This supplementary material data file contains figures and tables for each chapter of a PhD thesis titled "Genome-based systematics of Bradyrhizobium and its species". There are 4 folders, each labeled Chapter 2 to Chapter 5. Figures and tables depict information of various topics discussed in the thesis such as Bradyrhizobium supergroups based on phylogenomics, photosynthesis genes and synteny patterns found in Bradyrhizobium as well as the description of novel Bradyrhizobium species from South Africa. Chapters given as files correspond to the chapters in the PhD thesis.