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Background   Borrelia bavariensis  is one of the agents of Lyme Borreliosis (or Lyme disease) in Eurasia. The genome of the  Borrelia burgdorferi  sensu lato species complex, that includes  B. bavariensis , is known to be very complex and fragmented making the assembly of whole genomes with next-generation sequencing data a challenge.    Results  We present a genome reconstruction for 33  B. bavariensis  isolates from Eurasia based on long-read (Pacific Bioscience, for three isolates) and short-read (Illumina) data. We show that the combination of both sequencing techniques allows proper genome reconstruction of all plasmids in most cases but use of a very close reference is necessary when only short-read sequencing data is available.  B. bavariensis  genomes combine a high degree of genetic conservation with high plasticity: all isolates share the main chromosome and five plasmids, but the repertoire of other plasmids is highly variable. In addition to plasmid losses and gains through horizontal transfer, we also observe several fusions between plasmids. Although European isolates of  B. bavariensis  have little diversity in genome content, there is some geographic structure to this variation. In contrast, each Asian isolate has a unique plasmid repertoire and we observe no geographically based differences between Japanese and Russian isolates. Comparing the genomes of Asian and European populations of  B. bavariensis  suggests that some genes which are markedly different between the two populations may be good candidates for adaptation to the tick vector, ( Ixodes ricinus  in Europe and  I. persulcatus  in Asia).    Conclusions  We present the characterization of genomes of a large sample of  B. bavariensis  isolates and show that their plasmid content is highly variable. This study opens the way for genomic studies seeking to understand host and vector adaptation as well as human pathogenicity in Eurasian Lyme Borreliosis agents.

High conservation combined with high plasticity: genomics and evolution of Borrelia bavariensis