Dynamic Genome Evolution of the Oryza Genomes

摘要

Comparative genomics is a powerful tool to decipher gene and genome evolution. Placing multiple genome comparisons in a phylogenetic context improves the sensitivity of evolutionary inferences. A large genomic region surrounding the MONOCULMI (MOCI) locus was chosen for study in 14 Oryza species. Sequencing and annotation of 18 bacterial artificial chromosome clones for these spe-cies revealed highly conserved gene colinearity and structure in the MOCI region. Since the Oryza radiation about 14 million years ago, differences in transposon amplification appear to be responsible for the different current sizes of the Oryza genomes. In the MOCl region, transposons were only con-served between genomes of the same type. In addition to the conserved gene content, several appar-ent genes have been generated de novo or uniquely retained in the AA lineage. Large and apparently non-coding sequences flanking the MOCI gene were observed to be under strong purifying selection. The allotetraploids Oryza alta and Oryza minuta were found to be products of recent polyploidiza-tion, less than 1.6 and 0.4 mya, respectively. In allotetraploids, pseudogenization of duplicated genes was common, caused by large deletions, small frameshifting insertions/deletions or nonsense muta-tions. Comparative sequence analysis of a few other genomic regions will be discussed as well.