PubMedCrossRef 65. Hanahan D: Studies on transformation of Escherichia coli with plasmids. J Mol Biol 1983, 166:557–580.PubMedCrossRef 66. Kessler B, de Lorenzo V, Timmis KN: A general system to integrate lacZ fusion into the chromosome of gram negative bacteria: regulation of the Pm promoter of the TOL plasmid studied with all controlling elements in monocopy. Mol Gen Genet 1992, 233:293–301.PubMedCrossRef Authors’ contributions BMS202 nmr JRM and MA performed the majority of the experiments, participated in bioinformatics analysis, study design, and in crafting of the manuscript. MRB, MJ, and FIG performed some growth experiments and RMN analyses. JJN and CV conceived the study, participated

in the design, coordination, bioinformatic analysis, and crafting of the manuscript. All authors have read and approved the final manuscript.”
“Background Historically, taxonomic selleck analyses have been performed using

a diverse and often arbitrary selection of morphological and phenotypic characteristics. Today, these characteristics are generally considered unsuitable for generating reliable and consistent taxonomies for prokaryotes, as there is no rational basis for choosing which morphological or phenotypic properties should be examined. Moreover, it is doubtful that individual phenotypes or small collections of phenotypes can consistently and correctly represent evolutionary Lck relationships [1]. The unsuitability of phenotypic traits, along with the advent of DNA sequencing, LY333531 order has led to 16S rRNA gene sequence comparisons becoming the standard technique

for taxonomic analyses [1], although it has been argued that the cpn60 gene allows for greater evolutionary discrimination [2]. Over time, the trend has moved toward using a greater number of genes to infer phylogenetic relationships–in part due to the increasing ease and reduced cost associated with DNA sequencing, but also due to doubts about the accuracy of evolutionary relationships inferred from a single gene. Phylogeny can be inferred from a number of universally conserved housekeeping genes using multi-locus sequence analysis (MLSA) [3, 4]. While 16S rRNA gene sequence analysis and MLSA have proven to be effective tools for phylogenetics, a major deficiency inherent in these techniques is that only a small amount of information is used to represent an entire organism. This practice has largely been accepted due to the time and cost of genome sequencing. However, recent improvements in sequencing technology have substantially reduced the resources necessary to sequence a genome, and there are now numerous genome sequences available in publicly accessible databases. The accelerating pace of genome sequencing provides the opportunity to explore the use of entire genomes in analyzing evolutionary relationships.