UC Riverside

Genome evolution is responsible for generating phenotypic differences between individuals, which has cumulated in the extraordinary variation in organism development, morphology, and life history present in the tree of life. Genomes vary in size, structure, and content and this variation is especially apparent among plants, who as sessile organisms must adapt rapidly to face environmental stress. In this dissertation, I examine the causes and consequences of plant genome evolution in three disparate species in an attempt to understand the patterns by which these lineages have undergone genome evolution while adapting to their respective ranges. In Chapter 1, I develop a novel method to summarize genomes from high-throughput sequencing reads and apply the method to describe genome content evolution in over 1,000 resequenced Arabidopsis thaliana genomes. In Chapter 2, I examine the subgenome evolution of the recent allopolyploid Capsella bursa-pastoris and describe the genetic factors that enabled this species to colonize every continent except for Antarctica. In Chapter 3, I develop a resource for genome-wide association mapping in Vigna unguiculata (cowpea) and demonstrate the effectiveness of this utility by mapping the genetic basis of seed pigmentation phenotypes. Overall, the work in this dissertation contributes insight into the genetic and environmental factors affecting plant genome evolution