Effects of crown gall disease on natural microbiota of Vitis vinifera - genome annotations

Young grapevines (Vitis vinifera) frequently die due to the crown gall (CG) disease induced by the plant pathogen Allorhizobium vitis (Rhizobiaceae). Virulent members of A. vitis harbour a tumor-inducing (Ti) plasmid and cause formation of CGs due to genes encoded on the T-DNA. Expression of the oncogenes by transformed host cells induce cell proliferation, metabolic and physiological changes. The CG produces opines uncommon to plants, which provide an important nutrient source for A. vitis harbouring opine catabolism enzymes. CGs host a defined bacterial community and the mechanisms establishing a CG-specific bacterial community are currently unknown. Thus, we were interested in whether genes homologous to those of the Ti-plasmid coexist in the genomes of the microbial species coexisting in CGs. We isolated eight bacterial strains from grapevine CGs, sequenced their genomes and tested their virulence and opine utilization ability in bioassays. In addition, the eight genome sequences were aligned to the sequences of a Ti-plasmid and seven published bacterial genomes, including closely related plant associated bacteria but not from CGs. Homologous genes for virulence and opine anabolism were only present in the virulent Rhizobiaceae. By contrast, homologs of the opine catabolism genes were present in all strains including the non-virulent members of the Rhizobiaceae and non-Rhizobiaceae, indicating horizontal gene transfer of the opine degradation cluster from virulent to non-virulent strains. These results along with those of the opine utilization assay support the important role of opine utilization for co-colonization of virulent and non-virulent bacteria in CGs, thereby shaping the CG community.

This dataset contains the prokka annotations of the genomes as used in "Opportunistic bacteria of grapevine crown galls are equipped with the genomic repertoire for opine utilization"