Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

Maintenance Of Duplicated Regulatory Genes In Arabidopsis thaliana Driven By Expression Pattern Shifts

Jill Ricker¹ , Qing Zhang³ , Kerr Wall¹ , Liying Cui¹ , Xiaohong Zhang^1,2 , Jim Leebens-Mack^1,2 , Naomi Altman³ , Hong Ma^1,2 , Claude dePamphilis^1,2

¹  Dept. of Biology, The Pennsylvania State University, University Park, PA, 16802, USA

²  Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA

³  Dept. of Statistics, The Pennsylvania State University, University Park, PA, 16802, USA

Gene duplication is highly prevalent in the nuclear genomes of plants, and plays an important role in the diversity of form and function by providing raw material for molecular evolution. Gene duplicates (paralogs) have a variety of fates – nonfunctionalization, subfunctionalization, and neofunctionalization. However, it is not known if these fates primarily occur through changes in gene expression regulation or changes in the protein sequence. This study attempts to identify the role of expression pattern shifts in the maintenance of paralogs. A total of 280 paralogous sets of Arabidopsis thaliana genes were identified from an initial set of 1700 regulatory genes using phylogenetic clustering based on maximum parsimony phylogenies from amino acid sequences from Arabidopsis and Oryza. A 2-way ANOVA was performed to identify gene, tissue, and gene by tissue interactions within each paralogous set based on Affymetrix whole genome microarray data from wild-type root, stem, leaf, inflorescence, stage 12 flower, and silique tissues. Results indicate that an overwhelming majority of paralogous sets have statistically significant gene by tissue interactions. Calculation of Ka/Ks ratios for each paralogous set indicates that paralogous sets with gene by tissue interactions have maintained protein constraint while lowly expressed genes over all tissues have decreased protein constraint. We conclude that maintenance of duplicated regulatory genes in Arabidopsis thaliana is driven by expression pattern shifts rather than changes in the protein sequence.