UC Berkeley

Plants possess functional, layered, and very often successful immune systems without the use of antibodies or circulating immune cells. Plant immune receptors are encoded by DNA, and diversity in receptor DNA sequences increases the capacity for recognition of disease proteins across populations. The central question of this dissertation is how plants generate and maintain enough diversity at their immune receptor sequences to recognize and defend themselves against rapidly evolving pathogens, focusing on the contribution from mutation. Mutation is the food of evolution, supplying the variation on which natural selection acts. Most genic mutations are deleterious, but immune systems present a case in which high mutation is beneficial and may even be required for success. However, our understanding of immune system diversity generation outside of bacteria and vertebrates is limited. In Chapter 1, I provide a literature review of plant immune system diversity and propose a theoretical framework for how this diversity is generated. To understand the contribution of mutation to the evolution of plant immune systems, I first characterized how the variability of immune receptor genes is related to genomic and epigenetic features in the model plant, Arabidopsis thaliana (Chapter 2). I identified several genomic features associated with rapid evolution and observed a distinct subset of immune receptors with a higher likelihood of mutation. I expanded on my initial finding through work on Zea mays (maize), in which I looked at variation in immune receptor expression and regulation across tissue types and individuals, contributing to our understanding of immune receptor evolution in agricultural crops (Chapter 3). Mutation and natural selection are occurring concurrently, making their relative contributions difficult to disentangle from available sequencing data. Therefore, measurement of newly occurring mutations is required to quantify whether there is elevated mutation in plant immune genes compared to other genes in the genome. New mutations are at very low frequencies and require ultra-accurate sequencing techniques to distinguish them from errors. I adapted these techniques from human tissue to Arabidopsis and determined the de novo mutation spectra across Arabidopsis tissues, finding that the somatic and germline mutation rates are remarkably similar. I then tested how activation of the immune system and disruption of DNA repair influences mutation rate, identifying that activation of the immune system does not increase the global mutation rate and DNA repair knockouts impart distinct signatures of mutation related to their mechanism (Chapter 4). Finally, I conclude with the future directions and implications of this work, including expansion into how other non-human innate immune systems evolve.