Detail
Article
Online article
FT
Medvik - BMC
  • Something wrong with this record ?

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

S. Natsume, H. Takagi, A. Shiraishi, J. Murata, H. Toyonaga, J. Patzak, M. Takagi, H. Yaegashi, A. Uemura, C. Mitsuoka, K. Yoshida, K. Krofta, H. Satake, R. Terauchi, E. Ono,

. 2015 ; 56 (3) : 428-41. [pub] 20141120

Language English Country Japan

Document type Journal Article, Research Support, Non-U.S. Gov't

Persistent link   https://www.medvik.cz/link/bmc16000528

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.

References provided by Crossref.org

000      
00000naa a2200000 a 4500
001      
bmc16000528
003      
CZ-PrNML
005      
20160127101655.0
007      
ta
008      
160108s2015 ja f 000 0|eng||
009      
AR
024    7_
$a 10.1093/pcp/pcu169 $2 doi
035    __
$a (PubMed)25416290
040    __
$a ABA008 $b cze $d ABA008 $e AACR2
041    0_
$a eng
044    __
$a ja
100    1_
$a Natsume, Satoshi $u Iwate Biotechnology Research Center (IBRC), 174-4, Narita 22, Kitakami, Iwate, 024-0003 Japan.
245    14
$a The Draft Genome of Hop (Humulus lupulus), an Essence for Brewing / $c S. Natsume, H. Takagi, A. Shiraishi, J. Murata, H. Toyonaga, J. Patzak, M. Takagi, H. Yaegashi, A. Uemura, C. Mitsuoka, K. Yoshida, K. Krofta, H. Satake, R. Terauchi, E. Ono,
520    9_
$a 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.
650    12
$a pivo $7 D001515
650    _2
$a dieta $7 D004032
650    _2
$a květy $x genetika $7 D035264
650    _2
$a stanovení celkové genové exprese $7 D020869
650    _2
$a regulace genové exprese u rostlin $7 D018506
650    _2
$a rostlinné geny $7 D017343
650    _2
$a délka genomu $7 D059646
650    12
$a genom rostlinný $7 D018745
650    _2
$a Humulus $x genetika $x metabolismus $7 D027582
650    _2
$a organely $x genetika $7 D015388
650    _2
$a fylogeneze $7 D010802
650    _2
$a kvantitativní znak dědičný $7 D019655
650    _2
$a repetitivní sekvence nukleových kyselin $x genetika $7 D012091
650    _2
$a polymerázová řetězová reakce s reverzní transkripcí $7 D020133
650    _2
$a sekvenční analýza DNA $7 D017422
650    _2
$a sekvenční analýza RNA $7 D017423
655    _2
$a časopisecké články $7 D016428
655    _2
$a práce podpořená grantem $7 D013485
700    1_
$a Takagi, Hiroki $u Iwate Biotechnology Research Center (IBRC), 174-4, Narita 22, Kitakami, Iwate, 024-0003 Japan.
700    1_
$a Shiraishi, Akira $u Bioorganic Research Institute, Suntory Foundation for Life Sciences (SUNBOR), 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka, 618-8503 Japan.
700    1_
$a Murata, Jun $u Bioorganic Research Institute, Suntory Foundation for Life Sciences (SUNBOR), 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka, 618-8503 Japan.
700    1_
$a Toyonaga, Hiromi $u Research Institute, Suntory Global Innovation Center (SIC) Ltd., 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka, 618-8503 Japan.
700    1_
$a Patzak, Josef $u Hop Research Institute Co., Ltd., 438-01 Zatec, Kadanska 2525, Czech Republic.
700    1_
$a Takagi, Motoshige $u Technology Development Department, Suntory System Technology (SST) Ltd., 2-1-5, Dojima, Kita-ku, Osaka, 530-8204 Japan.
700    1_
$a Yaegashi, Hiroki $u Iwate Biotechnology Research Center (IBRC), 174-4, Narita 22, Kitakami, Iwate, 024-0003 Japan.
700    1_
$a Uemura, Aiko $u Iwate Biotechnology Research Center (IBRC), 174-4, Narita 22, Kitakami, Iwate, 024-0003 Japan.
700    1_
$a Mitsuoka, Chikako $u Iwate Biotechnology Research Center (IBRC), 174-4, Narita 22, Kitakami, Iwate, 024-0003 Japan.
700    1_
$a Yoshida, Kentaro $u Iwate Biotechnology Research Center (IBRC), 174-4, Narita 22, Kitakami, Iwate, 024-0003 Japan.
700    1_
$a Krofta, Karel $u Hop Research Institute Co., Ltd., 438-01 Zatec, Kadanska 2525, Czech Republic.
700    1_
$a Satake, Honoo $u Bioorganic Research Institute, Suntory Foundation for Life Sciences (SUNBOR), 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka, 618-8503 Japan.
700    1_
$a Terauchi, Ryohei $u Iwate Biotechnology Research Center (IBRC), 174-4, Narita 22, Kitakami, Iwate, 024-0003 Japan.
700    1_
$a Ono, Eiichiro $u Research Institute, Suntory Global Innovation Center (SIC) Ltd., 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka, 618-8503 Japan eiichiro_ono@suntory.co.jp.
773    0_
$w MED00003836 $t Plant & cell physiology $x 1471-9053 $g Roč. 56, č. 3 (2015), s. 428-41
856    41
$u https://pubmed.ncbi.nlm.nih.gov/25416290 $y Pubmed
910    __
$a ABA008 $b sig $c sign $y a $z 0
990    __
$a 20160108 $b ABA008
991    __
$a 20160127101820 $b ABA008
999    __
$a ok $b bmc $g 1102809 $s 924734
BAS    __
$a 3
BAS    __
$a PreBMC
BMC    __
$a 2015 $b 56 $c 3 $d 428-41 $e 20141120 $i 1471-9053 $m Plant and Cell Physiology $n Plant Cell Physiol $x MED00003836
LZP    __
$a Pubmed-20160108

Find record

Citation metrics

Archiving options