Open AccessA draft phased assembly of the diploid Cascade hop ( Humulus lupulus ) genome
Author(s) -
PadgittCobb Lillian K.,
Kingan Sarah B.,
Wells Jackson,
Elser Justin,
Kronmiller Brent,
Moore Daniel,
Concepcion Gregory,
Peluso Paul,
Rank David,
Jaiswal Pankaj,
Henning John,
Hendrix David A.
Publication year - 2021
Publication title -
the plant genome
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.403
H-Index - 41
ISSN - 1940-3372
DOI - 10.1002/tpg2.20072
Subject(s) - humulus lupulus , hop (telecommunications) , genome , biology , retrotransposon , genetics , computational biology , whole genome sequencing , gene , computer science , transposable element , computer network
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 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.