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Article|13 Dec 2023|OPEN
Telomere-to-telomere and gap-free genome assembly of a susceptible grapevine species (Thompson Seedless) to facilitate grape functional genomics
Xianhang Wang1 ,† , Mingxing Tu1 ,† , Ya Wang2 , Yali Zhang1 , Wuchen Yin2 , Jinghao Fang2 , Min Gao2 , Zhi Li2 , Wei Zhan3 , Yulin Fang1 , Junyang Song4 , , Zhumei Xi1 , and Xiping Wang,2 ,
1College of Enology, College of Food Science and Engineering, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
2State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
3Xi’an Haorui Genomics Technology Co., Ltd, Xi’an 710116, China
4College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
*Corresponding author. E-mail: songjunyang@nwsuaf.edu.cn,xizhumei@nwafu.edu.cn,wangxiping@nwafu.edu.cn
Both authors contributed equally to the study.

Horticulture Research 11,
Article number: uhad260 (2024)
doi: https://doi.org/10.1093/hr/uhad260
Views: 28

Received: 25 Jun 2023
Accepted: 26 Nov 2023
Published online: 13 Dec 2023

Abstract

Grapes are globally recognized as economically significant fruit trees. Among grape varieties, Thompson Seedless holds paramount influence for fresh consumption and for extensive applications in winemaking, drying, and juicing. This variety is one of the most efficient genotypes for grape genetic modification. However, the lack of a high-quality genome has impeded effective breeding efforts. Here, we present the high-quality reference genome of Thompson Seedless with all 19 chromosomes represented as 19 contiguous sequences (N50 = 27.1 Mb) with zero gaps and prediction of all telomeres and centromeres. Compared with the previous assembly (TSv1 version), the new assembly incorporates an additional 31.5 Mb of high-quality sequenced data with annotation of a total of 30 397 protein-coding genes. We also performed a meticulous analysis to identify nucleotide-binding leucine-rich repeat genes (NLRs) in Thompson Seedless and two wild grape varieties renowned for their disease resistance. Our analysis revealed a significant reduction in the number of two types of NLRs, TIR-NB-LRR (TNL) and CC-NB-LRR (CNL), in Thompson Seedless, which may have led to its sensitivity to many fungal diseases, such as powdery mildew, and an increase in the number of a third type, RPW8 (resistance to powdery mildew 8)-NB-LRR (RNL). Subsequently, transcriptome analysis showed significant enrichment of NLRs during powdery mildew infection, emphasizing the pivotal role of these elements in grapevine’s defense against powdery mildew. The successful assembly of a high-quality Thompson Seedless reference genome significantly contributes to grape genomics research, providing insight into the importance of seedlessness, disease resistance, and color traits, and these data can be used to facilitate grape molecular breeding efforts.