The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding

Abstract

Grapevine is one of the most economically important crops worldwide. However, the previous versions of the grapevine reference genome tipically consist of thousands of fragments with missing centromeres and telomeres, limiting the accessibility of the repetitive sequences, the centromeric and telomeric regions, and the study of inheritance of important agronomic traits in these regions. Here, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the cultivar PN40024 using PacBio HiFi long reads. The T2T reference genome (PN_T2T) is 69 Mb longer with 9018 more genes identified than the 12X.v0 version. We annotated 67% repetitive sequences, 19 centromeres and 36 telomeres, and incorporated gene annotations of previous versions into the PN_T2T assembly. We detected a total of 377 gene clusters, which showed associations with complex traits, such as aroma and disease resistance. Even though PN40024 derives from nine generations of selfing, 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 constitutes an important resource for grapevine genetic studies and breeding programs.

Acknowledgements

This work was supported by the National Natural Science Fund for Excellent Young Scientists Fund Program (Overseas) to Y.Z., the National Key Research and Development Program of China (grant 2019YFA0906200), the Agricultural Science and Technology Innovation Program (CAAS-ZDRW202101), the Shenzhen Science and Technology Program (grant KQTD2016113010482651), and 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 from the COST Innovators Grant GRAPEDIA (IG17111), supported by COST (European Cooperation in Science and Technology). JTM is supported by PID2021-128865NB-I00 and RYC-2017-23 645 grants from AEI (Spain).

Author contributions

Y.Z. conceived and designed the project with H.X., Z.C., and C.R. The PN40024 sample was provided by Z.C. under an MTA signed with INRAE. X.S., W.L., X.X., and Z.M. performed the tissue culture of the sample in the greenhouse. X.S., X.W., H.X., N.W., F.Z., H.X., H.Z. and Y.W. performed the bioinformatic analyses. A.V., K.A., D.H., J.G., J.T.M., D.W., Z.L., X.L., and W.L. performed the gene annotation. Y.P., S.H., Z.L., W.L., X.W., Y.F., Y.W., H.W. and C.L. assisted in bioinformatics analyses. X.S., S.C., X.W., H.X., and Y.Z. wrote the manuscript with comments and input from all authors.

Data availability

All PacBio sequence data have been deposited in the NCBI Sequence Read Archive under project number PRJNA882193 and the National Genomics Data Center (NGDC) Genome Sequence Archive (GSA) (https://ngdc.cncb.ac.cn/gsa/), with BioProject number PRJCA012093. The assembly and annotation as well as the sequences of centromeres and heterozygous regions have been deposited in zenodo: https://zenodo.org/record/7751391#. ZBgVmcJBy3A. The assembly and its annotation will be also hosted in the GRAPEDIA portal (https://grapedia.org/).

Code availability

All the scripts and pipelines used in this study have been archived in GitHub: https://github.com/zhouyflab.

Conflict of interest statement

The authors declare no conflict of interest.

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