HOP (HUMULUS LUPULUS) IS KNOWN FOR THE UNIQUE ARRAY OF BIOACTIVE COMPOUNDS THAT IT PRODUCES. IT HAS A LONG HISTORY OF USE IN TRADITIONAL MEDICINE. HOP PRODUCES XANTHOHUMOL, WHICH HAS ANTICANCER ACTIVITY, AND BITTER ACIDS, WHICH IMPART FLAVOR IN BREWING AND POSSESS ANTIMICROBIAL ACTIVITY. HOP IS ALSO SUSCEPTIBLE TO DISEASES INCLUDING POWDERY MILDEW (PM), WHICH REDUCES THE QUALITY AND QUANTITY OF HOP CONE YIELD. THE GENOME OF HOP IS LARGE AND COMPLEX, CHALLENGING EARLY ASSEMBLY EFFORTS. BECAUSE OF ADVANCES IN SEQUENCING AND ASSEMBLY, WE NOW HAVE A CHROMOSOME-LEVEL ASSEMBLY THAT WE CAN ANALYZE FOR GENE CONTENT AND OTHER GENOMIC FEATURES. WITH A COMPREHENSIVE ANNOTATION OF GENES, WE CAN INVESTIGATEEVOLUTIONARY PATTERNS IN HOP AND EXTENSIVELY ANALYZE GENE EXPRESSION AND FUNCTION. FIRST, LARGE-SCALE STRUCTURAL SIMILARITIES BETWEEN HOP AND CLOSELY RELATED SPECIES, INCLUDING HEMP AND MULBERRY,WILL BE IDENTIFIED BY ALIGNING GENES FROM THE HOP ASSEMBLY TO THE GENES OF THESE OTHER SPECIES. SIGNIFICANTLY SIMILAR GENE SEQUENCES WILL BE ORDERED BASED ON THEIR GENOMIC COORDINATES TO DETECT REGIONS OF CONSERVED GENE ORDER BETWEEN THE ASSEMBLIES. IN THE NEXT PHASE OF THE PROJECT, GENE EXPRESSION DURING HOP CONE DEVELOPMENT WILL BE ASSESSED. FIRST, RNA WILL BE EXTRACTED FROM CONE AND LEAF TISSUES AT FIVE DEVELOPMENTAL TIME POINTS IN CONES, FOLLOWED BY SEQUENCING AND ALIGNMENT OF RNA TO THE HOP ASSEMBLY. OVERALL, THE PURPOSE OF THIS STUDY IS TO 1) FIND GENES THAT SHOW VARIABLE EXPRESSION DURING DEVELOPMENT; 2) PREDICT THE FUNCTION OF THESE GENES BY COMPARING THEM TO GENES FROM OTHER SPECIES WITH KNOWN FUNCTION THAT HAVE A HIGHLY SIMILAR DNA SEQUENCE; 3) DETERMINE THE LOCATION OF GENES ALONG THE CHROMOSOME; AND 4) IDENTIFY OTHER GENES AND GENOMIC FEATURES SURROUNDING THESE GENES OF INTEREST.THE RESULTS OF THIS STUDY WILL HAVE AN IMPACT ON IMPROVING HOP HEALTH AND PRODUCTION. MY GOAL IS TO UNCOVER GENES THAT BOTH SHOW VARIABLE EXPRESSION DURING DEVELOPMENT AND CONTRIBUTE TO THE PRESENTATION OF DESIRED TRAITS, INCLUDING DISEASE RESISTANCE AND SYNTHESIS OF BIOACTIVE COMPOUNDS. MAPPING SIMILARITIES BETWEEN THE GENOMES OF HOP AND CLOSELY RELATED SPECIESWILL IMPROVE OUR UNDERSTANDING ABOUT THE EVOLUTIONARY HISTORY OF HOP. IT WILL ALSO PROVIDE INSIGHT ABOUT WHETHER GENES INVOLVED IN TRAITS OF INTEREST ARE CONSERVED BETWEEN SPECIES OR SHOW EVIDENCE OF SELECTIVE PRESSURE AND DUPLICATION. THE RESULTS OF THIS STUDY WILL INFORM THE DEVELOPMENT OF DISEASE-RESISTANT HOP CULTIVARS CONTAINING A DESIRED PROFILE OF BIOACTIVE COMPOUNDS THROUGH IMPROVED GENOMICS-ASSISTED BREEDING STRATEGIES. TAKEN TOGETHER, THE CHROMOSOME-LEVEL ASSEMBLY OF HOP WILL TRANSFORM HOP GENOMICS.