BACKGROUND: Due to its overarching role in genome function, sequence-dependent 
DNA curvature continues to attract great attention. The DNA double helix is not 
a rigid cylinder, but presents both curvature and flexibility in different 
regions, depending on the sequence. More in depth knowledge of the various 
orders of complexity of genomic DNA structure has allowed the design of 
sophisticated bioinformatics tools for its analysis and manipulation, which, in 
turn, have yielded a better understanding of the genome itself. Curved DNA is 
involved in many biologically important processes, such as transcription 
initiation and termination, recombination, DNA replication, and nucleosome 
positioning. CpG islands and tandem repeats also play significant roles in the 
dynamics and evolution of genomes.
RESULTS: In this study, we analyzed the relationship between these three 
structural features within rice (Oryza sativa) and Arabidopsis (Arabidopsis 
thaliana) genomes. A genome-scale prediction of curvature distribution in rice 
and Arabidopsis indicated that most of the chromosomes of both genomes have 
maximal chromosomal DNA curvature adjacent to the centromeric region. By 
analyzing tandem repeats across the genome, we found that frequencies of repeats 
are higher in regions adjacent to those with high curvature value. Further 
analysis of CpG islands shows a clear interdependence between curvature value, 
repeat frequencies and CpG islands. Each CpG island appears in a local minimal 
curvature region, and CpG islands usually do not appear in the centromere or 
regions with high repeat frequency. A statistical evaluation demonstrates the 
significance and non-randomness of these features.
CONCLUSIONS: This study represents the first systematic genome-scale analysis of 
DNA curvature, CpG islands and tandem repeats at the DNA sequence level in plant 
genomes, and finds that not all of the chromosomes in plants follow the same 
rules common to other eukaryote organisms, suggesting that some of these genomic 
properties might be considered as specific to plants.