Fig. 3.

—Mechanisms of cluster evolution. (A) Different types of events affecting evolution of a single cluster. The evolution of a CSEP cluster comprising six genes is depicted in relation to divergence of two species: species 1 (in blue) keeps the ancestral organization of the cluster while species 2 (in green) undergoes evolutionary changes. Corresponding expected Circos diagrams for the two species are depicted for four cases. (B) Example of cluster family 9. Circos diagram showing relationships between homologous gene clusters. Outer ring: contigs/chromosomes. First inner ring: CSEP clusters as detected (dark gray) and homology extensions (light gray). Significance codes are as follow: <0.001 (***), <0.01 (**), <0.05 (*), <0.1(.), > 0.1 (nonsignificant, NS). Second inner ring: genes. CSEP genes are shaded in black, transposase-related genes in gray. Inner part: gene similarities, a link between two genes implies at least one blast hit with an E value < 1e-6. Thin gray highlighted links correspond to genes with at least 40% protein identity on 10% of their length, thick black links to genes with at least 50% identity on 20% of their length. (C) Relationships between homologous clusters for cluster family 9 showing subfamilies and cluster sizes (see Materials and Methods for a description of the clustering algorithm).