Hop (Humulus lupulus L. var Lupulus) is a diploid, dioecious plant with a history of cultivation spanning more than one thousand years. Hop cones are valued for their use in brewing, and around the world, hop has been used in traditional medicine to treat a variety of ailments. Efforts to determine how biochemical pathways responsible for desirable traits are regulated have been challenged by the large, repetitive, and heterozygous genome of hop. We present the first report of a haplotype-phased assembly of a large plant genome. Our assembly and annotation of the Cascade cultivar genome is the most extensive to date. PacBio long-read sequences from hop were assembled with FALCON and phased with FALCON-Unzip. Using the diploid assembly to assess haplotype variation, we discovered genes under positive selection enriched for stress-response, growth, and flowering functions. Comparative analysis of haplotypes provides insight into large-scale structural variation and the selective pressures that have driven hop evolution. Previous studies estimated repeat content at around 60%. With improved resolution of long terminal retrotransposons (LTRs) due to long-read sequencing, we found that hop is nearly 78% repetitive. Our quantification of repeat content provides context for the size of the hop genome, and supports the hypothesis of whole genome duplication (WGD), rather than expansion due to LTRs. With our more complete assembly, we have identified a homolog of cannabidiolic acid synthase (CBDAS) that is expressed in multiple tissues. The approaches we developed to analyze a phased, diploid assembly serve to deepen our understanding of the genomic landscape of hop and may have broader applicability to the study of other large, complex genomes.

Hop (Humulus lupulus L.) cones are used extensively in beer brewing to enhance flavor and impart bittering. Verifying hops cultivar identity has traditionally been accomplished by morphological characteristics or a chemical analysis of lupulin glands but these traits may vary according to environmental influences. The objective of this research was to develop an AFLP (amplified fragment length polymorphism) protocol for analyzing DNA extracted from dried hop cones. The DNA was extracted from dried cones of six hop genotypes by a technique published for grapes (Vitis spp). The reagents, MseI primers, and protocol were part of a commercially available kit, while the 6‐carboxyfluorescein‐labeled EcoRI primers were purchased separately. Eleven primer combinations amplified an average of 546.5 scorable fragments with an average of 49.7 fragments per primer combination. All genotypes were differentiated with the primer combinations studied. Average genetic similarity estimates ranged between 0.956 and 0.995 among the six hop genotypes studied. This research provides the hops industry with a powerful technique to verify accurately hops cultivar identity and purity through an analysis of dried cone DNA.