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Comparative whole genome analysis of six diagnostic brucellaphages
Authors:Jason Farlow  Andrey A Filippov  Kirill V Sergueev  Jun Hang  Adam Kotorashvili  Mikeljon P Nikolich
Institution:1. Ilia State University, Tbilisi, Georgia;2. Department of Emerging Bacterial Infections, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA;3. Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA;4. Richard G. Lugar Center for Public Health Research, Tbilisi, Georgia
Abstract:Whole genome sequencing of six diagnostic brucellaphages, Tbilisi (Tb), Firenze (Fz), Weybridge (Wb), S708, Berkeley (Bk) and R/C, was followed with genomic comparisons including recently described genomes of the Tb phage from Mexico (TbM) and Pr phage to elucidate genomic diversity and candidate host range determinants. Comparative whole genome analysis revealed high sequence homogeneity among these brucellaphage genomes and resolved three genetic groups consistent with defined host range phenotypes. Group I was composed of Tb and Fz phages that are predominantly lytic for Brucella abortus and Brucella neotomae; Group II included Bk, R/C, and Pr phages that are lytic mainly for B. abortus, Brucella melitensis and Brucella suis; Group III was composed of Wb and S708 phages that are lytic for B. suis, B. abortus and B. neotomae. We found that the putative phage collar protein is a variable locus with features that may be contributing to the host specificities exhibited by different brucellaphage groups. The presence of several candidate host range determinants is illustrated herein for future dissection of the differential host specificity observed among these phages.
Keywords:°  C  degrees Celsius  μm  micrometer  μl  microliter  acc  no    accession number  BIC  Bayesian Information Criterion  Bk  Berkeley phage  BS  bootstrap  C  cytidine  CRISPRs  clustered regularly interspaced short palindromic repeats  dN - dS statistic  the ratio of the number of non-synonymous substitutions per non-synonymous site to the number of synonymous substitutions per synonymous site  DNA  Deoxyribonucleic acid  DnaA  a protein that activates initiation of DNA replication in prokaryotes  DNase I  deoxyribonuclease I  Fz  Firenze phage  g  gravity  G  guanosine  h  hours  IG  intergenic  InDel  insertion&ndash  deletion  Iz  Izatnagar phage  Kb  kilobasepair  L  confluent lysis  L  liter  LPS  lipopolysaccharide  min  minutes  ml  milliliter  MOI  multiplicity of infection  NA  not applicable  NL  no lysis  nm  nanometer  ORF  open reading frame  oriC  origin of replication  PL  partial lysis  RNase A  ribonuclease A  RTD  routine test dilution  SDA  serum dextrose agar  SDS  sodium dodecyl sulfate  SNPs  single nucleotide polymorphisms  Tb  Tbilisi phage  TbM  Tbilisi phage variant sequenced in Mexico  TbW  Tbilisi phage variant sequenced at WRAIR  U  S    United States  Wb  Weybridge phage  WRAIR  Walter Reed Army Institute of Research
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