Evolutionary classification of tumor- and root-inducing plasmids based on T-DNAs and virulence regions

Tumor-inducing (Ti) and root-inducing (Ri) plasmids of Agrobacterium that display a large diversity are involved in crown gall and hairy root plant diseases. Their phylogenetic relationships were inferred from an exhaustive set of Ti and Ri plasmids (including 36 new complete Ti plasmids) by focusing on T-DNA and virulence regions. The opine synthase gene content of T-DNAs revealed 13 opine types corresponding to former classifications based on opines detected in diseased plants, while the T-DNA gene content more finely separate opine types in 18 T-DNA organizations. This classification was supported by the phylogeny of T-DNA oncogenes of Ti plasmids. The five gene organizations found in Ti/Ri vir regions was supported by the phylogeny of common vir genes. The vir organization was found to be likely an ancestral plasmid trait separating classic Ti plasmids (with one or two TDNAs) and Ri and vine-Ti plasmids. A scenario generally supported by the repABC phylogeny. T-DNAs likely evolved later with the acquisition of opine characteristics as last steps in the Ti/Ri plasmid evolution. This novel evolutionary classification of Ti/Ri plasmids was found to be relevant for accurate crown gall and hairy root epidemiology.

Automated summary

The phylogenetic relationships of Ti and Ri plasmids of Agrobacterium, which are involved in crown gall and hairy root plant diseases, were studied. A classification based on T-DNA and virulence regions was proposed, showing the diversity of opine types and gene organizations. This evolutionary classification is important for the epidemiology of crown gall and hairy root diseases.