The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding

被引：95

作者：

Shi, Xiaoya ^{[1
,2
]}

Cao, Shuo ^{[2
,3
]}

Wang, Xu ^{[2
,4
]}

Huang, Siyang ^{[2
,5
]}

Wang, Yue ^{[2
,6
]}

Liu, Zhongjie ^{[2
]}

Liu, Wenwen ^{[2
]}

Leng, Xiangpeng ^{[1
]}

Peng, Yanling ^{[2
]}

Wang, Nan ^{[2
]}

Wang, Yiwen ^{[2
]}

Ma, Zhiyao ^{[2
]}

Xu, Xiaodong ^{[2
]}

Zhang, Fan ^{[2
]}

Xue, Hui

Zhong, Haixia ^{[7
]}

Wang, Yi ^{[8
]}

Zhang, Kekun ^{[9
]}

Velt, Amandine ^{[10
]}

Avia, Komlan ^{[10
]}

Holtgraewe, Daniela ^{[11
,12
]}

Grimplet, Jerome ^{[13
]}

Matus, Jose Tomas ^{[14
]}

Ware, Doreen ^{[15
,16
]}

Wu, Xinyu ^{[7
]}

Wang, Haibo ^{[17
]}

Liu, Chonghuai ^{[18
]}

Fang, Yuling ^{[9
]}

Rustenholz, Camille ^{[10
]}

Cheng, Zongming ^{[19
]}

Xiao, Hua ^{[2
,7
]}

Zhou, Yongfeng ^{[2
,20
]}

机构：

[1] Qingdao Agr Univ, Coll Hort, Qingdao 266109, Peoples R China

[2] Chinese Acad Agr Sci, Shen Branch,Key Lab Synthet Biol,State Key Lab Tr, Guangdong Lab Lingan Modern Agr, Agr Genom Inst Shenzhen,Minist Agr & Rural Affair, Shenzhen 518120, Peoples R China

[3] Huazhong Agr Univ, Coll Hort & Forestry Sci, Key Lab Hort Plant Biol, Minist Educ, Wuhan 430070, Peoples R China

[4] Univ Coll Dublin, Sch Agr & Food Sci, Dublin 4, Ireland

[5] Guangxi Univ, Coll Agr, Natl Demonstrat Ctr Expt Plant Sci Educ, Nanning 530004, Peoples R China

[6] Southwest Univ, State Key Lab Resource Insects, Chongqing 400715, Peoples R China

[7] Xinjiang Acad Agr Sci, Inst Hort Crops, Urumqi 830091, Peoples R China

[8] Chinese Acad Sci, Inst Bot, Beijing Key Lab Grape Sci & Enol, Beijing 100093, Peoples R China

[9] Northwest A&F Univ, Coll Enol, Yangling 712100, Peoples R China

[10] Univ Strasbourg, SVQV, INRAE, F-68000 Colmar, France

[11] Bielefeld Univ, Genet & Genom Plants, CeBiTec, D-33615 Bielefeld, Germany

[12] Bielefeld Univ, Fac Biol, D-33615 Bielefeld, Germany

[13] Ctr Invest & Tecnol Agroalimentaria Aragon CITA, Unidad Hortofruticultura, Zaragoza 50059, Spain

[14] Univ Valencia, Inst Integrat Syst Biol I2SysBio, Syst Biotech Program, CSIC, Valencia 46908, Spain

[15] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA

[16] ARS, USDA ARS NEA Robert W Holley Ctr Agr & Hlth, Ithaca, NY 14853 USA

[17] Chinese Acad Agr Sci, Fruit Res Inst, Key Lab Biol & Genet Improvement Hort Crops Germp, Minist Agr,Key Lab Mineral Nutr & Fertilizers Eff, Xingcheng 125100, Liaoning Provin, Peoples R China

[18] Chinese Acad Agr Sci, Zhengzhou Fruit Res Inst, Zhengzhou 450004, Peoples R China

[19] Nanjing Agr Univ, Coll Hort, Nanjing 210095, Peoples R China

[20] Chinese Acad Trop Agr Sci, Trop Crops Genet Resources Inst, State Key Lab Trop Crop Breeding, Haikou 571101, Peoples R China

来源：

HORTICULTURE RESEARCH | 2023年 / 10卷 / 05期

关键词：

SEQUENCE; INSTABILITY;

D O I：

10.1093/hr/uhad061

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

Grapevine is one of the most economically important crops worldwide. However, the previous versions of the grapevine reference genome tipically consist of thousands of fragments with missing centromeres and telomeres, limiting the accessibility of the repetitive sequences, the centromeric and telomeric regions, and the study of inheritance of important agronomic traits in these regions. Here, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the cultivar PN40024 using PacBio HiFi long reads. The T2T reference genome (PN_T2T) is 69 Mb longer with 9018 more genes identified than the 12X.v0 version. We annotated 67% repetitive sequences, 19 centromeres and 36 telomeres, and incorporated gene annotations of previous versions into the PN_T2T assembly. We detected a total of 377 gene clusters, which showed associations with complex traits, such as aroma and disease resistance. Even though PN40024 derives from nine generations of selfing, we still found nine genomic hotspots of heterozygous sites associated with biological processes, such as the oxidation-reduction process and protein phosphorylation. The fully annotated complete reference genome therefore constitutes an important resource for grapevine genetic studies and breeding programs.

引用

页数：13

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