Genetic tree of all rdhA genes identified in the genomes of strains CF,DCA,PERK,UNSWDHB,and E (Figure S). Of the rdhA genes in strain PERK lots of are equivalent to each other (Figure S). One example is,two rdhA genes (Dehre_ and Dehre_) share an amino acid sequence identity of . and also a nucleotide identity of . . Moreover,similar rdhA genes are normally close to one another within the genome within the two rdhA clusters (Figure S). A related scenario exists within the comprehensive genomes of strains CF and DCA. Analysis with the two rdhA clusters in these genomes revealed the presence of very equivalent regions (nucleotide similarity ranging from to ; pairwise blocks in Figure S),potentially resulting from sequence duplication events.Insertion Sequence TranspositionTransposition events (TEs) are known to possess constructive,neutral and damaging effects on the host (Rebollo et al. TEs may be typically PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/24683347 effective towards the entire population regardless of deleterious effects on folks (Rebollo et al. The comparison with the comprehensive genomes of strain CF,strain DCA,and strain PERK reveals several strainspecific transposition events and some of them clearly show gene disruptions (information not shown). On the other hand,most TEs detected in these 3 Dehalobacter genomes reside in noncoding regions and consequently their effects cannotTwo rdhA Clusters in Dehalobacter GenomesSimilar to FRAX1036 Dehalococcoides genomes,Dehalobacter genomes possess a number of,nonidentical rdhA genes (Table. In Dehalococcoides genomes,many of the rdhA genes are located in two higher plasticity (HP) regions connected with hot recombination web sites like some tRNA genes and the tmRNAFrontiers in Microbiology www.frontiersin.orgFebruary Volume ArticleTang et alparative Dehalobacter Genome Analysisbe evaluated without more understanding of gene regulation. Considering the fact that TEs commonly exist as interspersed repeats (direct or inverted) within a genome,they’re hot genome rearrangement web-sites through intragenomic homologous recombination. Several lines of evidence exist to suggest that insertion sequence (IS) transposition has played an important function in shaping Dehalobacter genomes. A big quantity of ISs were located in the three comprehensive Dehalobacter genomes (,and in strains CF,DCA,and PERK,respectively),and many strainspecific transposition events were identified when aligning the genomes of strains CF and DCA. Within the genome of strain CF,distinct ISs have been identified,of which exist in more than one particular copy inside the CF genome; an extreme case is the fact that of IS (DCF_p) that exists in nine copies within the genome. While strains CF and DCA share all ISs,their copy numbers differ in some instances,revealing lots of strainspecific transposition events which have happened because the differentiation of the two strains (Figure The genome of strain PERK has distinct ISs,of which five are shared with strain CF.Homologous RecombinationGenes crucial for homologous recombination had been located in all Dehalobacter genomes including recA,recFOR and ruvABC (Table S; tab. The presence of a big quantity of intragenomic repeats such as rRNA operons and ISs supplies prospective recombination websites for intragenomic homologous recombination,contributing to genome plasticity. 3 copies in the rRNA operons exist within the genomes of strains CF and DCA,while strain PERK genome has 4. As pointed out earlier,the strain CF (or DCA) genome features a global GCskew profile markedly diverse from that of strain PERK (Figure. 3 intragenomic sequence rearrangement events could clarify the distinction (Figure. Two o.
