title: Acquisition and loss of virulence-associated factors during genome evolution and speciation in three clades of Bordetella species.
abstract: The genus Bordetella consists of nine species that include important respiratory pathogens such as the 'classical' species B. bronchiseptica, B. pertussis and B. parapertussis and six more distantly related and less extensively studied species. Here we analyze sequence diversity and gene content of 128 genome sequences from all nine species with focus on the evolution of virulence-associated factors.
  
  
  
  Both genome-wide sequence-based and gene content-based phylogenetic trees divide the genus into three species clades. The phylogenies are congruent between species suggesting genus-wide co-evolution of sequence diversity and gene content, but less correlated within species, mainly because of strain-specific presence of many different prophages. We compared the genomes with focus on virulence-associated genes and identified multiple clade-specific, species-specific and strain-specific events of gene acquisition and gene loss, including genes encoding O-antigens, protein secretion systems and bacterial toxins. Gene loss was more frequent than gene gain throughout the evolution, and loss of hundreds of genes was associated with the origin of several species, including the recently evolved human-restricted B. pertussis and B. holmesii, B. parapertussis and the avian pathogen B. avium.
  
  
  
  Acquisition and loss of multiple genes drive the evolution and speciation in the genus Bordetella, including large scale gene loss associated with the origin of several species. Recent loss and functional inactivation of genes, including those encoding pertussis vaccine components and bacterial toxins, in individual strains emphasize ongoing evolution.
authors.affiliation: Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA. bxl29@psu.edu.
authors.forename: Bodo
authors.initials: B
authors.lastname: Linz
authors.affiliation: Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Yury V
authors.initials: YV
authors.lastname: Ivanov
authors.affiliation: The Millner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Bath, UK.
authors.forename: Andrew
authors.initials: A
authors.lastname: Preston
authors.affiliation: J. Craig Venter Institute, Rockville, MD, USA.
authors.forename: Lauren
authors.initials: L
authors.lastname: Brinkac
authors.affiliation: Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.affiliation: J. Craig Venter Institute, Rockville, MD, USA.
authors.forename: Maria
authors.initials: M
authors.lastname: Kim
authors.affiliation: Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Simon R
authors.initials: SR
authors.lastname: Harris
authors.affiliation: Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Laura L
authors.initials: LL
authors.lastname: Goodfield
authors.affiliation: Public Health England, Respiratory and Vaccine Preventable Bacteria Reference Unit, London, UK.
authors.forename: Norman K
authors.initials: NK
authors.lastname: Fry
authors.affiliation: Public Health England, Porton Down, Salisbury, UK.
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Gorringe
authors.affiliation: USDA, Agricultural Research Service, National Animal Disease Center, Ames, IA, USA.
authors.forename: Tracy L
authors.initials: TL
authors.lastname: Nicholson
authors.affiliation: USDA, Agricultural Research Service, National Animal Disease Center, Ames, IA, USA.
authors.forename: Karen B
authors.initials: KB
authors.lastname: Register
authors.affiliation: J. Craig Venter Institute, Rockville, MD, USA.
authors.forename: Liliana
authors.initials: L
authors.lastname: Losada
authors.affiliation: Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA. Harvill@uga.edu.|Singapore Centre on Environmental Life Sciences Engineering, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 637551, Singapore. Harvill@uga.edu.|Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA. Harvill@uga.edu.
authors.forename: Eric T
authors.initials: ET
authors.lastname: Harvill
mesh_terms: D000818:Animals; D058947:Bacterial Secretion Systems / Q000235:genetics; D001884:Bordetella / Q000145:classification* / Q000235:genetics*; D001885:Bordetella Infections / Q000382:microbiology; D066264:Datasets as Topic; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D014644:Genetic Variation; D016680:Genome, Bacterial; D023281:Genomics; D005838:Genotype; D006801:Humans; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D037521:Virulence Factors / Q000235:genetics*
chemical_list: D058947:Bacterial Secretion Systems; D037521:Virulence Factors
keywords: Bordetella; Evolution; Gene acquisition; Gene loss; Virulence factor