Research article

Characterization of paralogous protein families in rice

Haining Lin^1,3,7 , Shu Ouyang¹ , Amy Egan^1,6 , Kan Nobuta² , Brian J Haas^1,5 , Wei Zhu¹ , Xun Gu^3,4 , Joana C Silva^1,6 , Blake C Meyers² and C Robin Buell^1,7

¹  The Institute for Genomic Research, 9712 Medical Center Dr., Rockville, MD 20850, USA and J.Craig Venter Institute, 9704 Medical Center Dr., Rockville, MD 20850, USA

²  Department of Plant and Soil Sciences & Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA

³  Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA

⁴  Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA

⁵  The Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA

⁶  Institute for Genome Sciences & Department of Microbiology & Immunology, University of Maryland, Baltimore, School of Medicine, HSF-II, Rm S-445, 20 Penn St., Baltimore, MD 21201, USA

⁷  Department of Plant Biology, Michigan State University, 166 Plant Biology Building, East Lansing, MI 48824, USA

author email corresponding author email

BMC Plant Biology 2008, 8:18doi:10.1186/1471-2229-8-18

Published:	19 February 2008

Abstract

Background

High gene numbers in plant genomes reflect polyploidy and major gene duplication events. Oryza sativa, cultivated rice, is a diploid monocotyledonous species with a ~390 Mb genome that has undergone segmental duplication of a substantial portion of its genome. This, coupled with other genetic events such as tandem duplications, has resulted in a substantial number of its genes, and resulting proteins, occurring in paralogous families.

Results

Using a computational pipeline that utilizes Pfam and novel protein domains, we characterized paralogous families in rice and compared these with paralogous families in the model dicotyledonous diploid species, Arabidopsis thaliana. Arabidopsis, which has undergone genome duplication as well, has a substantially smaller genome (~120 Mb) and gene complement compared to rice. Overall, 53% and 68% of the non-transposable element-related rice and Arabidopsis proteins could be classified into paralogous protein families, respectively. Singleton and paralogous family genes differed substantially in their likelihood of encoding a protein of known or putative function; 26% and 66% of singleton genes compared to 73% and 96% of the paralogous family genes encode a known or putative protein in rice and Arabidopsis, respectively. Furthermore, a major skew in the distribution of specific gene function was observed; a total of 17 Gene Ontology categories in both rice and Arabidopsis were statistically significant in their differential distribution between paralogous family and singleton proteins. In contrast to mammalian organisms, we found that duplicated genes in rice and Arabidopsis tend to have more alternative splice forms. Using data from Massively Parallel Signature Sequencing, we show that a significant portion of the duplicated genes in rice show divergent expression although a correlation between sequence divergence and correlation of expression could be seen in very young genes.

Conclusion

Collectively, these data suggest that while co-regulation and conserved function are present in some paralogous protein family members, evolutionary pressures have resulted in functional divergence with differential expression patterns.