%0 Journal Article
%T Bacterial phylogenetic tree construction based on genomic translation stop signals
%A Lijing Xu
%A Jimmy Kuo
%A Jung-Kang Liu
%A Tit-Yee Wong
%J Microbial Informatics and Experimentation
%D 2012
%I BioMed Central
%R 10.1186/2042-5783-2-6
%X A 16SrRNA-alignment tree of 19 well-studied ¦Á-, ¦Â- and ¦Ã-Proteobacteria Type species is used as standard reference for bacterial phylogeny. The genomes of sixty-one bacteria, belonging to the ¦Á-, ¦Â- and ¦Ã-Proteobacteria subphyla, are used for this study. The stop codons and PSC are collectively termed ¡°Translation Stop Signals¡± (TSS). A gene is represented by nine scalars corresponding to the numbers of counts of TAA, TAG, and TGA on each of the three reading-frames of that gene. ¡°Translation Stop Signals Ratio¡± (TSSR) is the ratio between the TSS counts. Four types of TSSR are investigated. The TSSR-1, TSSR-2 and TSSR-3 are each a 3-scalar series corresponding respectively to the average ratio of TAA: TAG: TGA on the first, second, and third reading-frames of all genes in a genome. The Genomic-TSSR is a 9-scalar series representing the ratio of distribution of all TSS on the three reading-frames of all genes in a genome. Results show that bacteria grouped by their similarities based on TSSR-1, TSSR-2, or TSSR-3 values could only partially resolve the phylogeny of the species. However, grouping bacteria based on thier Genomic-TSSR values resulted in clusters of bacteria identical to those bacterial clusters of the reference tree. Unlike the 16SrRNA method, the Genomic-TSSR tree is also able to separate closely related species/strains at high resolution. Species and strains separated by the Genomic-TSSR grouping method are often in good agreement with those classified by other taxonomic methods. Correspondence analysis of individual genes shows that most genes in a bacterial genome share a similar TSSR value. However, within a chromosome, the Genic-TSSR values of genes near the replication origin region (Ori) are more similar to each other than those genes near the terminus region (Ter).The translation stop signals on the three reading-frames of the genes on a bacterial genome are interrelated, possibly due to frequent off-frame recombination facilitated by translati
%U http://www.microbialinformaticsj.com/content/2/1/6/abstract