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

Abstract

We present a chromosome-level assembly of the Cascade hop (Humulus lupulus L. var. lupulus) genome. The hop genome is large (2.8 Gb) and complex, and early attempts at assembly were fragmented. Recent advances have made assembly of the hop genome more tractable, transforming the extent of investigation that can occur. The chromosome-level assembly of Cascade was developed by scaffolding the previously reported Cascade assembly generated with PacBio long-read sequencing and polishing with Illumina short-read DNA sequencing. We developed gene models and repeat annotations and used a controlled bi-parental mapping population to identify significant sex-associated markers. We assessed molecular evolution in gene sequences, gene family expansion and contraction, and time of divergence from Cannabis sativa and other closely related plant species using Bayesian inference. We identified the putative sex chromosome in the female genome based on significant sex-associated markers from the bi-parental mapping population. While the estimate of repeat content (~64%) is similar to the estimate for the hemp genome, syntenic blocks in hop contain a greater percentage of LTRs. Hop is enriched for disease resistance-associated genes in syntenic gene blocks and expanded gene families. The Cascade chromosome-level assembly will inform cultivation strategies and serve to deepen our understanding of the hop genomic landscape, benefiting hop researchers and the Cannabaceae genomics community.

Acknowledgements

We thank Dovetail Genomics for Hi-C sequencing and assembly. We thank Chris Sullivan and Kenneth Lett at the Center for Quantitative Life Sciences (CQLS) at Oregon State University for assistance with the computing infrastructure. Funding for sequencing was provided by Hopsteiner and USDA-ARS CRIS Project 5358-21000-040-00D. LKPC is supported by an AFRI Predoctoral Fellowship (grant no. 2020-67034-31722) from the USDA National Institute of Food and Agriculture. The authors have no conflicts of interests to declare.

Author contribution

LPC, PM, JH, and DH designed the study. LPC polished and annotated the genome, analyzed and interpreted data, created figures, and wrote the manuscript. NP prepared RNA-seq samples and contributed text about RNA-seq preparation. DH analyzed and interpreted data and provided guidance about figure design and significant edits to the manuscript. JH developed the mapping population and genetic map and developed the associated figures and manuscript sections for the mapping population and genetic map. LPC, PM, JH, and DH reviewed and edited the manuscript. JH and PM acquired funds to perform the study.

Data availability

The data that support the findings of this study are openly available on the Downloads page of http://hopbase.cqls.oregonstate.edu/ and under NCBI BioProject ID PRJNA562558. Analysis pipelines, scripts, and specific commands are included on the GitHub project page,at https://github.com/padgittl/CascadeDovetail.

Conflict of interest statement

None declared.

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