Rhizobium skierniewicense Ch11 Genome sequencing and assembly. Rhizobium skierniewicense Ch11

This is an overview of the main important regions within Tumor-inducing (Ti) and Root-inducing (Ri) plasmid sequences belonging to various Agrobacterium isolates and several reference strains using high-throughput sequencing technology. Characterization was based on the delimitation of the biovar, determination of the opine type, gene organization within the T-DNA region and analysis of genes involved in virulence. Various subgroups were then identified based on gene organization within T-DNA region. For each opine type, the plasmid was also dispatched into several subgroups with common gene content and organization of the virulence region. For the first time, the phylogenetic relationships between representatives of all 50 Agrobacterium plasmids have been investigated using T-DNA and virulence regions. The monophyly of the plasmid types is demonstrated for the first time using molecular data. The monophyly of the major subgroups proposed are supported in this study. Comparative sequences analysis showed that these plasmids displayed high diversity level, especially within T-DNA regions. The knowledge acquired in our work highlights a key role of opine type in affecting plasmid sequence structures, gene content and organization. Here we propose an improved classification of Ti and Ri plasmids which will be used to discern crown gall epidemiology.