首页|Telomere-to-telomere and gap-free genome assembly of a susceptible grapevine species(Thompson Seedless)to facilitate grape functional genomics

Telomere-to-telomere and gap-free genome assembly of a susceptible grapevine species(Thompson Seedless)to facilitate grape functional genomics

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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 duringpowdery 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.

Xianhang Wang、Mingxing Tu、Ya Wang、Yali Zhang、Wuchen Yin、Jinghao Fang、Min Gao、Zhi Li、Wei Zhan、Yulin Fang、Junyang Song、Zhumei Xi、Xiping Wang

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College 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

State Key Laboratory of Crop Stress Biology in Arid Areas,College of Horticulture,Northwest A&F University,Yangling,Shaanxi 712100,China

Xi'an Haorui Genomics Technology Co.,Ltd,Xi'an 710116,China

College of Landscape Architecture and Arts,Northwest A&F University,Yangling,Shaanxi 712100,China

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国家自然科学基金国家自然科学基金国家自然科学基金Key Research and Development Program of ShaanxiChina National GeneBank(CNGB)

U160323432002000322024232023-YBNY-075

2024

10.1093/hr/uhad260

园艺研究(英文)

园艺研究(英文)

CSTPCD
ISSN：
年,卷(期)：2024.11(1)
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