Background: Individuals in the same species are assumed to share the same genomic set. However, it is not unusual to find an orthologous gene only in small subset of the species, and recent genomic studies suggest that structural rearrangements are very frequent between genomes in the same species. Two recently sequenced rice genomes Oryza sativa L. var. Nipponbare and O. sativa L. var. 93-11 provide an opportunity to systematically investigate the extent of the gene repertoire polymorphism, even though the genomic data of 93-11 derived from whole-short-gun sequencing is not yet as complete as that of Nipponbare.
Results: We compared gene contents and the genomic locations between two rice genomes. Our conservative estimates suggest that at least 10% of the genes in the genomes were either under presence/absence polymorphism (5.2%) or asymmetrically located between genomes (4.7%). The proportion of these "asymmetric genes" varied largely among gene groups, in which disease resistance (R) genes and the RLK kinase gene group had 11.6 and 7.8 times higher proportion of asymmetric genes than housekeeping genes (Myb and MADS). The significant difference in the proportion of asymmetric genes among gene groups suggests that natural selection is responsible for maintaining genomic asymmetry. On the other hand, the nucleotide diversity in 17 R genes under presence/absence polymorphism was generally low (average nucleotide diversity = 0.0051).
Conclusion: The genomic symmetry was disrupted by 10% of asymmetric genes, which could cause genetic variation through more unequal crossing over, because these genes had no allelic counterparts to pair and then they were free to pair with homologues at non-allelic loci, during meiosis in heterozygotes. It might be a consequence of diversifying selection that increased the structural divergence among genomes, and of purifying selection that decreased nucleotide divergence in each R gene locus.