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Article|02 Dec 2022|OPEN
Telomere-to-telomere and gap-free reference genome assembly of the kiwifruit Actinidia chinensis 
Junyang Yue1,2 , ,† , Qinyao Chen1 ,† , Yingzhen Wang1 ,† , Lei Zhang3 ,† , Chen Ye4 , Xu Wang2 , Shuo Cao2 , Yunzhi Lin5 , Wei Huang6 , He Xian7 , Hongyan Qin8 , Yanli Wang8 , Sijia Zhang1 , Ying Wu1 , Songhu Wang1 and Yi Yue4 , Yongsheng Liu,1,5 ,
1School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
2Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
3Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, China
4School of Information and Computer, Anhui Agricultural University, Hefei, Anhui 230036, China
5Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulic and Mountain River Engineering, Sichuan University, Chengdu, Sichuan 610064, China
6Department of Bioinformatics, Anhui Double Helix Gene Technology Corporation, Hefei, Anhui 230022, China
7Comprehensive Testing Ground, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830012, China
8Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, Jilin 130112, China
*Corresponding author. E-mail: yuejy@ahau.edu.cn,liuyongsheng1122@ahau.edu.cn
†Junyang Yue,Qinyao Chen and Yingzhen Wang,Lei Zhang contributed equally to the study.

Horticulture Research 10,
Article number: uhac264 (2023)
doi: https://doi.org/10.1093/hr/uhac264
Views: 307

Received: 21 Aug 2022
Accepted: 21 Nov 2022
Published online: 02 Dec 2022

Abstract

Kiwifruit is an economically and nutritionally important fruit crop with extremely high contents of vitamin C. However, the previously released versions of kiwifruit genomes all have a mass of unanchored or missing regions. Here, we report a highly continuous and completely gap-free reference genome of Actinidia chinensis cv. ‘Hongyang’, named Hongyang v4.0, which is the first to achieve two de novo haploid-resolved haplotypes, HY4P and HY4A. HY4P and HY4A have a total length of 606.1 and 599.6 Mb, respectively, with almost the entire telomeres and centromeres assembled in each haplotype. In comparison with Hongyang v3.0, the integrity and contiguity of Hongyang v4.0 is markedly improved by filling all unclosed gaps and correcting some misoriented regions, resulting in ~38.6–39.5 Mb extra sequences, which might affect 4263 and 4244 protein-coding genes in HY4P and HY4A, respectively. Furthermore, our gap-free genome assembly provides the first clue for inspecting the structure and function of centromeres. Globally, centromeric regions are characterized by higher-order repeats that mainly consist of a 153-bp conserved centromere-specific monomer (Ach-CEN153) with different copy numbers among chromosomes. Functional enrichment analysis of the genes located within centromeric regions demonstrates that chromosome centromeres may not only play physical roles for linking a pair of sister chromatids, but also have genetic features for participation in the regulation of cell division. The availability of the telomere-to-telomere and gap-free Hongyang v4.0 reference genome lays a solid foundation not only for illustrating genome structure and functional genomics studies but also for facilitating kiwifruit breeding and improvement.