Telomere-to-telomere assembly detects genomic diversity in Canadian strains of <i>Borrelia burgdorferi</i>
Bibliographic record
Abstract
Abstract Borrelia burgdorferi, the bacteria causing Lyme disease, has a complex genome comprising a linear chromosome and a combination of linear and circular plasmids. The atypical hairpin structure at the telomere of linear replicons and the highly paralogous plasmids make the genome assembly challenging. We developed a genome assembly pipeline using Oxford Nanopore Technologies (ONT) long read and Illumina short read to overcome these challenges. Using ONT reads enabled us to completely assemble the hairpin telomeres of the linear replicons along with a novel lp28 subtype plasmid and the complete circular plasmids of nine B. burgdorferi strains from five geographical regions in Canada. Although these strains are highly similar across the conserved genomic regions, variability was observed predominantly at the right telomeric ends. Comparative analyses revealed that all nine strains carry a ∼2-10 kb right telomeric end identical to the linear plasmid lp28-1, which leads to variability in the telomere length and the gene content. Additionally, we observed diversity at the hairpin telomeric sequences of the linear chromosomes. Further analysis showed that the nine strains belong to seven ospC types and have diverse plasmid profile, highlighting the genomic diversity among the strains from the same geographical locations. Overall, these findings suggest that even the B. burgdorferi strains from close geographical locations can carry substantial genomic variation, especially at the telomeres and with respect to their plasmid content, emphasizing it to be a possible mechanism of rapid evolution within these Canadian strains.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".