Abstract
<title>Abstract</title> <p> <italic>Pseudomonas fluorescens</italic> is a highly diverse species complex which is renowned for its plant growth-promoting and biocontrol capabilities across diverse ecological niches. In this study, we investigated pan-genomic nature, plant growth promoting genes and biosynthetic gene clusters of complete genomes to unveil their genomic diversity, functional adaptability, plant growth-promoting potential, and secondary metabolite repertoire. A number of 40 high-quality genomes data were collected from the NCBI database and re-annotated using Prokka. After that, pan-genome analysis was conducted using BPGA and Roary. From gene-presence absence matrix of Roary output, PGP gene heatmap was created across genomes. Antismash platform was used for predicting biosynthetic gene clusters. The findings revealed that an exceptionally open pan-genome, consisting of 82,011 gene clusters, dominated by cloud (89.3%) and shell (10.5%) genes, while only 19 genes constituted the core genome.Functional annotations analysis using COG and KEGG revealed that core genes are directly involved in cellular processes, on the other hand accessory genes are exerts action on metabolic functions, environmental sensing, and secondary metabolism. Plant growth-promoting (PGP) genesheatmap revealed a mosaic and strain-dependent distribution of traits such as pyrroloquinoline quinone biosynthesis, hydrogen cyanide production, ACC deaminase activity, and denitrification pathways. Those also depicting plant-beneficial properties are ecotype-specific rather than universally conserved. AntiSMASH based screening elucidated a rich and diverse repertoire of biosynthetic gene clusters, including NRPS, RiPPs, siderophores, terpenes, and stress-related metabolites, with both conserved and strain-unique distributions. Multivariate analyses further highlighted lineage-specific clustering driven by accessory gene content and biosynthetic diversity.Overall, is a genetically flexible species complex with strong potential for sustainable agriculture and natural product discovery. </p>