Plant Physiol. Illumina
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH
QUICK SEARCH:   [advanced]


     

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

OPEN ACCESS ARTICLE
This Article
Free via Open Access: OA
Right arrow Full Text (Plant Physiology Preview (PDF))
Right arrow Supplemental Data
Right arrowOA All Versions of this Article:
147/4/1763    most recent
pp.108.122416v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via CrossRef
Right arrow Citing Articles via Web of Science (4)
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Krom, N.
Right arrow Articles by Ramakrishna, W.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Krom, N.
Right arrow Articles by Ramakrishna, W.
Agricola
Right arrow Articles by Krom, N.
Right arrow Articles by Ramakrishna, W.

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.






HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH
ASPB Publications PLANT PHYSIOLOGY® THE PLANT CELL
Copyright © 2008 by the American Society of Plant Biologists