Plant F-Box Protein Evolution Is Determined by Lineage-Specific Timing of Major Gene Family Expansion Waves
A, Average Ka/Ks [ω by Yang  and g by Comeron ] ratios calculated over the complete coding sequence of all stable and unstable genes in A. thaliana by comparison to A. lyrata orthologs. Error bars represent SE. The difference is significant according to Kruskal-Wallis test (P<0.01). B, Sliding window plots for the four stable genes. C, Sliding window plots for randomly chosen unstable genes. For sliding window analysis, nucleotide sequences of A. thaliana (indicated by Arabidopsis Genome Initiative identifier) and orthologous nucleotide sequences of A. lyrata (indicated by protein identifier according to the Joint Genome Institute) were used. Window size was 150 bp, and step size was 9 bp. Light gray boxes highlight the position of the F-box domain, and dark gray boxes highlight the FBA-D position.