Unravelling the genomic landscape of Canadian Borrelia burgdorferi: a comparison across global strains

The main agent of Lyme borreliosis (LB) in North America, the bacteria Borrelia burgdorferi , is spreading in Canada following the northward expansion of its primary tick vectors, Ixodes scapularis and Ixodes pacificus . Despite the importance of this pathogen for human health, the precise geographical origin and genome structure of Canadian B. burgdorferi strains remain to be determined, and no complete genome sequence from this region is available. The complex genome structure of Borrelia species makes their assembly challenging, but the latest long-read sequencing technologies and bioinformatics software now enable de novo assembly of Borrelia genomes with high efficacy. In this study, we sequenced and assembled the genomes of six Canadian B. burgdorferi strains to compare their content and structure to additional Borrelia genomes from the USA and Europe. We successfully reconstructed the genome, comprising chromosomes and plasmids of the six Canadian strains. These genomes showed an overall similar structure compared to other B. burgdorferi strains. Phylogenetic inferences highlighted topological differences in the placement of B. burgdorferi strains between the chromosome and the cp26 and lp54 plasmids. Synteny analyses revealed important replicon sequence conservation across strains while highlighting a high proportion of shared gene sequences among the replicons of the same strain, especially for cp32 plasmids. We describe the first complete genomes of Canadian B. burgdorferi strains and present a strategy for the assembly, annotation, comparative analysis of plasmids and their evolution in the same bacterial genus. While the genome content and structure of Canadian strains are similar to other B. burgdorferi strains, the information in the plasmids and genes they harbour will be useful to elucidate the origins and evolution of LB in Canada.