FIG 3.

Phylogenetic lineage of M. avium subsp. paratuberculosis strains from France. A maximum likelihood phylogenetic tree was inferred using IQ-Tree (K3Pu+F model), showing the relatedness of 192 French isolates and the K-10 strain. PICSAR77 was used as the reference, being completely assembled and belonging to the largest clade of the phylogeny (i.e., clade A), and homoplasic sites were removed. The tree was midpoint rooted. The scale of the tree is by site substitution. Bootstrap phylogenetic clades have been highlighted (light blue, clade A; dark blue, clade A1; green, clade B; yellow, clade C). The other strains have been shaded in gray. From left to right are shown the isolate name, host breed, MLVA-INMV (INRA Nouzilly MIRU VNTR) profiles, animal identifier, herd identifier, and year of strain isolation. The legends for breed and MLVA profile are shown in the lower left. Colored dots on the tree indicate M. avium subsp. paratuberculosis isolates from 2003 (pink) or the K-10 strain (brown). The monophyletic group carrying the synonymous mutation in the gyrB gene at position 1124 is indicated by a red box.