The Draft Genome of Hop (Humulus lupulus), an Essence for Brewing

Abstract

The female flower of hop (Humulus lupulus var. lupulus) is an essential ingredient that gives characteristic aroma, bitterness and durability/stability to beer. However, the molecular genetic basis for identifying DNA markers in hop for breeding and to study its domestication has been poorly established. Here, we provide draft genomes for two hop cultivars [cv. Saazer (SZ) and cv. Shinshu Wase (SW)] and a Japanese wild hop [H. lupulus var. cordifolius; also known as Karahanasou (KR)]. Sequencing and de novo assembly of genomic DNA from heterozygous SW plants generated scaffolds with a total size of 2.05 Gb, corresponding to approximately 80% of the estimated genome size of hop (2.57 Gb). The scaffolds contained 41,228 putative protein-encoding genes. The genome sequences for SZ and KR were constructed by aligning their short sequence reads to the SW reference genome and then replacing the nucleotides at single nucleotide polymorphism (SNP) sites. De novo RNA sequencing (RNA-Seq) analysis of SW revealed the developmental regulation of genes involved in specialized metabolic processes that impact taste and flavor in beer. Application of a novel bioinformatics tool, phylogenetic comparative RNA-Seq (PCP-Seq), which is based on read depth of genomic DNAs and RNAs, enabled the identification of genes related to the biosynthesis of aromas and flavors that are enriched in SW compared to KR. Our results not only suggest the significance of historical human selection process for enhancing aroma and bitterness biosyntheses in hop cultivars, but also serve as crucial information for breeding varieties with high quality and yield.

Identification and characterization of microRNAs in Humulus lupulus using high-throughput sequencing and their response to Citrus bark cracking viroid (CBCVd) infection

“…The filtered reads obtained from CIP and HP were processed using the plant-specific parameterized probabilistic-model-based miR-PREFeR core algorithm [43] by exploring the scoring system, which includes the secondary structure, the dicer cleavage site, the minimum free energy, the presence of star miRNA evidence and other criteria mentioned earlier [44]. The remaining non-redundant cleaned reads were mapped to the hop draft genome sequence [45] using bowtie-align-reads.py script, which is a wrapper for the bowtie mapper. The main script miR_PREFeR.py was used for de-novo identification of novel miRNAs, using a bowtie aligned SAM file, a hop reference genome with the following configuration parameters (GFF File = none, Precursor Len = 600 and Reads depth cutoff = 3).…”

Plant Glandular Trichomes: Natural Cell Factories of High Biotechnological Interest

“…The (draft) genome sequences of a number of plant species with glandular trichomes are now available. A nonexhaustive list includes different tomato species (Solanum lycopersicum and Solanum pimpinellifolium [Tomato Genome Consortium, 2012] and Solanum pennellii [Bolger et al, 2014]), potato (Solanum tuberosum [Xu et al, 2011]), cucumber (Cucumis sativus [Huang et al, 2009]), tobacco (Nicotiana tabacum [Sierro et al, 2014;Edwards et al, 2017]) and its related species (Nicotiana sylvestris and Nicotiana tomentosiformis [Sierro et al, 2013]), hot pepper (Capsicum annuum ), mint (Mentha longifolia [Vining et al, 2017]), cannabis (Cannabis sativa [van Bakel et al, 2011]), and hop (Humulus lupulus [Natsume et al, 2015]). …”

Methods for verifying the authenticity of hops - an effective tool against falsification

“…The majority of SSR markers occur in non-coding regions of the genome. The increasing information by Next Generation Sequencing (NGS) about transcriptome (Nagel et al, 2008;Clark et al, 2013;Xu et al, 2013) and whole genome sequences (Natsume et al, 2015) complemented hop DNA gene sequences in GeneBank EST databases, which have provided the possibility to look for new gene specifi c molecular markers. From this information, a new type of molecular markers was derived such as Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR) (Patzak and Matoušek, 2011;Jakše et al, 2011;Koelling et al, 2012;Singh et al, 2012) and Single Nucleotide Polymorphism (SNP) markers (Matthews et al, 2013;Yamauchi et al, 2014;Henning et al, 2015).…”