Abstract
<title>Abstract</title> <p> Rhizobium species are important symbiotic nitrogen fixers and potential bioinoculants, yet the comparative genomic characteristics of <italic>Rhizobium bangladeshense</italic> BLR175, <italic>Rhizobium binae</italic> BLR195, and <italic>Rhizobium lentis</italic> BLR27 remain insufficiently characterized. This study applied a standardized workflow comprising Prokka annotation, dRep-based identity analysis, Roary pan-genome reconstruction, functional screening, and Proksee visualization. Genome sizes ranged from 5.96 to 6.81 Mb, with 7,287–7,884 predicted coding sequences. <italic>R. lentis</italic> exhibited an N50 of 5,067 bp and the highest hypothetical-protein fraction among the three genomes. Pairwise average nucleotide identity values of 88.47–89.84% and assignment to distinct secondary clusters confirmed substantial genomic divergence among the three strains. The pan-genome contained 18,646 gene clusters, including 1,336 core and 17,310 accessory clusters. All genomes carried major genes associated with nodulation, nitrogen fixation, microaerobic respiration, surface-polysaccharide biosynthesis, dicarboxylate transport, and cytochrome-c maturation. BLR175 showed the broadest inventories of genes associated with metal homeostasis, siderophore production, and colonization; BLR195 was enriched in phosphate-utilization genes and uniquely carried <italic>merA</italic> ; and BLR27 exhibited the most extensive phytohormone and stress-mitigation-related gene profile. These findings identify three genomically distinct candidate bioinoculants with complementary functional potential. </p>