Polymorphic Segmental Duplication In The Nematode Caenorhabditis elegans

Background: The nematode Caenorhabditis elegans was the first multicellular organism to have itsgenome fully sequenced. Over the last 10 years since the original publication in 1998, the C. elegansgenome has been scrutinized and the last gaps were filled in November 2002, which present aunique opportunity for examining genome-wide segmental duplications.Results: Here, we performed analysis of the C. elegans genome in search for segmental duplicationsusing a new tool–OrthoCluster–we have recently developed. We detected 3,484 duplicatedsegments–duplicons–ranging in size from 234 bp to 108 Kb. The largest pair of duplicons, 108 kbin length located on the left arm of Chromosome V, was further characterized. They are nearlyidentical at the DNA level (99.7% identity) and each duplicon contains 26 putative protein codinggenes. Genotyping of 76 wild-type strains obtained from different labs in the C. elegans communityrevealed that not all strains contain this duplication. In fact, only 29 strains carry this large segmentalduplication, suggesting a very recent duplication event in the C. elegans genome.Conclusion: This report represents the first demonstration that the C. elegans laboratory wildtypeN2 strains has acquired large-scale differences.