Intron gain and loss in segmentally duplicated genes in rice

Analysis of segmental duplication in rice revealed that 159 Mb of the 371 Mb genome and 21,570 of the 43,719 non-transposable element-related genes were contained within a duplicated region. In these duplicated regions, 3,101 collinear paired genes were present. Using this set of segmentally duplicated genes, we investigated intron evolution from full-length cDNA-supported non-transposable element-related gene models of rice. Using gene pairs that have an ortholog in the dicotyledonous model species Arabidopsis thaliana, we identified more intron loss (49 introns within 35 gene pairs) than intron gain (5 introns within 5 gene pairs) following segmental duplication. We were unable to demonstrate preferential intron loss at the 3' end of genes as previously reported in mammalian genomes. However, we did find that the four nucleotides of exons that flank lost introns had less frequently used 4-mers.We observed that intron evolution within rice following segmental duplication is largely dominated by intron loss. In two of the five cases of intron gain within segmentally duplicated genes, the gained sequences were similar to transposable elements.Introns are under less selection pressure than exons, and consequently, their sequences diverge faster than exons. However, the position of the intron with respect to the protein sequence is relatively conserved and conservation of intron position has been observed between distinct eukaryotic lineages throughout about 1.5 billion years of evolution such as between animal and fungal genes [1] and between the malaria parasite Plasmodium falciparum and other eukaryotes [2]. With respect to intron position within genes, introns within intron-sparse species as well as single intron genes are preferentially located near the 5' end of the gene [3,4], suggesting a biased pattern of intron distribution. Indeed, recent studies on 684 eukaryotic orthologous genes from eight eukaryotic species of animals, plants, fungi, and protists showed