The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems
The gene contents of the “short” and “long” Myxo NF-T3SSs are displayed on the 16S rRNA phylogeny of the group. The 16S rRNA maximum likelihood tree was built with RAxML  (General time-reversible model + 4-categories-discretized Gamma distribution for rate variations among sites) and chosen from the best of 200 starting trees. The numbers in the tree nodes refer to bootstrap values out of 100 replicates. The identified NF-T3SS genes are represented by boxes containing the last letter of the “sct” gene name, and colored according to the color code of Figure 1A. Dashed transparent boxes correspond to genes showing hits for Hmmer sequence profiles with i-evalue above the 10−3 threshold. Empty boxes correspond to genes not annotated in our analysis, and boxes with three dots correspond to several (4 to 16) consecutive non-annotated genes. Proteins encoded in the loci are colored on the NF-T3SS structure drawings, whereas parts of the structure whose corresponding gene could not be found remain unfilled.