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

Abstract

Overlapping genes (OGs) represent one type of widespread genomic feature in bacterial genomes and have been used as rare genomic markers in phylogeny inference of closely related bacterial species. However, the inference may experience a decrease in performance for phylogenomic analysis of too closely or too distantly related genomes. Another drawback of OGs as phylogenetic markers is that they usually take little account of the effects of genomic rearrangement on the similarity estimation, such as intra-chromosome/genome translocations, horizontal gene transfer, and gene losses. To explore such effects on the accuracy of phylogeny reconstruction, we combine phylogenetic signals of OGs with collinear genomic regions, here called locally collinear blocks (LCBs). By putting these together, we refine our previous metric of pairwise similarity between two closely related bacterial genomes. As a case study, we used this new method to reconstruct the phylogenies of 88 Enterobacteriale genomes of the class Gammaproteobacteria. Our results demonstrated that the topological accuracy of the inferred phylogeny was improved when both OGs and LCBs were simultaneously considered, suggesting that combining these two phylogenetic markers may reduce, to some extent, the influence of gene loss on phylogeny inference. Such phylogenomic studies, we believe, will help us to explore a more effective approach to increasing the robustness of phylogeny reconstruction of closely related bacterial organisms.

Cyanobacterial phylogenetic analysis based on phylogenomics approaches render evolutionary diversification and adaptation: an overview of representative orders

“…The overlapping genes (OGs) are adjoining genes whose coding sequences are partially or completely overlapped (Jiang et al 2008). Overlapping genes (OGs) correspond to widely available genomic feature of bacterial genomes and are also used as rare genomic markers for phylogenetic analysis of closely related bacterial species (Zhang and Lin 2015). OGs are potentially involved in different important processes including regulation of gene expression or development of genome compaction (Zhang and Lin 2015).…”

“…Overlapping genes (OGs) correspond to widely available genomic feature of bacterial genomes and are also used as rare genomic markers for phylogenetic analysis of closely related bacterial species (Zhang and Lin 2015). OGs are potentially involved in different important processes including regulation of gene expression or development of genome compaction (Zhang and Lin 2015). In fact, OGs are much conserved among species rather than non-OGs (Jiang et al 2008).…”