Updated map of duplicated regions in the yeast genome

We have updated the map of duplicated chromosomal segments in the Saccharom yces cerevisiae genome originally published by Wolfe and Shields in 1997 (N ature 387, 708-713). The new analysis is based on the more sensitive Smith- Waterman search method instead of BLAST. The parameters used to identify du plicated chromosomal regions were optimized such as to maximize the amount of the genome placed into paired regions, under the assumption that the hyp othesis that the entire genome was duplicated in a single event is correct. The core of the new map, with 52 pairs of regions containing three or more duplicated genes, is largely unchanged from our original map. 39 tRNA gene pairs and one snRNA pair have been added. To find additional pairs of gene s that may have been formed by whole genome duplication, we searched throug h the parts of the genome that are not covered by this core map, looking fo r putative duplicated chromosomal regions containing only two duplicate gen es instead of three, or having lower-scoring gene pairs. This approach iden tified a further 32 candidate paired regions, bringing the total number of protein-coding genes on the duplication map to 905 (16% of the proteome). T he updated map suggests that a second copy of the ribosomal DNA array has b een deleted from chromosome IV. (C) 1999 Elsevier Science B.V. All rights r eserved.