Intron gain, a dominant evolutionary process supporting high levels of gene expression in rice

Presence of introns in eukaryotic genes, their evolution and biological function has been a subject of considerable debate ever since their discovery in 1977. To understand the effect of number of introns on the structural and functional characteristics of rice genes, we carried out whole genome analysis of the relationship of the number of introns per gene with predicted cDNA sequence (CDS) length, average exon length and gene expression patterns. There was a direct correlation between the number of introns and the average CDS length among the expressed rice genes, as determined by expressed sequence tags (EST) support. The percentage of expressed genes in groups of rice genes representing different intron numbers showed a significant positive correlation with the number of introns providing evidence for higher level of expression for intron-rich genes. This was further supported by higher abundance of ESTs for the intron-rich genes in the rice EST database. Higher number of introns may be providing post-transcriptional stability to the mRNA leading to higher expression levels. Here we first report the detailed genome wide analysis of distribution pattern of introns in rice that provides important insight in to understanding the evolution, structure and expression of genes in plant species. Particularly, the complex gene structure and functional advantage of the intron containing genes supports the gain of intron theory for the evolution of eukaryotic genes.