A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome

Authors: PADGITT-COBB, LILLIAN - Oregon State University; KINGAN, SARAH - Pacific Biosciences Inc; WELLS, JACKSON - Oregon State University; ELSER, JUSTIN - Oregon State University; KRONMILLER, BRENT - Oregon State University; Moore, Daniel; CONCEPCION, GREGORY - Pacific Biosciences Inc; PELUSO, PAUL - Pacific Biosciences Inc; RANK, DAVID - Pacific Biosciences Inc; JAISWAL, PANKAJ - Oregon State University; Henning, John; HENDRIX, DAVID - Oregon State University

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/3/2020
Publication Date: 2/18/2021
Citation: Padgitt-Cobb, L.K., Kingan, S.B., Wells, J., Elser, J., Kronmiller, B., Moore, D.L., Concepcion, G., Peluso, P., Rank, D., Jaiswal, P., Henning, J.A., Hendrix, D.A. 2021. A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome. The Plant Genome. 14(1). Article e20072. https://doi.org/10.1002/tpg2.20072.
DOI: https://doi.org/10.1002/tpg2.20072

Interpretive Summary: Hop (Humulus lupulus L. var Lupulus) is an important crop with a long 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. This research is the first report of a draft genome of a diploid plant whereby DNA sequences from both the mother and father are reported. We investigated presence and absence of genes from close family members and noted that hops and cannabis share genes and gene orders that appear to be specific to that plant family. We also report on genes which appear to be under strong evolutionary pressure and noted that these genes fall within controlling plant growth and flowering along with plant response to abiotic and biotic stress. Finally, our data supports the hypothesis that the hop genome arose by whole genome duplication rather than expansion due to small, multi-replication events.

Technical Abstract: 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.