De novo genome assembly and analysis unveil biosynthetic and metabolic potentials of Pseudomonas fragi A13BB

Opeyemi K. Awolope, Noelle H. O’Driscoll, Alberto Di Salvo, Andrew J. Lamb

The role of rhizosphere microbiome in supporting plant growth under biotic stress is well documented. Rhizobacteria ward off phytopathogens through various mechanisms including antibiosis. We sought to recover novel antibiotic-producing bacterial strains from soil samples collected from the rhizosphere. Pseudomonas fragi A13BB was recovered as part of this effort, and the whole genome was sequenced to facilitate mining for potential antibiotic-encoding biosynthetic gene clusters. Here, we report the complete genome sequence of P. fragi A13BB obtained from de novo assembly of Illumina MiSeq and GridION reads. The 4.94 Mb genome consists of a single chromosome with a GC content of 59.40%. Genomic features include 4410 CDSs, 102 RNAs, 3 CRISPR arrays, 3 prophage regions, and 37 predicted genomic islands. Two β-lactone biosynthetic gene clusters were identified; besides, metabolic products of these are known to show antibiotic and/or anticancer properties. A siderophore biosynthetic gene cluster was also identified even though P. fragi is considered a non-siderophore producing pseudomonad. Other gene clusters of broad interest identified include those associated with bioremediation, biocontrol, plant growth promotion, or environmental adaptation. This dataset unveils various un-/underexplored metabolic or biosynthetic potential of P. fragi and provides insight into molecular mechanisms underpinning these attributes.