Build Of Genome Context Networks And Its Application In Phylogenetic Construction

With the complement of the sequencing of the human genome and the accumulation more and more genome sequences of both bacterial and eukaryotes of, the study of genome is moving to a new era called post-genomics and the main research focus has shift to functional genomics.The genome context analysis method one of the many methods used in post-genomics era. It uses multi-genomes to gain the knowledge of the functional linkage of coding genes as well as proteins. Apart from their traditional usage in protein-protein interaction prediction, genome context methods can be used in comparative genomics and we used them to construct a tree of life of near 200 species. Since the prevalence of the usage of this kind of method, it is necessary to provide an automatic tool for. This article consists of the following three parts:1. Introduction of genome context method. Introduce the principle of phylogenetic profile method, gene neighbor method, gene fusion method and the statistical methods used to find the significance.2. Tool used to build the genome context networks. By implement the three methods mentioned before, we provide a tool for calculation, drawing and demonstration of the genome context networks. It's a good complement of the existence database and renders user the power to get the result of their data for further analysis.3. Phylogenetic analysis based on genome context methods. Based on the genomic data, we appled the gene relationships to reconstruct a tree of life which includes 195 fully sequenced representative species. We assumed that the organism is a system and the relationships of the parts in the system are the essence of organism. Compared with previous phylogenomic studies, our strategy highlights the relationships among genes on genome level. It does not use any point mutation information in the primary sequences but provides an independent testing of current phylogenetic knowledge. In the resulting tree, the monophylies of three superkingdoms and most taxonomic sub-divisions are well confirmed, indicating the existence of distinct gene network evolved in each taxonomic group. Our result suggests the high G+C gram positive origin of Bacteria and challenges some traditional taxonomies. Our strategy according to gene networks sheds new light on the phylogeny of species and taxonomy.