Comparative Genomics And Protein Protein Interaction Network Prediction For Rhizobia

Rhizobia are important agricultural micro-organisms which live in a symbiotic relationship with the host (mainly legumes) and fix nitrogen inside root nodules. Rhizobia supply nitrogen to the host and reduce the use level of fertilizers.Traditional classification of organisms is based on16SrRNA and several other conserved genes, not the genome, thus some controversy still exist in the classification system. In this paper, by utilizing bioinformatics tools, we compared19genomes of rhizobia and found that the characteristics of LCBs (Locally Coilinear Blocks) distribution can be used to define genera. This provides a rapid classification method for newly discovered rhizobia. We also analyzed the codon usage and expression levels of nifA and nodA genes which are important in symbiotic nitrogen fixation. It is revealed that nifA genes trend to use codons benefit to high expression. Our results provide new insight for obtaining more effective rhizobial strains.Protein-protein interaction (PPI) network plays a key role in molecular processes. But the research of rhizobia PPI network is still in its infancy. Here, we use two different methods to predict PPI networks of19species (strains) of Rhizobia on genomic scale. We also analyze the topology properties of the PPI networks. Our study provides a way to find new symbiotic nitrogen fixation gene and a foundation for the further exploration of Rhizobia PPI network evolution and bacteria-plant PPI networks.