Ti plasmids in A. tumefaciens and Ri plasmids in A. rhizogenes cause plant tumor and hairy root diseases by their T-DNA transfer into plant chromosomes, respectively. The first complete sequencing of Ti (Suzuki et al., 2000) and Ri (Moriguchi et al., 2001) plasmids revealed the presence of 195 ORFs in 206,479 bp pTi-SAKURA DNA and of 173 ORFs in 217,594 bp pRi1724 DNA. The identified genes consisted of several functional gene clusters. Except for common genes including T-DNA, vir, tra and rep genes, there were 84 and 27 unknown ORFs in Ti and Ri plasmids, respectively. Extensive phylogenetic analyses of tra, vir, oriV and their homolog genes interestingly indicated that Ri plasmids are closer to Rhizobium symbiotic plasmids rather than Ti plasmids. This was confirmed by cross-hybridization of a total of annoted genes in the plasmids. We discussed the origin and evolution of these plasmids focusing on gene transfer systems.
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