Analysis of the genome sequence of plant beneficial strain Pseudomonas sp. RU47

Pseudomonas sp. RU47 (RU47) is a rhizosphere-competent strain showing plant growth-promoting and biocontrol activities. In this study, the genome sequence of strain RU47 was obtained and phylogenetic and comparative genome analyses were performed. Multilocus sequence analysis (MLSA) coupled with the calculation of average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) values suggested that strain RU47 belongs to the P. koreensis group of the P. fluorescens complex, but cannot be assigned to any known Pseudomonas species. Multiple genes and operons encoding functions that likely contribute to its previously reported high rhizosphere competence, biocontrol of Rhizoctonia solani and plant growth promotion in soils with reduced fertilization were identified. Putative genes and gene clusters for the production of hydrogen cyanide, cyclic lipopeptides, bacteriocins, siderophores, indole-3-acetic acid, spermidine, alkaline protease A, chitinase and ß-1,3-glucanase were identified, as well as loci associated with solubilization of inorganic phosphate. Several of these functions were also confirmed by in vitro testing. Distribution of putative genes and gene clusters that may contribute to the plant growth-promoting and biocontrol activities was largely similar among strains belonging to P. koreensis group, as revealed by comparative genome analysis. Data presented in this study further support the potential of RU47 for its application in agriculture and may be a valuable resource for further studies.