02263nas a2200337   4500000000100000000000100001008004100002260001300043653001300056653001800069653001300087653001500100653001200115100002500127700001700152700001800169700001700187700002100204700001700225700002300242700001600265700001500281700001900296700001700315700001800332245008100350300001100431490000700442520146200449022001401911       2021                            d  c2021 Mar10aDiploidy10aGenome, Plant10aGenomics10aHaplotypes10aHumulus1 aLillian Padgitt-Cobb1 aSarah Kingan1 aJackson Wells1 aJustin Elser1 aBrent Kronmiller1 aDaniel Moore1 aGregory Concepcion1 aPaul Peluso1 aDavid Rank1 aPankaj Jaiswal1 aJohn Henning1 aDavid Hendrix00aA draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome.  ae200720 v143 a<p>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 contain compounds of therapeutic interest including xanthohumol. Efforts to determine how biochemical pathways responsible for desirable traits are regulated have been challenged by the large (2.8 Gb), repetitive, and heterozygous genome of hop. We present a draft haplotype-phased assembly of the Cascade cultivar genome. Our draft assembly and annotation of the Cascade genome is the most extensive representation of the hop genome to date. PacBio long-read sequences from hop were assembled with FALCON and partially phased with FALCON-Unzip. Comparative analysis of haplotype sequences provides insight into selective pressures that have driven evolution in hop. We discovered genes with greater sequence divergence enriched for stress-response, growth, and flowering functions in the draft phased assembly. With improved resolution of long terminal retrotransposons (LTRs) due to long-read sequencing, we found that hop is over 70% repetitive. We identified a homolog of cannabidiolic acid synthase (CBDAS) that is expressed in multiple tissues. The approaches we developed to analyze the draft phased 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.</p>
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