Pangenome analysis indicates evolutionary origins and genetic diversity: emphasis on the role of nodulation in symbiotic Bradyrhizobium

Abstract

The Bradyrhizobium genus is widely known for encompassing many species capable of forming nodules and establishing the biological nitrogen fixation process with several legumes, significantly contributing to agriculture and environmental sustainability. Despite its importance, questions about the evolution, pangenome, and symbiotic genes of Bradyrhizobium are still poorly understood. In this study, we analyzed the pangenome of a set of Bradyrhizobium symbiotic species using the Roary and GET_HOMOLOGUES tools in strains originated from the Northern and Southern Hemispheres. We also investigated the presence and correlation of the fix, nif, nod, Type III secretion system (T3SS) and their effector proteins, and T4SS genes, trying to find differences between clades, hosts, and biogeographic origin. Pangenome analysis of Bradyrhizobium species from the Northern and Southern Hemispheres provided valuable insights into their diversity, biogeography, origin, and co-evolution with their legume host plants. The genus possesses a relatively small core genome compared to the expanded accessory genome, a key feature that facilitates genetic exchange and acquisition of new genes, allowing adaptation to a variety of environments. Notably, the presence or absence of T3SS effector proteins varied significantly according to the geographic location, suggesting specific environmental adaptations, as well as a direct relationship with nodulation genes. Comparative analysis indicated that symbiotic Bradyrhizobium species originated in the Northern Hemisphere and present a greater diversity of orthologous groups than those from the Southern Hemisphere. These results contribute to our understanding of the evolutionary history of these symbiotic bacteria.

Keywords: Bradyrhizobium; Fix/Nif; Nod factors; biogeography; environmental adaptation; nodulation; pangenome; type III secretion system.

Figure 1

Representation of the absence and presence of genes involved in the metabolism of biological nitrogen fixation, nodulation, the T3SS, and candidate genes for T3SS and T3E effectors in symbiotic Bradyrhizobium. The phylogenetic tree is classified according to the clades: B. japonicum (purple), B. elkanii (green), and B. jicamae (orange). Red upward arrows indicate bacteria isolated in the Northern Hemisphere, whereas yellow downward arrows indicate bacteria isolated in the Southern Hemisphere. The colors in the heatmap represent the number of proteins found in each strain, following a variation scale. The scale bar represents the number of amino acid substitutions per site.

Figure 2

Pangenome characteristics of 44 species of symbiotic Bradyrhizobium. (A) Core genome curve (B) Accessory genome curve.

Figure 3

Global distribution of orthologous clusters of the Bradyrhizobium accessory genome by geographic region and between hemispheres. The main graph highlights the hemisphere groupings and specific regions. The secondary graph highlights the African-specific accessory genome clusters, highlighting the specificity of accessory genomes between North Africa and South Africa.

Figure 4

Global distribution and genetic interaction among Bradyrhizobium species, according to the accessory genome. White boxes indicate the sharing of accessory genome gene clusters. Each species is identified by a number: 1. Bradyrhizobium elkanii; 2. B. frederickii; 3. B. ottawaense; 4. B. septentrionale; 5. B. quebecense; 6. B. baranii; 7. B. diazoefficiens; 8. B. jicamae; 9. B. pachyrhizi; 10. B. canariense; 11. B. rifense; 12. B. cytisi; 13. B. valentinum; 14. B. retamae; 15. B. algeriense; 16. B. hipponense; 17. B. nanningense; 18. B. zhengyangense; 19. B. guangzhouense; 20. B. zhanjiangense; 21. B. lablabi; 22. B. daqingense; 23. B. japonicum; 24. B. embrapense; 25. B. paxllaeri; 26. B. icense; 27. B. forestalis; 28. B. manauense; 29. B. tropiciagri; 30. B. centrolobii; 31. B. neotropical; 32. B. uaiense; 33. B. brasilense; 34. B. stylosanthis; 35. B. viridifuturi; 36. B. vignae; 37. B. altum; 38. B. acaciae; 39. B. australafricanum; 40. B. diversitatis; 41. B. archetypum; 42. B. australiense; 43. B. murdochi; 44. B. agreste.

Figure 5

Functional distribution of accessory genes in the pangenome according to COG categories: (A) Northern and Southern Hemisphere groups. (B) Specific subgroups of species isolated in North America, South America, Africa, Asia, and Oceania.