Population genomics of the legume symbionts Sinorhizobium meliloti and S. medicae

Abstract

The nitrogen-fixing mutualism between legumes and rhizobia is ecologically and agriculturally important and is a model for the molecular genetics of plant microbe interactions and the evolution of mutualism. The goal of this research was to investigate the evolutionary forces shaping genetic diversity in two species of rhizobia, <italic>Sinorhizobium meliloti</italic> and <italic>S. medicae</italic> by integrating population genetic tools, experimental evolution, and whole-genome sequencing. In Chapter 1, I characterize the diversity and divergence of <italic>S. meliloti</italic> and <italic>S. medicae</italic> and ask how selection and horizontal gene transfer (HGT) have shaped nucleotide variation. I find limited evidence for HGT between <italic>S. meliloti</italic> and <italic>S. medicae</italic>, indicating that recombination with closely related species does not have much impact on nucleotide diversity in <italic>Sinorhizobium spp.</italic> and does not prevent species from diverging. I also find that the targets of strong positive selection are different in the two species, suggesting that <italic>S. meliloti</italic> and <italic>S. medicae</italic> may be subject to different selective pressures in nature. The goal of Chapter 2 was to examine gene content and copy number variation. While I find that S. meliloti and S. medicae both have extensive variation in content and copy number, most of this variation seems to be deleterious. This suggests that the large size of bacterial pangenomes is due, in part, to many short-lived, deleterious gains and losses of genes rather than adaptation. Finally, in Chapter 3, I use experimental evolution to tests for costs of mutualism. I do not find clear evidence of costs, but I do identify a mutation in the <italic>purM</italic> gene that may affect host range. Overall, this contributes to our understanding of both the evolution of rhizobia, and the evolutionary forces shaping variation in prokaryotes.