159. Searching for Synteny: A Whole-Genome Comparison of Caenorhabditis elegans with Saccharomyces cerevisiae 

Karen L. Diemer and Kelly A. Frazer 
Genome Sciences Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road MS 84-171, Berkeley, CA 94720  
kelly@mhgc.lbl.gov 

Characterizing the syntenic relationships of genes in different species has been a valuable tool for deciphering a variety of biological phenomenons. The completely sequenced yeast Saccharomyces cerevisiae and the extensively sequenced worm Caenorhabditis elegans genomes provide us with the opportunity to search on a whole-genome wide basis for conservation of gene order between these distantly related eukaryotic organisms. The yeast and worm genomes diverged approximately 965 million years ago (Doolittle et al. 1996), therefore any conservation of gene order is likely due to biological forces dictating genome organization rather than a lack of shuffling of genes that were neighbors in the last common ancestor. We compared protein translations of the 6221 yeast ORFs to the available worm sequence data (85% of total) to determine whether any paired genes, loci that are consecutive (neighbors) in both organisms, exist. Ten pairs of adjacent yeast ORFs were identified that have significant matches (TBLASTN expect values <1e-21) adjacent to each other in the worm genome. Four of these paired ORFs consist of genes encoding for different core histones, three consist of genes that encode for proteins of no known related function, and three consist of ORFs that are part of the same gene in yeast but had not yet been identified as such. These data indicate that the study of conserved gene pairs in distantly related eukaryotes may provide insights into the selective pressures governing the clustering of certain genes as well as serve to facilitate the assignment of putative ORFs into protein encoding units.