Access to genome sequences and accompanying -omic data have revolutionized plant biology. In this dissertation, I report on generation of genome assemblies and associated analyses for Mitragyna speciosa (kratom), a medicinal plant species, Salvia hispanica (Chia pinta), a cultural food crop from Mesoamerica, and a comparative of species that produce tubers. Mitragyna speciosa produces monoterpene indole alkaloids with potential clinical use as opioid agonists. Through generation of a chromosome-scale chia genome and comparison to other chia genomes, structural variation in terpene biosynthetic pathway components was revealed. Additionally, the first population structure of chia was described with rampant introgressions from other Salvia species. Genomic assemblies of multiple tuber-producing species as well as their sister or closely related species were generated and compared to determine the evolutionary origin(s) of the trait of tuberization. The conserved expression of three transcription factors: POTH1, BRC1b, and BEL5 were found in tuberizing species suggesting co-option of these genes across angiosperms. A central role for POTH1 was also demonstrated in development of rhizomes, a parallel under-ground structure to the stolon.
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