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

Abstract

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 interspecies conservation of divergent and convergent gene pairs in three plant species: rice (Oryza sativa), Arabidopsis (Arabidopsis thaliana), and black cottonwood (Populus trichocarpa). 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 overrepresented or underrepresented in Arabidopsis and Populus gene pairs, while only two GO classes were underrepresented in rice divergent gene pairs. Three cis-regulatory elements common to both Arabidopsis and rice were overrepresented in the intergenic regions of strongly correlated divergent gene pairs compared to those of noncorrelated 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.

A 3,000-Loci Transcription Map of Chromosome 3B Unravels the Structural and Functional Features of Gene Islands in Hexaploid Wheat

“…Furthermore, the expression profiles that we established may not reflect the exact expression profiles of genes located on chromosome 3B since microarray hybridization does not allow discrimination between the homoeologous A, B, and D copies that are potentially present and transcribed for each individual gene in hexaploid wheat. However, studies in various model organisms demonstrated that organization in clusters was not only found for coexpressed genes but also for genes involved in the same metabolic pathway and/or associated in protein-protein complexes (Cohen et al, 2000;Lee and Sonnhammer, 2003;Krom and Ramakrishna, 2008;Xu et al, 2008). The mechanisms involved in neighbor gene regulation described above cannot explain the tendency of noncoexpressed cofunctional genes to occur in adjacent or nearby locations in the genome.…”

“…We also found a few coexpressed gene clusters that were conserved between wheat and rice or B. distachyon, suggesting that genes maintained their proximity during the evolution and that common regulatory mechanisms are also conserved between plant genomes. Other examples have been reported of coexpressed and cofunctional gene pairs conserved between Arabidopsis, rice, and poplar (Krom and Ramakrishna, 2008;Liu and Han, 2009). However, in addition to the syntenic genes, we found that more than two-thirds of the coexpression clusters also contained nonsyntenic genes when compared to rice and/or B. distachyon genes.…”

A Collection of Conserved Noncoding Sequences to Study Gene Regulation in Flowering Plants

“…To obtain possible mechanistic insights from the presence of conserved binding sites on gene regulation, we investigated the effect on the coexpression of a conserved binding site located between divergent gene pairs. Previously, Krom and Ramakrishna (2008) reported that specific regulatory elements were overrepresented in divergent or convergent gene pairs with a strong correlation in gene expression. In this analysis, we were able to show that the presence of a conserved binding site leads to a significant increase in transcriptional coherence compared with divergent gene pairs that did not share a conserved binding site.…”

“…In this section, we explore whether we can detect more complex transcriptional units, focusing on divergent gene pairs that have been shown to have a higher correlation in expression than random gene pairs (Krom and Ramakrishna, 2008). First, 6,501 divergent gene pairs were identified in the genome of Arabidopsis.…”

Assessing the Influence of Adjacent Gene Orientation on the Evolution of Gene Upstream Regions inArabidopsis thaliana

“…A few studies have investigated the patterns of coexpression or shared gene ontology categories among gene neighbors in A. thaliana, the best annotated plant genome (Williams and Bowles 2004;Krom and Ramakrishna 2008;Wang et al 2009). Yet, surprisingly Notefew studies have investigated the evolutionary dynamics of plant noncoding regions (but see de Meaux et al 2005 andMiyashita 2001).…”