Comparative genomic analysis of HAB-5 reveals genes associated with antimicrobial and plant growth-promoting activities.

HAB-5 is a plant growth-promoting rhizobacterium (PGPR) that exhibits several biotechnological traits, such as enhancing plant growth, colonizing the rhizosphere, and engaging in biocontrol activities. In this study, we conducted whole-genome sequencing of HAB-5 using the single-molecule real-time (SMRT) sequencing platform by Pacific Biosciences (PacBio; United States), which has a circular chromosome with a total length of 4,083,597 bp and a G + C content of 44.21%. The comparative genomic analysis of HAB-5 with other strains, DSM7, SRCM101359, FZB42, HAB-2, and 168, revealed that these strains share 2,465 CDSs, while 599 CDSs are exclusive to the HAB-5 strain. Many gene clusters in the HAB-5 genome are associated with the production of antimicrobial lipopeptides and polypeptides. These gene clusters comprise distinct enzymes that encode three NRPs, two Transat-Pks, one terpene, one lanthipeptide, one T3PKS, one Ripp, and one thiopeptide. In addition to the likely IAA-producing genes ( and ), there are probable genes that produce volatile chemicals ( and ). Moreover, HAB-5 contained genes linked to iron transportation ( and ), sulfur metabolism ( and ), phosphorus solubilization (, and ), and nitrogen fixation ( and ). In conclusion, this study provides a comprehensive genomic analysis of HAB-5, pinpointing the genes and genomic regions linked to the antimicrobial properties of the strain. These findings advance our knowledge of the genetic basis of the antimicrobial properties of and imply that HAB-5 may employ a variety of commercial biopesticides and biofertilizers as a substitute strategy to increase agricultural output and manage a variety of plant diseases.