A phased, diploid assembly of the Cascade hop (Humulus lupulus) genome reveals patterns of selection and haplotype variation

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.

Identification and Characterization of Verticillium Nonalfalfae-responsive Micrornas in the Roots of Resistant and Susceptible Hop Cultivars

“…After processing the raw sequencing data, we obtained from 1,771,295 to 4,636,681 sequencing reads with a mean read length of 18 bp to 22 bp per library. Processed reads from each library were aligned against the hop draft genome [30,31] disallowing mismatches (Table 1). NS = not signi cant.…”

Genomic analysis of powdery mildew resistance in a hop (Humulus lupulus L.) bi-parental population segregating for “R6-locus”

“…geneious.com) to identify putative genes involved in disease resistance. Contigs containing SNPs that were observed within a QTL were annotated with RNAseq data from Cascade stem, leaf and apical meristem (Padgitt-Cobb et al 2019). Gene prediction was performed on all contigs containing significant SNPs using the Augustus (Stanke and Morgenstern 2005) as an internal plugin.…”

“…Three putative R-genes were identified on contig 002196F. A visual observation of RNAseq data (Padgitt-Cobb et al 2019) obtained from USDA cultivar 'Cascade' (that was exposed to PM infection prior to collecting RNA samples) showed complex expression amongst these three with multiple variations of exons combined into putative isoform mRNA molecules with only two that appear to be complete transcripts (TCONS_00051515 and TCONS_00051522 Quantitative expression levels (black color graphs) were all normalized between tissues similar role in hop. Contig 002196F also contains a putative gene for polygalacturonase (Q40312) as well as a putative gene for Heat stress transcription factor B-1 (O22230.1) ( Table 2).…”

Genomic Analysis of Powdery Mildew Resistance in a Hop (Humulus lupulusL.) Bi-parental Population Segregating for “R6-locus”

“…We utilized Geneious Pro 11.0.5 (https://www.geneious.com) to identify putative genes involved in disease resistance. Contigs containing SNPs that were observed within a QTL were annotated with RNAseq data from Cascade stem, leaf and apical meristem (Padgitt-Cobb et al 2019). Gene prediction was performed on all contigs containing significant SNPs using the Augustus (Stanke and Morgenstern.…”

“…Three putative R-genes were identified on contig 002196F. A visual observation of RNAseq data (Padgitt-Cobb et al, 2019) obtained from USDA cultivar 'Cascade' (that was exposed to PM infection prior to collecting RNA samples) showed complex expression amongst these three with multiple variations of exons combined into putative isoform mRNA molecules with only two that appear to be complete transcripts (TCONS_00051515 and TCONS_00051522). The Augustus-predicted gene located at 002196F: 39443-41061 contains a full CC-NB-LRR complement exhibiting high similarity to XP_024032005, disease resistance protein RGA2-like [Morus notabilis].…”