An improved assembly of the “Cascade” hop (Humulus lupulus) genome uncovers signatures of molecular evolution and refines time of divergence estimates for the Cannabaceae family

Authors: PADGITT-COBB, LILLIAN - Oregon State University; PITRA, NICHOLI - Hopsteiner; MATTHEWS, PAUL - Hopsteiner; Henning, John; HENDRIX, DAVID - Oregon State University

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/17/2022
Publication Date: 12/22/2022
Citation: Padgitt-Cobb, L.K., Pitra, N.J., Matthews, P.D., Henning, J.A., Hendrix, D.A. 2022. An improved assembly of the “Cascade” hop (Humulus lupulus) genome uncovers signatures of molecular evolution and refines time of divergence estimates for the Cannabaceae family. Horticulture Research. 10(2). Article uhac281. https://doi.org/10.1093/hr/uhac281.
DOI: https://doi.org/10.1093/hr/uhac281

Interpretive Summary: Hop (Humulus lupulus L. var Lupulus) is a valuable minor crop plant with an extensive history of cultivation and use in brewing, as a textile, and for its therapeutic properties. The hop genome is large and complex, and early attempts at assembling DNA sequence into a genome were fragmented and incomplete, limiting its use in science. Our new effort created a separate DNA assembly for each of the 10 chromosomes of hop, which is known as a chromosome-level assembly. This version of the Cascade hop genome is the most complete hop assembly to-date, providing an improved resource to investigate evolutionary patterns across related species, as well as provide identification of genes and genetic markers for plant breeding purposes. The approaches we developed to analyze the Cascade hop genome will deepen our understanding of the organization of hop genes and other non-gene DNA sequences and may have broad applicability to the study of other large, complex genomes. Taken together, the development of the chromosome-level assembly will inform cultivation strategies, provide breeding targets for all traits of economic importance and benefit hop researchers and the Cannabaceae genomics community.

Technical Abstract: Hop (Humulus lupulus L. var Lupulus) is a diploid, dioecious plant with an extensive history of cultivation and use in brewing, as a textile, and for its therapeutic properties. The hop genome is large (2.8 Gb) and complex, and early attempts at assembly resulted in fragmented and incomplete assemblies, limiting the extent of investigation that could occur. Fragmented assemblies do not sufficiently capture the surrounding genomic context of genes, including transposable elements and gene duplication. Recent advances in sequencing technology and assembly algorithms have made assembly of the hop genome tractable and have transformed the extent of investigation that can occur. Our new chromosome-level assembly of the Cascade hop genome is the most complete hop assembly to-date, providing an improved resource to investigate evolutionary patterns across species, including large-scale regions of sequence conservation containing collinear orthologs, as well as evidence of whole genome duplication. We assess molecular evolution in collinear gene pairs using the rate of synonymous substitutions (Ks) and the rate of transversions at four-fold synonymous codon positions (4DTv), as well as functional enrichment of collinear genes. We also assess gene family expansion and contraction, and calculate a more-precise estimate of the date of species divergence in hop and closely related species, which allows for a comprehensive investigation of the evolutionary trajectory of biosynthetic enzymes, as well as genomic features underlying growth, flowering, and stress response. The approaches we developed to analyze the Cascade hop genome serve to deepen our understanding of the hop genomic landscape and may have broader applicability to the study of other large, complex genomes. Taken together, the development of the chromosome-level assembly will inform cultivation strategies, benefiting hop researchers and the Cannabaceae genomics community.