15th International Conference on Arabidopsis Research - TAIR

T06-021
Gene Subfunctionalization and Neofunctionalization
in Arabidopsis Gene Families studied using Gene
Expression and Sequence Data
Kiana Toufighi(1), David Guttman(1), Nicholas J. Provart(1)
1-Dept. of Botany, University of Toronto, Toronto, ON. CANADA. M5S 3B2
The process of subfunctionalization (a gene acquiring different expression
patterns) and/or neofunctionalization (a gene acquiring a new biochemical
function) is thought to promote the preservation of duplicated genes (Lynch
and Force, 2000). Several papers have been published recently which provide
a theoretical framework for this process (Lynch and Force, 2000; Ohta,
2003).
Collections of gene expression data represent a rich resource for many
aspects of biology. In the case of Arabidopsis, one collection recently made
available is that from NASCArrays (Craigon et al., 2004), in which expression
levels for more than 22 000 genes in >124 samples have been measured
using the Affymetrix GeneChip technology platform. We have used the data in
an unbiased way, as proxies for promoter composition: the data were used to
calculate the similarity of expression patterns of all possible pairwise combinations
of genes in each of 3377 gene families in Arabidopsis. At the same
time, we performed pairwise global sequence alignments using ClustalW for
the same gene pairs, and calculated the similarity for each pair. These pairwise
comparision values for expression correlation and sequence similarity
were plotted against each other, and the process was repeated for all gene
families. Binning averages were generated in order to simplify the resultant
data sets. In general, even for gene which exhibit very high levels of sequence
similarity, expression levels did not correlate by more than 10-20%.
Furthermore, when we examined the pairwise sequence alignments and used
them to calculate Kn/Ks ratios, we found, as have others (Kondrashov et al.,
2002), that most pairs had a Kn/Ks ratio