Abstract
BackgroundHigh 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.ResultsUsing 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.ConclusionCollectively, 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.
Highlights
High gene numbers in plant genomes reflect polyploidy and major gene duplication events
A total of 11 paralogous protein families with more than one hundred member proteins were identified in rice which encoded proteins such as zinc finger proteins, protein kinases, Myb-like proteins, and transducins [see Additional file 2], similar to the largest protein families reported in Arabidopsis [30]
We demonstrated that even relatively small plant genomes such as rice and Arabidopsis have a significant portion of their proteomes in paralogous families, resulting in a partially redundant proteome
Summary
High gene numbers in plant genomes reflect polyploidy and major gene duplication events. 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. Genome duplication has been reported in rice (Oryza sativa), an important agricultural species and model species for the grass family (Poaceae) [15,16,17,18,19]. Paralogous families, composed of tandemly and segmentally duplicated genes, have been studied to a limited extent in rice, typically in a comparative context with the finished genome of the dicotyledonous plant species, Arabidopsis thaliana [22,23,24,25,26,27]. In Horan et al [28], Arabidopsis and rice proteins were co-clustered using Pfam domainbased or BLASTP-based similarity clustering which allowed for the clustering of proteins into families common between these two model species and for the identification of proteins that were species-specific
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