Comparison of sidedness and functional cluster indices in C. reinhardtii cpDNA to those of simulated genomes. (A)The sidedness index Cs observed in C. reinhardtii (indicated by an arrow) is significantly larger than Cs of gene orders simulated under the random breakage model (inversion only) and the estimated ancestral genome indicated in Figure 2B. (B) The functional cluster index Cf for C. reinhardtii (indicated by a solid horizontal line) is greater than that for the inferred ancestral genome (dashed line), in contrast to the decrease predicted by three sets of simulations under the random breakage model. Models 1, 2 and 3 specified the inversion/transposition ratios to be 1:0, 10:1 and 1:1, respectively, in simulations with 10,000 replicates. The box section of the box plot indicates the first quartile, median and the third quartile of the distribution.