BPhyOG: an interactive server for genome-wide inference of bacterial phylogenies based on overlapping genes

Abstract

Background: Overlapping genes (OGs) in bacterial genomes are pairs of adjacent genes of which the coding sequences overlap partly or entirely. With the rapid accumulation of sequence data, many OGs in bacterial genomes have now been identified. Indeed, these might prove a consistent feature across all microbial genomes. Our previous work suggests that OGs can be considered as robust markers at the whole genome level for the construction of phylogenies. An online, interactive web server for inferring phylogenies is needed for biologists to analyze phylogenetic relationships among a set of bacterial genomes of interest.

Description: BPhyOG is an online interactive server for reconstructing the phylogenies of completely sequenced bacterial genomes on the basis of their shared overlapping genes. It provides two tree-reconstruction methods: Neighbor Joining (NJ) and Unweighted Pair-Group Method using Arithmetic averages (UPGMA). Users can apply the desired method to generate phylogenetic trees, which are based on an evolutionary distance matrix for the selected genomes. The distance between two genomes is defined by the normalized number of their shared OG pairs. BPhyOG also allows users to browse the OGs that were used to infer the phylogenetic relationships. It provides detailed annotation for each OG pair and the features of the component genes through hyperlinks. Users can also retrieve each of the homologous OG pairs that have been determined among 177 genomes. It is a useful tool for analyzing the tree of life and overlapping genes from a genomic standpoint.

Conclusion: BPhyOG is a useful interactive web server for genome-wide inference of any potential evolutionary relationship among the genomes selected by users. It currently includes 177 completely sequenced bacterial genomes containing 79,855 OG pairs, the annotation and homologous OG pairs of which are integrated comprehensively. The reliability of phylogenies complemented by annotations make BPhyOG a powerful web server for genomic and genetic studies. It is freely available at http://cmb.bnu.edu.cn/BPhyOG.

Figure 1

Flow chart of the phylogenetic tree of 30 gamma-proteobacterial genomes reconstructed on the basis of conserved OG pairs. The left panel shows a phylogenetic UPGMA tree for the 30 gamma-proteobacterial genomes based on the number of their shared OG pairs. Each branch is labeled by the species name and the total number of OG pairs in the genome in square brackets. The right upper panel shows all the conserved OG pairs in the genome of interest when the species name is clicked on the tree, e.g. Escherichia coli K12. The right lower panel describes the information about one OG pair (e.g. 83333_44) and the list of its orthologous OG pairs within the subtree-specific genomes.

Figure 2

The detailed features of one OG pair as an example, and a list of homologous OG pairs in all genomes. (a) The upper table describes the information about a selected OG pair, and the lower one lists details of the overlap features of each gene in the pair. (b) The list of predicted OG pairs homologous to the OG pair selected (OGid 83333_76) among all genomes. Two homologous OG pairs from two different genomes (g_i, g_j) are defined as two genes that overlap in genome g_i and have homologues that overlap in genome g_j.