title: African relapsing Fever borreliae genomospecies revealed by comparative genomics.
abstract: BACKGROUND
  Relapsing fever borreliae are vector-borne bacteria responsible for febrile infection in humans in North America, Africa, Asia, and in the Iberian Peninsula in Europe. Relapsing fever borreliae are phylogenetically closely related, yet they differ in pathogenicity and vectors. Their long-term taxonomy, based on geography and vector grouping, needs to be re-apprised in a genomic context. We therefore embarked into genomic analyses of relapsing fever borreliae, focusing on species found in Africa.
  
  
  RESULTS
  Genome-wide phylogenetic analyses group Old World Borrelia crocidurae, Borrelia hispanica, B. duttonii, and B. recurrentis in one clade, and New World Borrelia turicatae and Borrelia hermsii in a second clade. Accordingly, average nucleotide identity is 99% among B. duttonii, B. recurrentis, and B. crocidurae and 96% between latter borreliae and B. hispanica while the similarity is 86% between Old World and New World borreliae. Comparative genomics indicates that the Old World relapsing fever B. duttonii, B. recurrentis, B. crocidurae, and B. hispanica have a 2,514-gene pan genome and a 933-gene core genome that includes 788 chromosomal and 145 plasmidic genes. Analyzing the role that natural selection has played in the evolution of Old World borreliae species revealed that 55 loci were under positive diversifying selection, including loci coding for membrane, flagellar, and chemotaxis proteins, three categories associated with adaption to specific niches.
  
  
  CONCLUSIONS
  Genomic analyses led to a reappraisal of the taxonomy of relapsing fever borreliae in Africa. These analyses suggest that B. crocidurae, B. duttonii, and B. recurrentis are ecotypes of a unique genomospecies, while B. hispanica is a distinct species.
authors.affiliation: URMITE, UMR63, CNRS 7278, IRD 198, INSERM 1095, Aix Marseille Université , Marseille , France.
authors.forename: Haitham
authors.initials: H
authors.lastname: Elbir
authors.affiliation: Equipe ATIP, Centre National de la Recherche Scientifique, Laboratoire d'Analyse, Topologie, Probabilités - Unité Mixte de Recherche 7353, Aix Marseille Université , Marseille , France.
authors.forename: Laurent
authors.initials: L
authors.lastname: Abi-Rached
authors.affiliation: Equipe EBM, Centre National de la Recherche Scientifique, Laboratoire d'Analyse, Topologie, Probabilités - Unité Mixte de Recherche 7353, Aix-Marseille Université , Marseille , France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Pontarotti
authors.affiliation: URMITE, UMR63, CNRS 7278, IRD 198, INSERM 1095, Aix Marseille Université , Marseille , France.
authors.forename: Niyaz
authors.initials: N
authors.lastname: Yoosuf
authors.affiliation: URMITE, UMR63, CNRS 7278, IRD 198, INSERM 1095, Aix Marseille Université , Marseille , France.
authors.forename: Michel
authors.initials: M
authors.lastname: Drancourt
keywords: Borrelia; genomics; phylogeny; relapsing fever; speciation