UC Riverside

This dissertation advances our knowledge of allopolyploidy, genomic adaptations, and heat stress responses in plants, focusing on Nicotiana section Repandae and two Boechera species, Boechera arcuata and Boechera perennans. Through comparative genomic and transcriptomic analyses, it elucidates the genetic mechanisms underlying these processes and their evolutionary implications. In Nicotiana section Repandae, I investigate global gene expression and subgenome dominance among three allotetraploid species derived from hybridization between N. sylvestris and N. obtusifolia about 4.5 million years ago. My findings reveal consistent subgenome dominance of N. obtusifolia across various developmental stages, impacting flower size and morphology. This dominance plays a significant role in shaping the genetic architecture and evolutionary trajectory of these species. In Boechera, I examine genomic adaptations to extreme environments, focusing on B. arcuata and B. perennans, which inhabit distinct climatic regions. Through comparative genomics and functional analysis, I identify unique and expanded gene families associated with environmental resilience. Gene Ontology enrichment reveals significant terms related to photosynthesis and stress response, particularly in B. perennans. The results highlight the evolutionary processes enabling these species to thrive in diverse habitats. I further investigate gene expression profiles and evolutionary patterns of heat stress responses in B. arcuata and B. perennans. Using RNA sequencing data, I identify differentially expressed genes under control and basal heat stress conditions, with the top 50 upregulated genes predominantly being heat shock proteins. GO enrichment analysis reveals distinct metabolic and enzyme activity responses, indicating species-specific adaptations. Positive selection tests identify amino acid sites under evolutionary pressure, suggesting adaptive changes contributing to thermotolerance. By integrating comparative genomic and transcriptomic analyses, here I provide insights into the genetic and evolutionary mechanisms driving these processes in Nicotiana and Boechera species, offering valuable information for future research and potential applications in improving crop resilience.