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.

中文翻译：

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二倍体级联啤酒花（Humulus lupulus）基因组的分阶段组装草案

蛇麻草L. var Lupulus（L. var Lupulus）是一种二倍体雌雄异株的植物，已有超过一千多年的栽培历史。啤酒花球果因其在酿造中的用途而受到重视，并包含具有治疗意义的化合物，包括黄腐酚。啤酒花的大（2.8 Gb），重复性和杂合基因组挑战了决定如何调控负责所需性状的生化途径的努力。我们提出了Cascade栽培品种基因组的单倍型分阶段装配草案。我们的Cascade基因组图装配和注释草案是迄今为止跃点基因组最广泛的表示。蛇麻草的PacBio长读序列与FALCON组装在一起，并与FALCON-Unzip进行部分定相。单倍型序列的比较分析提供了洞察啤酒花进化的选择性压力的见解。我们发现具有更大序列差异的基因在分阶段装配的草稿中富含了应激反应，生长和开花功能。通过长时间阅读测序，长末端逆转录转座子（LTR）的分辨率得到了提高，我们发现跳段重复率超过70％。我们确定了在多个组织中表达的大麻二酸合酶（CBDAS）的同源物。我们开发的用于分析分阶段装配草案的方法有助于加深我们对啤酒花基因组格局的了解，并且可能对其他大型复杂基因组的研究具有更广泛的适用性。我们鉴定了在多个组织中表达的大麻二酸合酶（CBDAS）的同源物。我们开发的用于分析分阶段装配草案的方法有助于加深我们对啤酒花基因组格局的了解，并且可能对其他大型复杂基因组的研究具有更广泛的适用性。我们鉴定了在多个组织中表达的大麻二酸合酶（CBDAS）的同源物。我们开发的用于分析分阶段装配草案的方法有助于加深我们对啤酒花基因组格局的了解，并且可能对其他大型复杂基因组的研究具有更广泛的适用性。