Mohammad Kamruzzaman / Biology / Faculty Mentor: Woo Suk Chang
Bradyrhizobium japonicum is a soil bacterium capable of establishing a symbiotic relationship with legume plants such as soybean. This symbiosis leads to the formation of root nodules in which the bacteria convert atmospheric nitrogen into ammonia, an essential nutrient source for the plant. However, this mutualistic association is significantly impacted by drought, a prominent abiotic stressor in US soybean cultivation. Thus, developing drought-tolerant soybean cultivars and compatible rhizobial strains has become a growing concern in the US agricultural industry. In a previous study, we identified two drought-tolerant Bradyrhizobium strains, namely TXVA and TXEA, isolated from Texas soils. Subsequently, we sequenced the complete genomes of both strains, revealing that TXVA’s genome comprises 9,193,770 base pairs with 8,980 protein-coding genes, while TXEA’s genome contains 9,339,455 base pairs with 9,158 protein-coding genes. In this study, we employed a computational strategy to identify genes with analogous functions across different strains. Using OrthoFinder, we found genes exhibiting comparable activities in TXVA, TXEA, and seven other known rhizobial strains. Furthermore, employing the Pangenome pipeline, we identified unique gene clusters within all compared genomes. Additionally, the Phylogenetic Profiler for Single Genes (IMG, JGI) enabled us to pinpoint distinctive genes for both TXVA and TXEA. The pangenome analysis revealed that a gene encoding a hypothetical protein (IMG gene ID: 2929624621) and another gene encoding deoxycytidylate deaminase were identified as unique to TXVA and TXEA, respectively.
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