Figures and data
![](https://prod--epp.elifesciences.org/iiif/2/97870%2Fv1%2Fcontent%2F584580v2_fig1.tif/full/max/0/default.jpg)
The geography of the dataset.
(A) sample collection distribution by country; (B) the number of genomes of each lineage included from each continent.
![](https://prod--epp.elifesciences.org/iiif/2/97870%2Fv1%2Fcontent%2F584580v2_fig2.tif/full/max/0/default.jpg)
Boxplot showing the distribution of accessory genes within each lineage.
Lineages with a small number of genomes were excluded from the analysis. L6, La1 and M. microti have significantly smaller accessory genomes compared to other lineages.
![](https://prod--epp.elifesciences.org/iiif/2/97870%2Fv1%2Fcontent%2F584580v2_fig3.tif/full/max/0/default.jpg)
Analysis of the functional components in the core (A) and accessory (B) genome using EggNOG mapper and InterProScan.
![](https://prod--epp.elifesciences.org/iiif/2/97870%2Fv1%2Fcontent%2F584580v2_fig4.tif/full/max/0/default.jpg)
(A) phylogenetic tree based on MTBC core genome. PCA based on the accessory genome data from Panaroo (B) and pangraph (C).
![](https://prod--epp.elifesciences.org/iiif/2/97870%2Fv1%2Fcontent%2F584580v2_fig5.tif/full/max/0/default.jpg)
MTBC Accessory genome identified by Panaroo (A) and Pangraph (B).
![](https://prod--epp.elifesciences.org/iiif/2/97870%2Fv1%2Fcontent%2F584580v2_fig6.tif/full/max/0/default.jpg)
Sub-lineage specific regions of differences (RDs) identified using pangenome-based and genome alignment-based approaches.
Sub-lineages are shown on the Y-axis coloured as per the legend and clustered based on the RD presence/absence patterns. RDs are listed on the X-axis, grouped by their pattern of presence/absence.
![](https://prod--epp.elifesciences.org/iiif/2/97870%2Fv1%2Fcontent%2F584580v2_fig7.tif/full/max/0/default.jpg)
Visual presentation of deletion caused by RD702.
The truncated bglS gene was classified as a core gene with Panaroo but has specific deletions within, which can be problematic for pangenomic analyses.