Evolution of the gyrB gene and the molecular phylogeny of Enterobacteriaceae: a model molecule for molecular systematic studies.

Abstract

Phylogenetic trees showing the evolutionary relatedness ofEnterobacteriaceae based upon gyrB and 16S rRNA genes were compared. Congruence among trees of these molecules indicates that the genomes of these species are not completely mosaic and that molecular systematic studies can be carried out. Phylogenetic trees based on gyrB sequences appeared to be more reliable at determining relationships among Serratia species than trees based on 16S rRNA gene sequences. gyrB sequences from Serratia species formed a monophyletic group validated by significant bootstrap values. Serratia fonticola had the most deeply branching gyrB sequence in the Serratia monophyletic group, which was consistent with its atypical phenotypic characteristics. Klebsiella and Enterobacter genera seemed to be polyphyletic, but the branching patterns of gyrB and 16S rRNA gene trees were not congruent. Enterobacter aerogenes was grouped with Klebsiella pneumoniae on the gyrB phylogenetic tree, which supports that this species could be transferred to the Klebsiella genus. Unfortunately, 16S rRNA and gyrB phylogenetic trees gave conflicting evolutionary relationships for Citrobacter freundii because of its unusual gyrB evolutionary process. gyrB lateral gene transfer was suspected for Hafnia alvei. Saturation of gyrB genes was observed by the pairwise comparison of Proteus spp., Providencia alcalifaciens and Morganella morganii sequences. Depending on their level of variability, 16S rRNA gene sequences were useful for describing phylogenetic relationships between distantly related Enterobacteriaceae, whereas gyrB sequence comparison was useful for inferring intra-and some intergeneric relationships.

Application of Whole-Cell Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Rapid Identification and Clustering Analysis ofPantoeaSpecies

“…Amplification and sequencing of the gyrB gene were performed as described previously (45) by means of the HotStarTaq master mix kit (Qiagen, Basel, Switzerland) and the ABI PRISM BigDye Terminators version 1.1 cycle sequencing kit (Applied Biosystems, Foster City, CA), respectively. Two degenerate primers were used to amplify and sequence a 970-bp region of the gyrB gene, gyr-320 (5Ј-TAARTTYGAYGAYAACTCYTAYAAAGT-3Ј) and rgyr-1260 (5Ј-CMCCYTCCACCARGTAMAGTTC-3Ј) (15). The phylogenetic tree was generated on the basis of a 740-bp fragment of the gyrB amplicon.…”

Phylogeny and classification of Dickeya based on multilocus sequence analysis

“…Primers for PCR amplification of gyrB and dnaJ were modified for specificity to the genus Dickeya from existing primers made for members of the Enterobacteriaceae (Dauga, 2002;Nhung et al, 2007). Primers previously published for dnaX (Slawiak et al, 2009) were used for all Dickeya strains.…”

Gene and genome trees conflict at many levels

“…(c) Many methods and many data types Phylogenies based on housekeeping genes such as gyrB, tufA and atpD are often compared with those based on 16S rRNA phylogenies (Dauga 2002;Purkhold et al 2003;Paradis et al 2005). The goal of comparing genes is to examine linkage disequilibrium or recombination or to overcome systematic biases (Cooper & Feil 2004) that might be present in one molecule and not in another.…”