Shi Xiaoya, Cao Shuo, Wang Xu, Huang Siyang, Wang Yue, Liu Zhongjie, Liu Wenwen, Leng Xiangpeng, Peng Yanling, Wang Nan, Wang Yiwen, Ma Zhiyao, Xu Xiaodong, Zhang Fan, Xue Hui, Zhong Haixia, Wang Yi, Zhang Kekun, Velt Amandine, Avia Komlan, Holtgräwe Daniela, Grimplet Jérôme, Matus José Tomás, Ware Doreen, Wu Xinyu, Wang Haibo, Liu Chonghuai, Fang Yuling, Rustenholz Camille, Cheng Zongming, Xiao Hua, Zhou Yongfeng
College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China.
State 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.
Hortic Res. 2023 Apr 4;10(5):uhad061. doi: 10.1093/hr/uhad061. eCollection 2023 May.
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.
葡萄是全球经济上最重要的作物之一。然而，葡萄参考基因组的先前版本通常由数千个片段组成，缺少着丝粒和端粒，这限制了重复序列、着丝粒和端粒区域的可及性，以及这些区域重要农艺性状遗传的研究。在此，我们使用PacBio HiFi长读长为品种PN40024组装了一个从端粒到端粒（T2T）无间隙的参考基因组。与12X.v0版本相比，T2T参考基因组（PN_T2T）长69 Mb，鉴定出的基因多9018个。我们注释了67%的重复序列、19个着丝粒和36个端粒，并将先前版本的基因注释纳入PN_T2T组装中。我们总共检测到377个基因簇，它们与复杂性状相关，如香气和抗病性。尽管PN40024来自九代自交，但我们仍然发现了九个与生物过程相关的杂合位点基因组热点，如氧化还原过程和蛋白质磷酸化。因此，这个完全注释的完整参考基因组构成了葡萄遗传研究和育种计划的重要资源。
