3-D Visualization for Gene Rearrangement in Ternary Comparison

An increase of full genome sequences from wide range of species enables “comparative genomics”, the study of similarities and differences in structure and functions of genetic information across taxa. One line of research has focused on the conservation of order of genes within gene clusters in various species of bacteria [1]. However, the results of these studies were sometimes inconsistent with results obtained by other methods such as sequence-based phylogenetic analyses. Another problem of such analysis of gene order was the lack of a convenient way of visualizing order of genes in a cluster. We have been trying to devise a method of visualization to find out the conserved islands from the whole genomes and to recognize conservation, replacement, inversion, re-arrangement or deletion. We developed a 3-D modeling viewer application for ternary comparison as a solution. Currently we are focusing on the organellar genome sets (mitochondrial or chloroplast genome), each of which is monophyletic in origin. The monophyly is a pre-requisite for analysis of gene order, because orthology of genes is ascertained in this case. In addition, the organellar genomes are small in size and are convenient to assess validity of our methodology.