Fig. 3: Genes most strongly associated with protection are unique to ATUE2.

A Presence/absence variation of nine genes that are most strongly associated with protection. Strains are ordered by their phylogeny. Strains belonging to the ATUE2 group are indicated in magenta. Gene presence is indicated in grey, absence in white. Growth was measured as the change in green pixels between days 0 and 7 after infection, with the scale indicated on the right. B Daily median of plant green pixels among all strains (top panel) or the ATUE2 subset (bottom panel). Shades of magenta indicate the number of protective genes out of 9 present in each strain, as indicated by the scale on the bottom. Eight replicates per treatment. C Plant growth after co-infections with the pathogen p4.C9, binned by (i) the presence of at least one gene from the set of the nine protective genes (presented in panel A) in a given commensal strain, and (ii) membership in the ATUE2 group. In each group, raw data for individual replicates are shown as dots; the overlain shades of blue indicate the posterior predictive intervals, as indicated on the bottom right. The mean growth for each group is also shown; the dot indicates the median, the thin horizontal line the 95% credible interval, and the thick line the 67% credible interval. n = 8 replicates per strain, with the number of strains in the different categories as follows: non-ATUE2 with 0/9 genes = 67; ATUE2 with 0/9 genes = 20, and ATUE2 with at least 1/9 genes = 16.