Figure 3: Comparative analysis of gene synteny and rearrangements.

(a) A distance tree (DCJ distance) showing that the genome-wide gene rearrangement rates in modern vertebrates (chicken, human and mouse) sharply decreased after the 2R-WGD. (b) Comparison of the gene order in the protoMHC region between the Chinese and Florida lancelets. A total of 269 genes conserved between lancelet and human are shown in the analysis. The DCJ rearrangement rate between the protoMHC regions of the two lancelets is 120/269=0.45, which is almost twice the average genome-wide rate (0.23) between the two lancelets (P<1e−8, χ²-test), indicating highly active local gene order scrambling in the protoMHC region. (c–f) Dot plots of gene synteny and rearrangements between closely related genomes. Scaffolds and chromosomes were bidirectionally clustered according to their similarity in gene synteny conservation. Two additional species pairs (fruit flies and bony fishes) and the high-resolution figures are presented in Supplementary Figs 16–21. More information is provided in Supplementary Note 7.