SCIENCE AT THE EDGE SEMINAR Friday, September 15 at 11:30am Room 1400 Biomedical and Physical Sciences Bldg. Refreshments at 11:15 Speaker: Shin-Han Shiu Department of Plant Biology Michigan State University, East Lansing, MI Title: Genome Evolution and Gene Duplication in Eukaryotes Abstract: A typical eukaryote genome contains thousands to tens of thousands genes. Interestingly, most genes are related to at least one other gene in the same genome and form gene families of various sizes. There are several outstanding questions regarding the evolution of duplicate genes and gene families. One of the major mechanisms for gene duplication is polyploidization. However, it is not known if the duplicates are lost in a few generations or if gene loss is a slow, drawn-out process. To address this question, we examined sequence polymorphism in a recently created (~20,000 years ago) polyploid plant, Arabidopsis suecica, by hybridizing genomic DNA to a microarray that represents nearly the whole Arabidopsis thaliana genome. We found that there is little evidence for deletion of most genes after ~20,000 generations. In addition to the question of the rate of duplicate gene loss, we are also interested in determining whether certain types of genes are preferentially retained. To address this, we have examined the evolutionary histories of various gene families in both plants and animals. We found significant preferential retention in several gene families particularly those involved in sensing environmental cues. Analysis of gene families relies on thorough annotation of genomes. Recently, several studies have shown that most intergenic sequences are expressed indicating the presence of novel genes. I will introduce an analysis pipeline for identifying novel genes from 'intergenic' regions to improve genome annotation.