Pangenome graphs for pks+/- E. coli in the NORM hybrid assembly collection

Contains files for three pangenome graphs used in the study "Co-evolution between colibactin production and resistance is linked to clonal expansions in Escherichia coli": one for hybrid assemblies containing the colibactin production genes (pks+), one for assemblies without them (pks-), and a final graph with both datasets.

For pks+ assemblies, an interactive annotated graph is available as a set of .html files in the zip archive `NORM_pks_neighborhood_graph_html.zip`.

References

Data

Isolation, sequencing, and assembly are described in the following two studies:

[1] Gladstone et al. "Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002–17: a nationwide, longitudinal, microbial population genomic study". The Lancet Microbe (2021). doi: 10.1016/S2666-5247(21)00031-8.

[2] Arredondo-Alonso et al. "Plasmid-driven strategies for clone success in Escherichia coli". Nature communications (2025). doi: 10.1038/s41467-025-57940-1.

Sequencing data is available from the European Nucleotide Archive under accession numbers PRJEB45354 and PRJEB57633.

Genome annotation

Genome annotation was performed using bakta v1.10.4 (GitHub: oschwengers/bakta) against full database v5.1 dated 2024-01-19 (doi: 10.5281/zenodo.10522951):

[3] Schwengers et al. "Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification." Microbial genomics (2021). doi: 10.1099/mgen.0.000685.

Annotation files are available in a separate Zenodo upload: doi: 10.5281/zenodo.17453317.

Pangenome inference

Pangenome inference from the annotations was performed using panaroo v1.5.2 (GitHub: gtonkinhill/panaroo) with the “--clean-mode strict” and “--remove-invalid-genes” options:

[4] Tonkin-Hill et al. "Producing polished prokaryotic pangenomes with the Panaroo pipeline." Genome Biology (2020). doi: 10.1186/s13059-020-02090-4.