Conserved synteny as a measure of genomic distance

AbstractThe number of chromosomal segments conserved during the evolution of two species can be used to measure their genomic distance. The number of conserved segments containing homologous genes can be estimated by comparing synteny relations within and between the two genomes. There are three sources of underestimation, however. The first stems from conserved segments in which genes are yet to be identified in one or both species. The second results from repeated translocations or transpositions resulting in not just one, but several conserved segments from a chromosome in one species being located on a single chromosome in the other. We characterize the bias due to both effects and propose correct measures of syntenic distance. We also discuss underestimation due to intrachromosomal rearrangements such as inversion