Plant and Animal Genome XIII, San Diego, CA. Abstract P263.
Comparative genome analysis in mammals has advanced significantly as a result of progress in genome mapping and sequencing. We have studied the genome organization in phylogenetically distinct species to address fundamental questions relating to mammalian chromosomal evolution. Pairwise comparisons of the human genome sequence (NCBI build 33) with the sequence-based maps of two representative species of Rodentia (mouse, rat) were performed using the GRIMM-Synteny approach. In addition, comprehensive RH-based maps from representative species of three orders of mammals, Cetartiodactyla (pig, cattle), Carnivora (cat, dog), and Perissodactyla (horse), were included in the analysis. A standardized set of rules was used to define homologous chromosome segments in all eight species, as well as for the definition of breakpoint boundaries and regions. The combined sequence and RH map-based analysis was conducted with a new bioinformatics tool that allowed for the visualization of homologous synteny ("conserved" segments), and lineage-specific or reuse breakpoints between the genomes analyzed. Identification of a significant number of reuse breakpoints confirms and extends our previous findings. These results provide a clear exception to the Nadeau-Taylor random breakpoint model of chromosome evolution. Analysis of gene content within the breakpoint regions revealed both gene-rich and gene-poor intervals, thus suggesting some breaks to be neutral while others may be acted upon by natural selection. Further analysis of evolutionary breakpoints and repositioning of centromeres and telomeres is underway, in addition to the reconstruction of the chromosome organization of the putative mammalian ancestor of extant mammals.