The Genomic Characterization of Reproductive Systems in Myricaceae and Other Angiosperm Lineages

Abstract

The genomes of plants are shaped by the forces of recombination, structural variation, repetitive elements, and whole-genome duplication. These genomic innovations can have long-standing impacts on plant reproduction and diversification. In this thesis, I use comparative genomics to characterize the consequences of these innovations, particularly the evolution of sex chromosomes, across diverse angiosperm species, with a primary focus on the order Fagales. In Chapter 2, I present numerous genomic resources for the Myricaceae family and describe a shared ZZ/ZW sex-determining system in the Morella genus. We propose two candidate genes likely involved in the evolution of dioecy in this genus: ent-copalyl diphosphate synthase (CPS) and a sex-linked paralog of FLOWERING LOCUS T (FT). I also describe a novel XX/XY system in the polyploid Myrica gale and recover two ancestral lineages from it that inform the biogeographic history of the family. In Chapter 3, I explore the prevalence of flowering time genes across thirty-six dioecious species, spanning over fifteen plant families and more than twenty independent evolutions of dioecy. Here, I show that FT paralogs are repeatedly associated with sex chromosomes and sex-determining regions and suggest that flowering-time genes are likely targets of sexually antagonistic selection. In Chapter 4, I present a haplotype-resolved, chromosome-scale genome for the Southern Live Oak, Quercus virginiana. In this genome, I identified a unique centromeric architecture that has not been previously described in the genus. This work demonstrates how comparative genomics is a powerful tool for understanding the genomic basis of diverse traits.