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

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...

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Published in:	BMC genomics Vol. 21; no. 1; p. 702
Main Authors:	Becker, Noémie S, Rollins, Robert E, Nosenko, Kateryna, Paulus, Alexander, Martin, Samantha, Krebs, Stefan, Takano, Ai, Sato, Kozue, Kovalev, Sergey Y, Kawabata, Hiroki, Fingerle, Volker, Margos, Gabriele
Format:	Journal Article
Language:	English
Published:	England BioMed Central Ltd 08-10-2020 BioMed Central BMC
Subjects:	Adaptation Animals Asia Borrelia Borrelia bavariensis Borrelia burgdorferi Group Borreliosis Chromosomes Conservation Conserved Sequence - genetics Europe Gene sequencing Genes Genetic aspects Genetic plasticity Genetic research Genome assembly Genome, Bacterial - genetics Genomes Genomics Genotypes Horizontal transfer Humans Identification and classification Ixodes Lyme Borreliosis Lyme disease Lyme Disease - microbiology Next-generation sequencing Pathogenicity Pathogens Phylogeny Physiological adaptation Plasmids Plasmids - genetics Plastic properties Plasticity Populations Proteins Reconstruction Russia Spirochaetales - classification Spirochaetales - genetics Vector-borne diseases Asia Europe Russia Germany Lyme Borreliosis Genetic plasticity Genome assembly Plasmids Borrelia bavariensis
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Summary:	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. 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). 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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1471-2164 1471-2164
DOI:	10.1186/s12864-020-07054-3