title: 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.
authors.affiliation: Iwate Biotechnology Research Center (IBRC), 174-4, Narita 22, Kitakami, Iwate, 024-0003 Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Natsume
authors.affiliation: Iwate Biotechnology Research Center (IBRC), 174-4, Narita 22, Kitakami, Iwate, 024-0003 Japan.
authors.forename: Hiroki
authors.initials: H
authors.lastname: Takagi
authors.affiliation: Bioorganic Research Institute, Suntory Foundation for Life Sciences (SUNBOR), 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka, 618-8503 Japan.
authors.forename: Akira
authors.initials: A
authors.lastname: Shiraishi
authors.affiliation: Bioorganic Research Institute, Suntory Foundation for Life Sciences (SUNBOR), 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka, 618-8503 Japan.
authors.forename: Jun
authors.initials: J
authors.lastname: Murata
authors.affiliation: Research Institute, Suntory Global Innovation Center (SIC) Ltd., 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka, 618-8503 Japan.
authors.forename: Hiromi
authors.initials: H
authors.lastname: Toyonaga
authors.affiliation: Hop Research Institute Co., Ltd., 438-01 Zatec, Kadanska 2525, Czech Republic.
authors.forename: Josef
authors.initials: J
authors.lastname: Patzak
authors.affiliation: Technology Development Department, Suntory System Technology (SST) Ltd., 2-1-5, Dojima, Kita-ku, Osaka, 530-8204 Japan.
authors.forename: Motoshige
authors.initials: M
authors.lastname: Takagi
authors.affiliation: Iwate Biotechnology Research Center (IBRC), 174-4, Narita 22, Kitakami, Iwate, 024-0003 Japan.
authors.forename: Hiroki
authors.initials: H
authors.lastname: Yaegashi
authors.affiliation: Iwate Biotechnology Research Center (IBRC), 174-4, Narita 22, Kitakami, Iwate, 024-0003 Japan.
authors.forename: Aiko
authors.initials: A
authors.lastname: Uemura
authors.affiliation: Iwate Biotechnology Research Center (IBRC), 174-4, Narita 22, Kitakami, Iwate, 024-0003 Japan.
authors.forename: Chikako
authors.initials: C
authors.lastname: Mitsuoka
authors.affiliation: Iwate Biotechnology Research Center (IBRC), 174-4, Narita 22, Kitakami, Iwate, 024-0003 Japan.
authors.forename: Kentaro
authors.initials: K
authors.lastname: Yoshida
authors.affiliation: Hop Research Institute Co., Ltd., 438-01 Zatec, Kadanska 2525, Czech Republic.
authors.forename: Karel
authors.initials: K
authors.lastname: Krofta
authors.affiliation: Bioorganic Research Institute, Suntory Foundation for Life Sciences (SUNBOR), 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka, 618-8503 Japan.
authors.forename: Honoo
authors.initials: H
authors.lastname: Satake
authors.affiliation: Iwate Biotechnology Research Center (IBRC), 174-4, Narita 22, Kitakami, Iwate, 024-0003 Japan.
authors.forename: Ryohei
authors.initials: R
authors.lastname: Terauchi
authors.affiliation: Research Institute, Suntory Global Innovation Center (SIC) Ltd., 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka, 618-8503 Japan eiichiro_ono@suntory.co.jp.
authors.forename: Eiichiro
authors.initials: E
authors.lastname: Ono
mesh_terms: D001515:Beer; D004032:Diet; D035264:Flowers / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D059646:Genome Size; D018745:Genome, Plant; D027582:Humulus / Q000235:genetics* / Q000378:metabolism; D015388:Organelles / Q000235:genetics; D010802:Phylogeny; D019655:Quantitative Trait, Heritable; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA
keywords: Genomics; Hop; Humulus; Specialized metabolism; Transcriptome