Insights into the rice and Arabidopsis genomes: Intron fates, paralogs, and lineage-specific genes

With the availability of near-complete rice genome sequence, high-quality annotation data, and large expression profile datasets, we examined segmental duplication, intron turnover, and paralogous protein family composition in rice. These data suggest a large percentage of the rice genome was involved in segmental duplication creating a large number of paralogous families. We found that singleton and paralogous family genes differed substantially not only in their likelihood of encoding a protein of known or putative function but also in the distribution of specific gene function. We showed 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. We observed that intron evolution within the rice genome following segmental duplication is dominated by intron loss rather than intron gain. In addition, with the availability of more complete or near-complete plant genomes and transcriptomes across a wide range of species, we identified and characterized conserved Brassicaceae-specific genes and Arabidopsis lineage-specific genes. Lineage specific genes in the Brassicaceae and within Arabidopsis were enriched in genes of no known function and appear to be fast evolving at the protein sequence level.