UC Riverside

Cis-regulatory variation contributes to the diversification of gene expression and has strong implications for the evolution of diverse species. In this dissertation, I explored the genetic and epigenetic regulation of gene expression, with an emphasis on the diversification of cis-regulatory elements, using a combination of phased genome assemblies, chromatin accessibility profiling, and transcriptomics. Here, I identify the molecular signatures of cis-regulatory variants, uncover potential sources of cis-regulatory variation, and explore how they may contribute to the immense diversity observed in the genus Citrus. In Chapter 1, I use a locally phased genome assembly of ‘Fairchild’ mandarin to understand how allelic variation in the chromatin landscape reflects cis-regulatory variation between alleles. In Chapter 2, I develop the first atlas of non-coding sequence conservation in the genus Citrus and use it to explore how sequence evolution has shaped cis-regulatory activity during the speciation of Citrus. In Chapter 3, I performed a transcriptomics experiment in a parent-offspring trio to understand how cis-regulatory variation alters the response to one of the most destructive pathogens of Citrus in a disease-tolerant hybrid. The integration of multiple leading-edge genomics technologies improves our understanding of cis-regulatory evolution and provides key insights to develop superior cultivars for the citrus industry.