Description:

  • 2007/05/26: BPhyOG involves 177 prokaryotic genomes up to date (Version: V-1.0).

  • See documentation for more information about BPhyOG.

  • The article can be downloaded from here.

BPhyOG is an interactive web server for reconstruction of whole-genome bacterial phylogenies based on overlapping genes, and also allows users to browse overlapping genes to acquire more information about subtree-specific genomes or all the 177 genomes. Fukuda et al. and Johnson et al. show that the evolution of overlapping gene structures may be related to the evolutionary time scale [1-3]. Therefore, assuming a universal rate of the formation and degradation of overlapping genes across species, we can determine the evolutionary distance between two bacterial genomes on the basis of the number of their shared overlapping gene pairs [4]. It is a useful tool for analyzing the tree of life and overlapping genes from a genomic standpoint.

Overlapping genes (OGs) are pairs of adjacent genes of which the coding sequences overlap partly or entirely. Many OGs have been identified in the genomes of prokaryotes, bacteriophages, viruses, and mitochondria. Overlapping gene pairs can be divided into three types: unidirectional (->->), convergent (-><-), and divergent (<-->). Overlaps have been demonstrated to be potentially important in transcriptional and translational regulators of gene expression and to influence the evolution of genes [5]. Also, exploring the conservation of overlapping genes is an important way to study the evolution of prokaryotic genomes.

References:

  1. Fukuda Y, Nakayama Y, Tomita M: On dynamics of overlapping genes in bacterial genomes. Gene 2003, 323:181-187.
  2. Fukuda Y, Washio T, Tomita M: Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae. Nucleic Acids Res 1999, 27(8):1847-1853.
  3. Johnson ZI, Chisholm SW: Properties of overlapping genes are conserved across microbial genomes. Genome Research 2004, 14(11):2268-2272.
  4. Luo Y, Fu C, Zhang DY, Lin K: Overlapping genes as rare genomic markers: the phylogeny of gamma-Proteobacteria as a case study. Trends in Genetics 2006, 22(11):593-596
  5. Krakauer DC, Plotkin JB: Redundancy, antiredundancy, and the robustness of genomes.Proc Natl Acad Sci U S A 2002, 99(3):1405-1409.

 

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