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: camille.rustenholz@inrae.fr,zmc@njau.edu.cn,xiaohua01@caas.cn,zhouyongfeng@caas.cn †Xiaoya Shi and Shuo Cao,Xu Wang contributed equally to the study.
Received: 06 Dec 2022 Accepted: 02 Apr 2023 Published online: 04 Apr 2023
Abstract
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.
, Zongming Cheng18 ,
