Whole genome analysis of endophytic strain PM1 reveals promising plant Growth-Promoting mechanisms in pomegranate

Abstract

The plant ecosystem harbours diverse symbiotic microorganisms with plant growth promoting and biocontrol activities. The gram- negative endophytic bacterium PM1 strain, isolated from the nodal region of pomegranate. The strain PM1 was studied through whole-genome sequencing, functional annotation, and plant growth-promoting trait (PGPT) gene analysis. Phylogenetic tree analysis and 16S rDNA sequencing confirmed its classification within the genus Brucella. The assembled genome size was 5,200,895 bp with a G + C content of 56.4 %. The average nucleotide identity (ANI) analysis revealed a 97.62 % similarity between PM1 and B. anthropi ATCC 49188 T, a type strain derived from human clinical samples, indicating a close relationship with Brucella anthropi. The functional annotation revealed 2,945 PGPT-related genes, including 32 % linked to direct effects (phytohormone signal production, biofertilization, and bioremediation processes) and 67 % to indirect effects (plant colonization, biocontrol, and competitive exclusion). KEGG analysis revealed genes involved in nitrogen metabolism, phosphate solubilization, siderophore production, hormone biosynthesis (gibberellin, cytokinin, and auxin), root colonization, and stress mitigation. Virulence factor database (VFDB) data revealed the absence of complete virulence gene assemblies, indicating limited pathogenic potential. Furthermore, secondary metabolite analysis predicted the potential production of ochrobactin compounds, which are potent siderophores that are important traits associated with PGPTs. The complete genome analysis of Brucella sp. PM1 provides new insights into plant-bacteria interactions, laying a foundation for advanced postgenomic studies and facilitating the development of bioeffective strategies such as biofertilizers or biocontrol agents for sustainable improvement in crop yields.