De novo assembling a high-quality genome sequence of Amur grape ( Vitis amurensis Rupr . ) gives insight into Vitis divergence and sex determination

Abstract

To date, there has been no high-quality sequence for genomes of the East Asian grape species, hindering biological and breeding efforts to improve grape cultivars. This study presents ∼ 522 Mb of the Vitis amurensis ( Va ) genome sequence containing 27 635 coding genes. Phylogenetic analysis indicated that Vitis riparia ( Vr ) may have first split from the other two species, Va and Vitis vinifera ( Vv ). Divergent numbers of duplicated genes reserved among grapes suggests that the core eudicot-common hexaploidy (ECH) and the subsequent genome instability still play a non-negligible role in species divergence and biological innovation. Prominent accumulation of sequence variants might have improved cold resistance in Va, resulting in a more robust network of regulatory cold resistance genes, explaining why it is extremely cold-tolerant compared with Vv and Vr. In contrast, Va has preserved many fewer nucleotide binding site (NBS) disease resistance genes than the other grapes. Notably, multi-omics analysis identified one trans -cinnamate 4-monooxygenase gene positively correlated to the resveratrol accumulated during Va berry development. A selective sweep analysis revealed a hypothetical Va sex-determination region (SDR). Besides, a PPR-containing protein-coding gene in the hypothetical SDR may be related to sex determination in Va. The content and arrangement order of genes in the putative SDR of female Va were similar to those of female Vv. However, the putative SDR of female Va has lost one flavin-containing monooxygenase (FMO) gene and contains one extra protein-coding gene uncharacterized so far. These findings will improve the understanding of Vitis biology and contribute to the improvement of grape breeding.

Acknowledgements

This research was supported by the Key Research and Development Project of Shandong Province (2022CXGC010605; 2021LZGC025), the Improved Variety Program of Shandong Province (2022LZGCQY019; 2020LZGC008), Shandong Natural Science Funding (ZR2020QC145; ZR2023QC239; ZR2021QC022; ZR2022QC076; ZR2023QC249; ZR2023QC217), the Scientific Research Guide Foundation of Shandong Academy of Grape (SDAG2021A01; SDAG2021A02; SDAG2021B11), the Shandong Academy of Agricultural Sciences, Introduction and Training of High-level Talents (CXGC2022E15), the National Horticulture Germplasm Resources Center-Amur Grapevine Germplasm Resources Branch Center (NHGRC2022-NH04), and the Species and Variety Germplasm Resources Protection Project (2130135).

Author contributions

P.W., Y.Z., Y.Y., H.Z., and B.L. designed the experiments. T.D., H.L., F.W., S.F., K.L., and Q.Z. performed the experiments and wrote the manuscript. F.M., A.L., Z.M., and T.Z. analyzed the data. J.J., Y.Z., and X.W. edited the manuscript.

Data availability

The Va genome project was deposited at NCBI under BioProject number PRJNA868106 and BioSample SAMN30308461. All Va coding sequences, protein sequences, and gff files can be download from the TCMPG 2.0 database under number TCMPG20325 (http://cbcb.cdutcm.edu.cn/TCMPG2/genome/details/?id=TCMPG20325). The Va IBCAS1988 genome data can be downloaded from the NGDC database (https://ngdc.cncb.ac.cn/search/?dbId=gwh&q=PRJCA001564&page=1). Vitis vinifera cv. ‘Cabernet Sauvignon’ genome data can be downloaded from the grapegenomics.com database (https://www.grapegenomics.com/pages/VvCabSauv/download.php). Vitis riparia genome data can be downloaded from the NCBI database (https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=96939).

Conflict of interest

The authors declare no competing interests.

Supplementary data

Supplementary data is available at Horticulture Research online.

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