Chromosomal conservation and sequence diversity of ribosomal RNA genes of two distant Oryza species

Contrary to the chromosomal polymorphism of 45 S ribosomal genes (45 S rDNA) loci in other Oryza species, each of Oryza australiensis and Oryza brachyantha has only one 45 S rDNA locus at the most conserved position of 45 S rDNAs in Oryza. O. australiensis and O. brachyantha are known phylogenetically distant and have extremely different genome sizes among diploid Oryza species. This study reveals that the sequences and organizations of intergenic spacer (IGS) for 45 S rDNA of both O. australiensis and O. brachyantha are different from other Oryza species. The IGS of O. australiensis contains 13 tandem repeats and only one transcriptional initiation site, while there are four tandem repeats and three transcriptional initiation sites in the IGS of O. brachyantha. Our results suggest different evolution processes of orthologous rDNA loci in the genus Oryza. Here we also demonstrate an efficient strategy to study locus-specific IGS before whole genome sequences data are available.