Graduate Thesis Or Dissertation
 

Towards Resolving Functional and Evolutionary Mysteries of the Large and Heterozygous Genome of Hop (Humulus lupulus) and the Cannabaceae Family Using Genomic Data Science

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https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/x920g4930

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  • Hop (Humulus lupulus L. var. lupulus) is a diploid, dioecious plant with an extensive history of cultivation and use in brewing, as a textile, and for its therapeutic properties. Hop is prized for its ability to produce a variety of aromatic and flavor compounds, as well as compounds with anti-microbial properties and pharmacological relevance, including terpenes and prenylated flavonoids. Identification of genes and genomic loci involved in response to abiotic and biotic stressors, as well as biosynthesis of secondary metabolites, requires high-quality genomic resources. The hop genome is large (~2.8 Gb) and complex, and early attempts at assembly resulted in fragmented and incomplete assemblies, limiting the extent of investigation that could occur. Fragmented assemblies do not sufficiently capture the surrounding genomic context of genes, including transposable elements and gene duplication. Recent advances in sequencing technology and assembly algorithms have made assembly of the hop genome tractable and have transformed the extent of investigation that can occur. The development of genomic resources for the Cascade hop genome allows for a comprehensive investigation of the evolutionary trajectory of biosynthetic enzymes, as well as genomic features underlying growth, flowering, and stress response. The approaches that we developed to analyze the Cascade hop genome serve to deepen our understanding of the hop genomic landscape and may have broader applicability to the study of other large, complex genomes. Taken together, the genomic resources described in my thesis will inform cultivation strategies and benefit hop researchers and the Cannabaceae genomics community.
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  • Pending Publication
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  • 2022-08-05 to 2023-09-06

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