The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding
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Date
2023
Authors
Grimplet, JérômeShi, Xiaoya
Cao, Shuo
Wang, Xu
Huang, Xiyang
Wang, Yue
Liu, Zhongjie
Liu, Wenwen
Leng, Xiangpeng
Peng, Yanling
Wang, Nan
Wang, Yiwen
Ma, Zhiyao
Xu, Xiaodong
Zhang, Fan
Zhong, Haixia
Wang, Yi
Zhang, Kekun
Velt, Amandine
Avia, Komlan
Holtgräwe, Daniela
Matus, José Tomás
Ware, Doreen
Wu, Xinyu
Wang, Haibo
Liu, Chonghuai
Fang, Yuling
Rustenholz, Camille
Cheng, Zongming
Xiao, Hua
Zhou, Yongfeng
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Abstract
Grapevine is one of the most economically important crops worldwide. However, the previous versions of the grapevine reference genome consisted of thousands of fragments with missing centromeres and telomeres, which limited the accessibility of the repetitive sequences, the centromeric and telomeric regions, and the inheritance of important agronomic traits in these regions. Here, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the pinot noir cultivar (PN40024) using the PacBio HiFi long reads. The T2T reference genome (PN_T2T) was 69 Mb longer with 9026 more genes identified than the 12X.v2 version (Canaguier et al., 2017). We annotated 67% repetitive sequences, 19 centromeres and 36 telomeres, and incorporated gene annotations of previous versions into the PN_T2T. We detected a total of 377 gene clusters, which showed associations with complex traits, such as aroma and disease resistance. Even though the PN40024 sample had been selfed for nine generations, 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, provides important resources for grapevine genetics and breeding.
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Horticulture Research, 2023
AGROVOC subjects
ViticulturaEndogamia
Secuencia genética
Vid
Sponsorship
This work was supported by the National Natural Science Fund for Excellent Young Scientists Fund Program (Overseas) to Yongfeng Zhou, the National Key Research and Development Program of China(grant2019YFA0906200), the Agricultural Science and Technology Innovation Program (CAAS-ZDRW202101), the Shenzhen Science and Technology Program (grant KQTD2016113010482651), the BMBF funded de.NBI Cloud within the German Network for Bioinformatics Infrastructure (de.NBI). We thank Bianca Frommer, Marie Lahaye, David Navarro-Payá, Marcela K. Tello-Ruiz and Kapeel Chougule for their help in analyzing the RNA-Seq data and in running the gene annotation pipeline. This study is also based upon work from COST Action CA17111 INTEGRAPE and form COST Innovators Grant IG17111 GRAPEDIA, supported by COST (European Cooperation in Science and Technology).