title: An event-driven approach for studying gene block evolution in bacteria.
abstract: BACKGROUND
  Gene blocks are genes co-located on the chromosome. In many cases, gene blocks are conserved between bacterial species, sometimes as operons, when genes are co-transcribed. The conservation is rarely absolute: gene loss, gain, duplication, block splitting and block fusion are frequently observed. An open question in bacterial molecular evolution is that of the formation and breakup of gene blocks, for which several models have been proposed. These models, however, are not generally applicable to all types of gene blocks, and consequently cannot be used to broadly compare and study gene block evolution. To address this problem, we introduce an event-based method for tracking gene block evolution in bacteria.
  
  
  RESULTS
  We show here that the evolution of gene blocks in proteobacteria can be described by a small set of events. Those include the insertion of genes into, or the splitting of genes out of a gene block, gene loss, and gene duplication. We show how the event-based method of gene block evolution allows us to determine the evolutionary rateand may be used to trace the ancestral states of their formation. We conclude that the event-based method can be used to help us understand the formation of these important bacterial genomic structures.
  
  
  METHODS
  The software is available under GPLv3 license on http://github.com/reamdc1/gene_block_evolution.git. Supplementary online material: http://iddo-friedberg.net/operon-evolution
authors.affiliation: Department of Microbiology, Miami University, Oxford, OH, USA and Department of Computer Science and Software Engineering, Miami University, Oxford, OH, USA.
authors.forename: David C
authors.initials: DC
authors.lastname: Ream
authors.affiliation: Department of Microbiology, Miami University, Oxford, OH, USA and Department of Computer Science and Software Engineering, Miami University, Oxford, OH, USA.
authors.forename: Asma R
authors.initials: AR
authors.lastname: Bankapur
authors.affiliation: Department of Microbiology, Miami University, Oxford, OH, USA and Department of Computer Science and Software Engineering, Miami University, Oxford, OH, USA Department of Microbiology, Miami University, Oxford, OH, USA and Department of Computer Science and Software Engineering, Miami University, Oxford, OH, USA.
authors.forename: Iddo
authors.initials: I
authors.lastname: Friedberg
mesh_terms: D001419:Bacteria / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D009876:Operon; D012984:Software