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Article|13 Oct 2023|OPEN
The haplotype-resolved T2T genome of teinturier cultivar Yan73 reveals the genetic basis of anthocyanin biosynthesis in grapes
Kekun Zhang1,2 ,† , Mengrui Du2,3 ,† , Hongyan Zhang1 , Xiaoqian Zhang1 , Shuo Cao2 , Xu Wang2 , Wenrui Wang1 , Xueqiang Guan4 , Penghui Zhou5 , Jin Li5 , Wenguang Jiang6 , Meiling Tang7 , Qiuling Zheng7 , Muming Cao8 , Yongfeng Zhou2,9 , Keqin Chen1 , , Zhongjie Liu2 , , Yulin Fang,1 ,
1College of Enology, Heyang Viti-Viniculture Station, Ningxia Helan Mountain’s East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling 712100, China
2National 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
3College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
4Shandong Grape Research Institute, Shanda South Road, Jinan 250199, China
5Shandong Technology Innovation Center of Wine Grape and Wine, COFCO Great Wall Wine (Penglai) Co., Ltd., Yantai 265600, China
6Yantai Changyu Group Co., Ltd., Yantai 264001, China
7Yantai Academy of Agricultural Sciences, Gangcheng West Street, Yantai 264000, China
8Viticulture and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
9National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 570100, China
*Corresponding author. E-mail: chenkeqin1985@nwafu.edu.cn,liuzhongjie@caas.cn,fangyulin@nwsuaf.edu.cn
†Both authors contributed equally to the study.

Horticulture Research 10,
Article number: uhad205 (2023)
doi: https://doi.org/10.1093/hr/uhad205
Views: 101

Received: 30 Jul 2023
Accepted: 01 Oct 2023
Published online: 13 Oct 2023

Abstract

Teinturier grapes are characterized by the typical accumulation of anthocyanins in grape skin, flesh, and vegetative tissues, endowing them with high utility value in red wine blending and nutrient-enriched foods developing. However, due to the lack of genome information, the mechanism involved in regulating teinturier grape coloring has not yet been elucidated and their genetic utilization research is still insufficient. Here, the cultivar ‘Yan73’ was used for assembling the telomere-to-telomere (T2T) genome of teinturier grapes by combining the High Fidelity (HiFi)， Hi-C and ultralong Oxford Nanopore Technologies (ONT) reads. Two haplotype genomes were assembled, at the sizes of 501.68 Mb and 493.38 Mb, respectively. In the haplotype 1 genome, the transposable elements (TEs) contained 32.77% of long terminal repeats (LTRs), while in the haplotype 2 genome, 31.53% of LTRs were detected in TEs. Furthermore, obvious inversions were identified in chromosome 18 between the two haplotypes. Transcriptome profiling suggested that the gene expression patterns in ‘Cabernet Sauvignon’ and ‘Yan73’ were diverse depending on tissues, developmental stages, and varieties. The transcription program of genes in the anthocyanins biosynthesis pathway between the two cultivars exhibited high similarity in different tissues and developmental stages, whereas the expression levels of numerous genes showed significant differences. Compared with other genes, the expression levels of VvMYBA1 and VvUFGT4 in all samples, VvCHS2 except in young shoots and VvPAL9 except in the E-L23 stage of ‘Yan73’ were higher than those of ‘Cabernet Sauvignon’. Further sequence alignments revealed potential variant gene loci and structure variations of anthocyanins biosynthesis related genes and a 816 bp sequence insertion was found in the promoter of VvMYBA1 of ‘Yan73’ haplotype 2 genome. The ‘Yan73’ T2T genome assembly and comparative analysis provided valuable foundations for further revealing the coloring mechanism of teinturier grapes and the genetic improvement of grape coloring traits.