Reconstructing genome trees of prokaryotes using overlapping genes

Abstract

BackgroundOverlapping genes (OGs) are defined as adjacent genes whose coding sequences overlap partially or entirely. In fact, they are ubiquitous in microbial genomes and more conserved between species than non-overlapping genes. Based on this property, we have previously implemented a web server, named OGtree, that allows the user to reconstruct genome trees of some prokaryotes according to their pairwise OG distances. By analogy to the analyses of gene content and gene order, the OG distance between two genomes we defined was based on a measure of combining OG content (i.e., the normalized number of shared orthologous OG pairs) and OG order (i.e., the normalized OG breakpoint distance) in their whole genomes. A shortcoming of using the concept of breakpoints to define the OG distance is its inability to analyze the OG distance of multi-chromosomal genomes. In addition, the amount of overlapping coding sequences between some distantly related prokaryotic genomes may be limited so that it is hard to find enough OGs to properly evaluate their pairwise OG distances.ResultsIn this study, we therefore define a new OG order distance that is based on more biologically accurate rearrangements (e.g., reversals, transpositions and translocations) rather than breakpoints and that is applicable to both uni-chromosomal and multi-chromosomal genomes. In addition, we expand the term "gene" to include both its coding sequence and regulatory regions so that two adjacent genes whose coding sequences or regulatory regions overlap with each other are considered as a pair of overlapping genes. This is because overlapping of regulatory regions of distinct genes suggests that the regulation of expression for these genes should be more or less interrelated. Based on these modifications, we have reimplemented our OGtree as a new web server, named OGtree2, and have also evaluated its accuracy of genome tree reconstruction on a testing dataset consisting of 21 Proteobacteria genomes. Our experimental results have finally shown that our current OGtree2 indeed outperforms its previous version OGtree, as well as another similar server, called BPhyOG, significantly in the quality of genome tree reconstruction, because the phylogenetic tree obtained by OGtree2 is greatly congruent with the reference tree that coincides with the taxonomy accepted by biologists for these Proteobacteria.ConclusionsIn this study, we have introduced a new web server OGtree2 at http://bioalgorithm.life.nctu.edu.tw/OGtree2.0/ that can serve as a useful tool for reconstructing more precise and robust genome trees of prokaryotes according to their overlapping genes.

The distinction of CPR bacteria from other bacteria based on protein family content

“…3b) the correspondence between clusters based on the distribution of core protein families and phylogeny (Fig. 3c) is apparent consistent with previous studies 24,25 . Based on complete-linkage, the cophenetic correlation between a maximum-likelihood phylogenetic tree is 0.70, based on average-linkage 0.67, and based on single-linkage, 0.54 (Supplementary Fig.…”

Phylogeny Inference of Closely Related Bacterial Genomes: Combining the Features of Both Overlapping Genes and Collinear Genomic Regions

“…Considering only protein-coding genes, the putative orthologous genes between two genomes were determined using the approach of bidirectional best hit (BBH). In accordance with previous studies, 18,27 we tested two types of para meter settings for the NCBI BLAST (the Basic Local Alignment Search Tool) program 37 : (1) e-value ,10 −4 and identity .40%, used by Luo et al 18 and (2) e-value , 10 −8 , identity . 45%, and coverage .…”

“…Our results and the results of others show that there are indeed some phylogenetic signals within those orthologous OGs among closely related bacterial genomes. [24][25][26][27][28] However, it is obvious that OGs as phylogenetic markers may be inappropriate for comparing a set of too closely related bacterial genomes, such as complete strain genomes of one species, because it is possible that no evolutionary events of OGs would have occurred in a short time span. In addition, for too distantly related bacterial genomes, the OGs method used for phylogeny inference may also show poor performance, as a few orthologous OGs may be identified.…”

Exploration of multivariate analysis in microbial coding sequence modeling

“…This implies that no Positive has a complete overlap with another Positive. It is, however, typically accepted that functional genes in prokaryotes can overlap over short stretches [29]. Hence, a small fraction of our Negatives may actually be part of a gene, making Negatives difficult to classify correctly.…”