A comparative genomics study of 278 Bradyrhizobium strains revealed a pan-genome consisting of 84,078 gene families, including 824 core genes and 42,409 accessory genes. Bradyrhizobium strains showed significant genetic diversity, with most lacking the nif and nod gene clusters necessary for symbiotic nitrogen fixation. The pan-genome was characterized as "open," with a power-law coefficient of 0.45, indicating progressive expansion with new genomes. Core genes were mainly involved in essential cellular processes, while accessory genes had diverse functions, including nitrogen fixation and nodulation. Three distinct genetic profiles were identified based on the presence/absence of gene clusters related to nodulation, nitrogen fixation, and secretion systems. Most soil-derived Bradyrhizobium strains lacked major nif/nod genes and were evolutionarily more closely related. The study also identified 190 genes involved in nodulation and nitrogen fixation, with 5 core genes, 141 accessory genes, and 44 strain-specific genes. Bradyrhizobium strains isolated from legumes had more nodulation genes than those from soil. The study found that Bradyrhizobium strains from root nodules of various legumes had both nif and nod gene clusters, as well as the ysc gene cluster of the T3SS system, suggesting their potential as rhizobial inoculants. However, many soil-derived strains lacked these gene clusters, indicating they may not exhibit nod-dependent symbiotic nitrogen fixation. The study also identified carbon fixation genes, with 139 genes in the pan-genome, including 18 core genes, 95 accessory genes, and 26 strain-specific genes. Bradyrhizobium strains showed varying abilities to fix carbon dioxide via the Calvin cycle, with RuBisCo as the key enzyme. The study highlighted the genetic diversity of Bradyrhizobium, emphasizing the importance of studying their genomes to understand their nitrogen and carbon fixation capabilities. The results provide insights into the genetic characteristics and nitrogen fixation profile of Bradyrhizobium, which could have implications for agricultural applications. The study also identified the evolutionary relationships among Bradyrhizobium strains, showing host-specific clustering and significant genetic differentiation between species. The findings suggest that Bradyrhizobium strains have diverse genetic profiles, with some capable of nitrogen fixation and others unable to form nodules. The study underscores the need for further research to understand the mechanisms driving the evolution of mobile genetic elements in Bradyrhizobium.A comparative genomics study of 278 Bradyrhizobium strains revealed a pan-genome consisting of 84,078 gene families, including 824 core genes and 42,409 accessory genes. Bradyrhizobium strains showed significant genetic diversity, with most lacking the nif and nod gene clusters necessary for symbiotic nitrogen fixation. The pan-genome was characterized as "open," with a power-law coefficient of 0.45, indicating progressive expansion with new genomes. Core genes were mainly involved in essential cellular processes, while accessory genes had diverse functions, including nitrogen fixation and nodulation. Three distinct genetic profiles were identified based on the presence/absence of gene clusters related to nodulation, nitrogen fixation, and secretion systems. Most soil-derived Bradyrhizobium strains lacked major nif/nod genes and were evolutionarily more closely related. The study also identified 190 genes involved in nodulation and nitrogen fixation, with 5 core genes, 141 accessory genes, and 44 strain-specific genes. Bradyrhizobium strains isolated from legumes had more nodulation genes than those from soil. The study found that Bradyrhizobium strains from root nodules of various legumes had both nif and nod gene clusters, as well as the ysc gene cluster of the T3SS system, suggesting their potential as rhizobial inoculants. However, many soil-derived strains lacked these gene clusters, indicating they may not exhibit nod-dependent symbiotic nitrogen fixation. The study also identified carbon fixation genes, with 139 genes in the pan-genome, including 18 core genes, 95 accessory genes, and 26 strain-specific genes. Bradyrhizobium strains showed varying abilities to fix carbon dioxide via the Calvin cycle, with RuBisCo as the key enzyme. The study highlighted the genetic diversity of Bradyrhizobium, emphasizing the importance of studying their genomes to understand their nitrogen and carbon fixation capabilities. The results provide insights into the genetic characteristics and nitrogen fixation profile of Bradyrhizobium, which could have implications for agricultural applications. The study also identified the evolutionary relationships among Bradyrhizobium strains, showing host-specific clustering and significant genetic differentiation between species. The findings suggest that Bradyrhizobium strains have diverse genetic profiles, with some capable of nitrogen fixation and others unable to form nodules. The study underscores the need for further research to understand the mechanisms driving the evolution of mobile genetic elements in Bradyrhizobium.