Graphical analyses of codon usage patterns. (top) Plots of the two most significant axes generated by the COA of RSCU values for Nuphar (top left) and Ranunculus (top right). Each point represents one of the 59 degenerate codons. The points are coded S (black circle) if the 3rd position nucleotide is G or C, and W (red square) if the 3rd position nucleotide is A or T. (middle) Plots of ENc (effective number of codons) by GC3 (the percentage G + C at the 3rd position) for each of the 79 protein-coding genes in Nuphar (middle left) and Ranunculus (middle right). The line in each graph (middle left and right) indicates the relationship predicted if codon usage was determined solely by 3rd position composition. (bottom) Plots of the two most significant axes generated by COA on CU (codon usage) for genes in Nuphar (bottom left) and Ranunculus (bottom right). Each gene is categorized as related to photosynthesis (green diamonds), gene expression (black circles) or other (red squares).
Raubeson et al. BMC Genomics 2007 8:174 doi:10.1186/1471-2164-8-174