Nucleotide Composition of the Nelumbo nucifera Genome

Nucleotide composition of genomes varies among organisms and among genes within a genome. Knowing the variations of nucleotide composition and the consequences of these differences would provide fundamental information for understanding genome evolution. Lotus (Nelumbo nucifera Gaertn.), a basal eudicot, diverged from its closest sister lineage at 135-125 MYA. The unique phylogenetic position of lotus makes it important for evolutionary studies. With the draft genome sequence of lotus available, we analyzed the nucleotide composition of the lotus genome compared to other sequenced plant genomes. GC content of the lotus genome was between grasses and eudicots. The lotus genome had more coding sequences with high GC3 than did the core eudicots, and its GC3 composition exhibited a negative gradient along the transcription direction. The difference between purines and pyrimidines in the coding sequence of lotus was smallest among the selected eudicot species. The lotus genome had a lower observed/expected (O/E) ratio of CpG dinucleotide than did the selected dicots and monocots except for grape. The lower O/E ratio of CpG dinucleotide is likely caused by instability of transposable elements, rather than a higher mutation rate.