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Published on May 30, 2008; 10.1104/pp.108.122416

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Received May 1, 2008
Accepted May 27, 2008

Comparative Analysis of Divergent and Convergent Gene Pairs and Their Expression Patterns in Rice, Arabidopsis, and Populus

Nicholas Krom and Wusirika Ramakrishna *

Department of Biological Sciences, Michigan Technological University, Houghton, Michigan 49931, USA

* Corresponding author; email: wusirika{at}mtu.edu.

Comparative analysis of the organization and expression patterns of divergent and convergent gene pairs in multiple plant genomes can identify patterns that are shared by more than one species or are unique to a particular species. Here, we study the coexpression and inter-species conservation of divergent and convergent gene pairs in three plant species: rice, Arabidopsis, and Populus. Strongly correlated expression levels between divergent and convergent genes were found to be quite common in all three species, and the frequency of strong correlation appears to be independent of intergenic distance. Conservation of divergent or convergent arrangement among these species appears to be quite rare. However, conserved arrangement is significantly more frequent when the genes display strongly correlated expression levels or have one or more Gene Ontology (GO) classes in common. A correlation between intergenic distance in divergent and convergent gene pairs and shared GO classes was observed, in varying degrees, in rice and Populus but not in Arabidopsis. Furthermore, multiple GO classes were either over-represented or under-represented in Arabidopsis and Populus gene pairs while only two GO classes were under-represented in rice divergent gene pairs. Three cis-regulatory elements common to both Arabidopsis and rice were over-represented in the intergenic regions of strongly correlated divergent gene pairs compared to those of non-correlated pairs. Our results suggest that shared as well as unique mechanisms operate in shaping the organization and function of divergent and convergent gene pairs in different plant species.






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