Telomere-to-telomere assembly detects genomic diversity in Canadian strains of Borrelia burgdorferi

Borrelia burgdorferi, the bacteria causing Lyme disease, has a complex genome comprising a linear chromosome and multiple linear and circular plasmids. The atypical hairpin telomeres and the highly paralogous plasmids complicate genome assembly. We develop a genome assembly pipeline using both long and short reads to overcome these challenges. Using long reads, we assemble the hairpin telomeres of the linear replicons, an lp28-1a plasmid subtype, and circular plasmids of nine B. burgdorferi strains from five regions across Northwest Ontario and Manitoba, Canada. Although similar across the core conserved genomic regions, all strains carry a ∼2-10 kb right telomeric end identical to lp28-1, leading to variability in telomere length and gene content. Additionally, we observe diversity at the linear chromosome hairpin telomeric sequences, ospC types, and plasmid profiles, highlighting the genomic diversity among the geographically proximate strains and suggesting such variations as possible mechanisms of rapid evolution.