A genome must locate its coding genes on the chromosomes in a meaningful manner 
with the help of natural selection, but the mechanism of gene order evolution is 
poorly understood. To explore the role of selection in shaping the current order 
of coding genes and their cis-regulatory elements, a comparative genomic 
approach was applied to the baker's yeast Saccharomyces cerevisiae and its close 
relatives. S. cerevisiae have experienced a whole-genome duplication followed by 
an extensive reorganization process of gene order, during which a number of new 
adjacent gene pairs appeared. We found that the proportion of new adjacent gene 
pairs in divergent orientation is significantly reduced, suggesting that such 
new divergent gene pairs may be disfavored most likely because their 
coregulation may be deleterious. It is also found that such new divergent gene 
pairs have particularly long intergenic regions. These observations suggest that 
selection specifically worked against deletions in intergenic regions of new 
divergent gene pairs, perhaps because they should be physically kept away so 
that they are not coregulated. It is indicated that gene regulation would be one 
of the major factors to determine the order of coding genes.