Codon usage.

Shown is the codon distribution of all merged protein-coding genes for all considered species (for gene-wise analysis results see Supplementary Figure S6 in File S1). Color key: The green region around one implies that a codon was observed about 1 time in 60 codons, higher red and lower blue values indicate deviations of uniform distribution (as factors); thereby also amino acid distribution is implicitly visible. A Hierarchical clustering (Lance-Williams [85]; average linkage method) of codon patterns (y-axis) approximately groups together the examined families. Closely related species (i.e. from the same tribe) generally have highly similar codon usage. Clustering on codon frequencies (x-axis) facilitates the visual identification of deviations. B Synonymous codons are listed sequentially to allow for quick evaluation of relative synonymous codon usage. For instance, the first 4 columns depict the codon usage for Alanine, where obviously the codon GCG is hardly used and codons GCU, GCC and GCA are used by all species with a preference for GCC.