title: A genome-wide SNP-based phylogenetic analysis distinguishes different biovars of Brucella suis.
abstract: Brucellosis is an important zoonotic disease caused by Brucella spp. Brucella suis is the etiological agent of porcine brucellosis. B. suis is the most genetically diverged species within the genus Brucella. We present the first large-scale B. suis phylogenetic analysis based on an alignment-free k-mer approach of gathering polymorphic sites from whole genome sequences. Genome-wide core-SNP based phylogenetic tree clearly differentiated and discriminated the B. suis biovars and the vaccine strain into different clades. A total of 16,756 SNPs were identified from the genome sequences of 54 B. suis strains. Also, biovar-specific SNPs were identified. The vaccine strain B. suis S2-30 is extensively used in China, which was discriminated from all biovars with the accumulation of the highest number of SNPs. We have also identified the SNPs between B. suis vaccine strain S2-30 and its closest homolog, B. suis biovar 513UK. The highest number of mutations (22) was observed in the phosphomannomutase (pmm) gene essential for the synthesis of O-antigen. Also, mutations were identified in several virulent genes including genes coding for type IV secretion system and the effector proteins, which could be responsible for the attenuated virulence of B. suis S2-30.
authors.affiliation: Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India.
authors.forename: Jagadesan
authors.initials: J
authors.lastname: Sankarasubramanian
authors.affiliation: Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India.
authors.forename: Udayakumar S
authors.initials: US
authors.lastname: Vishnu
authors.affiliation: Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India.
authors.forename: Paramasamy
authors.initials: P
authors.lastname: Gunasekaran
authors.affiliation: Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India. Electronic address: jrajendhran@gmail.com.
authors.forename: Jeyaprakash
authors.initials: J
authors.lastname: Rajendhran
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics*; D001428:Bacterial Vaccines / Q000235:genetics; D001483:Base Sequence; D041021:Brucella suis / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D002006:Brucellosis / Q000453:epidemiology / Q000382:microbiology; D002681:China / Q000453:epidemiology; D002874:Chromosome Mapping; D016680:Genome, Bacterial; D009154:Mutation; D017875:Phosphotransferases (Phosphomutases) / Q000235:genetics; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D013552:Swine; D000069319:Type IV Secretion Systems / Q000235:genetics; D037521:Virulence Factors / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D001428:Bacterial Vaccines; D000069319:Type IV Secretion Systems; D037521:Virulence Factors; D017875:Phosphotransferases (Phosphomutases); C052799:phosphomannomutase
keywords: Alignment-free; B. suis; Biovar; Brucella; Phylogeny; SNP