinger, Department of Developmental Biology, Stanford University, Beckman Center, 279 Campus Drive B-341, Stanford, CA 94305, USA

Nematodes are an attractive group of organisms for studying the evolution of developmental processes. Pristionchus pacificus was established as a satellite organism for comparing vulva development and other processes to Caenorhabditis elegans. The generation of a genetic linkage map of P.pacificus has provided a first insight into the structure and organization of the genome of this species. Pristionchus pacificus and C.elegans are separated from one another by >100 000 000 years such that the structure of the genomes of these two nematodes might differ substantially. To evaluate the amount of synteny between the two genomes, we have obtained 126 kb of continuous genomic sequence of P.pacificus, flanking the developmental patterning gene pal-1. Of the 20 predicted open reading frames in this interval, 11 have C.elegans orthologs. Ten of these 11 orthologs are located on C.elegans chromosome III, indicating the existence of synteny. However, most of these genes are distributed over a 12 Mb interval of the C.elegans genome and only three pairs of genes show microsynteny. Thus, intrachromosomal rearrange ments occur frequently in nematodes, limiting the likelihood of identifying orthologous genes of P.pacificus and C.elegans based on positional information within the two genomes.


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