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Article|04 Apr 2023|OPEN
The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding
Xiaoya Shi1,2 ,† , Shuo Cao2,3 ,† , Xu Wang2,4 ,† , Siyang Huang2,5 , Yue Wang2,6 , Zhongjie Liu2 , Wenwen Liu2 , Xiangpeng Leng1 , Yanling Peng2 , Nan Wang2 , Yiwen Wang2 , Zhiyao Ma2 , Xiaodong Xu2 , Fan Zhang2 , Hui Xue2 , Haixia Zhong7 , Yi Wang8 , Kekun Zhang9 , Amandine Velt10 , Komlan Avia10 , Daniela Holtgräwe11 , Jérôme Grimplet12 , José Tomás Matus13 , Doreen Ware14,15 , Xinyu Wu7 and Haibo Wang16 , Chonghuai Liu17 , Yuling Fang9 , Camille Rustenholz10 , , Zongming Cheng18 , , Hua Xiao2,7 , , Yongfeng Zhou,2,19 ,
1College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
2State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
3Key Laboratory of Horticultural Plant Biology Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
4School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
5National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
6State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, China
7Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
8Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing 100093, China
9College of Enology, Northwest A&F University, Yangling 712100, China
10SVQV, INRAE - University of Strasbourg, 68000 Colmar, France
11Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
12Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), 50059 Zaragoza, Spain
13Institute for Integrative Systems Biology (I2SysBio), Systems Biotech Program, Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
14Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
15USDA ARS NEA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA
16Fruit Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization), Ministry of Agriculture/Key Laboratory of Mineral Nutrition and Fertilizers Efficient Utilization of Deciduous Fruit Tree, Liaoning Province, Xingcheng 125100, China
17Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450004, China
18College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
19State Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
*Corresponding author. E-mail:,,,
Xiaoya Shi and Shuo Cao,Xu Wang contributed equally to the study.

Horticulture Research 10,
Article number: uhad061 (2023)
Views: 209

Received: 06 Dec 2022
Accepted: 02 Apr 2023
Published online: 04 Apr 2023


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.