Nucleic Acids Research, 2007, Vol. 35, No. 20 6805 Figure 6. The mouse genome has diﬀerent CG clustering characteristics than those of the human genome. The optimization curve characteristics for mouse are clearly diﬀerent from those for human (a). The optimal mouse annotation contains fragments no longer than 585 nt with 24 or more CGs per fragment, fewer CGs in a longer stretch of DNA than for the human genome. In panel (b) it is again apparent that base composition criteria alone will fail to recognize a substantial proportion of CG-dense loci in this species. Figure 7. CG cluster analysis of 10 diﬀerent species. These CG fragment length frequency plots were generated using 30 CGs per fragment for each species. Genomes containing CG clusters are deﬁned by the distinct peak of short, uniquely CG-dense fragments. While the three non-methylating organisms on the left (Saccharomyces cerevisiae, Caenorhabditis elegans and D. melanogaster) show no uniquely CG-dense peak, it was surprising to ﬁnd that fugu has similar characteristics despite the fact that it methylates its genome (25). Zebraﬁsh, on the other hand, which also methylates its genome, has a distinct CG-dense peak, as do the other vertebrate genomes on the right. There is more CG decay in zebraﬁsh than fugu (O/E CG ratios of 0.525 and 0.571, respectively), but this marginal diﬀerence does not appear suﬃcient to account for the emergence of CG-dense clusters in zebraﬁsh. Methylation of the genome is not, therefore, always accompanied by the presence of CG-dense loci that avoid mutational decay. For a more detailed illustration of the CG cluster analysis of these genomes, see the Supplementary Data section.