A Novel Construction of Genome Space with Biological Geometry

Yu, Chenglong; Liang, Qian; Yin, Changchuan; He, Rong L.; Yau, Stephen S.-T.

Comparative genomics at the sequence level has existed for 20 years, since the time genome sequencing started in earnest. Already there have been many proposals to compare genomes. Boore and Brown 1 used gene order to study the evolutionary relationships of metazoan mitochondrial genomes. Snel et al. 2 later constructed the phylogenetic tree for completely sequenced prokaryotic genomes based on gene content. In Snel et al.'s method, the similarity between two genomes is defined as the number of genes that they have in common divided by their total number of genes. However, such techniques are time-consuming as they must first identify all the genes in one genome. These approaches, together with G þ C content, edit distance, and reversal and rearrangement distances, 3 -5 compare genomes using only partial genomic information. Thus, these results are usually controversial because single-gene sequences generally do not contain enough information to construct an evolutionary history of organisms.