A recent duplication revisited: phylogenetic analysis reveals an ancestral duplication highly-conserved throughout the <it>Oryza </it>genus and beyond

Abstract

Abstract Background The role of gene duplication in the structural and functional evolution of genomes has been well documented. Analysis of complete rice (Oryza sativa) genome sequences suggested an ancient whole genome duplication, common to all the grasses, some 50-70 million years ago and a more conserved segmental duplication between the distal regions of the short arms of chromosomes 11 and 12, whose evolutionary history is controversial. Results We have carried out a comparative analysis of this duplication within the wild species of the genus Oryza, using a phylogenetic approach to specify its origin and evolutionary dynamics. Paralogous pairs were isolated for nine genes selected throughout the region in all Oryza genome types, as well as in two outgroup species, Leersia perrieri and Potamophila parviflora. All Oryza species display the same global evolutionary dynamics but some lineage-specific features appear towards the proximal end of the duplicated region. The same level of conservation is observed between the redundant copies of the tetraploid species Oryza minuta. The presence of orthologous duplicated blocks in the genome of the more distantly-related species, Brachypodium distachyon, strongly suggests that this duplication between chromosomes 11 and 12 was formed as part of the whole genome duplication common to all Poaceae. Conclusion Our observations suggest that recurrent but heterogeneous concerted evolution throughout the Oryza genus and in related species has led specifically to the extremely high sequence conservation occurring in this region of more than 2 Mbp.