Haplotype-resolved assemblies provide insights into genomic makeup of the oldest grapevine cultivar (Munage) in China

Abstract

Munage, an ancient grape variety that has been cultivated for thousands of years in Xinjiang, China, is renowned for its exceptional fruit traits. There are two main types of Munage: white fruit (WM) and red fruit (RM). However, the lack of a high-quality genomic resources has impeded effective breeding and restricted the potential for expanding these varieties to other growing regions. In this study, we assembled haplotype-resolved genome assemblies for WM and RM, alongside integrated whole genome resequencing (WGS) data and transcriptome data to illuminate the origin, private mutations and selection in Munage. Our analyses suggest that Munage likely shares a common ancestor with Eurasian grapes that originated in West Asia. Selective analysis between Munage clones and Eurasian grapes mapped genomic signals of selection in Munage grapes, with genes enriched in processes including cell maturation, plant epidermal cell differentiation, and root epidermal cell differentiation. We also identified 283 somatic mutation sites between WM and RM, along with differential selection on genome and expressed genes. These findings provide crucial genetic resources for investigating the genetics of the ancient Chinese grape variety, Munage, and will facilitate the genetic improvement in grapevine using this ancient cultivar as a gene donor.

Acknowledgements

The financial assistance for this research is received from the Project of Fund for Stable Support to Agricultural Sci-Tech Renovation (xjnkywdzc-2025001-07, xjnkywdzc-2026001-18, xjnkywdzc-2025001-39), Tianshan Autonomous Region Talent Youth Top notch Talent—Young Science and Technology Innovation Talent Project (2024TSYCCX0097), the National Natural Science Foundation of China (No. 32160682, No. 32260732 and No. 32460722), Xinjiang Uygur Autonomous Region Tianchi Talent - Young Doctor approved for VIVEK YADAV (History and genetic mechanism of grape domestication in Asia), Xinjiang Uygur Autonomous Region Tianchi Talent—Special Expert Project (Whole genome design and breeding of grapes), Key research and development project of autonomous region (2022B02045-1-1, 2023B02029-1-1), National Key Laboratory of Tropical Crop Breeding (No. NKLTCB-RC202501), the China Agriculture Research System of MOF and MARA and Shenzhen Polytechnic University Research Project (6024330001K) to Tian Ling.

Authors contributions

Hua Xiao, Xinyu Wu, Ling Tian, Yongfeng Zhou, Haixia Zhong, Xiaoya Shi, Fuchun Zhang (Conceptualization), Haixia Zhong, Xiaoya Shi, Fuchun Zhang, Jin Yao, Xu Wang, Vivek Yadav, Xiaoming Zhou (Data curation), Xiaoya Shi, Fuchun Zhang, Xu Wang, Shuo Cao, Songlin Zhang, Chuan Zhang, Jiangxia Qiao, Zhongjie Liu, Yingchun Zhang, Yuting Liu, Hao Wang, Hui Xue, Mengyan Zhang (Data analysis), Xinyu Wu, Haixia Zhong, Ling Tian, Yongfeng Zhou (Funding acquisition), Haixia Zhong, Xiaoya Shi, Fuchun Zhang, Tianhao Zhang, Wenrui Wang, Ruoyan Zhao, Tianrong Fan, Zhongqi Liu, Jiacui Li, Ruirui Liu (Methodology), Haixia Zhong (Project administration), Haixia Zhong, Fuchun Zhang, Xiaoming Zhou, Xinyu Wu (Resources), Haixia Zhong, Xiaoya Shi, Fuchun Zhang (Validation), Haixia Zhong, Xiaoya Shi, Vivek Yadav, Hua Xiao (Writing—review & editing), and Hua Xiao, Xinyu Wu, Yongfeng Zhou (Supervision)

Data availability

All raw data have been deposited in the NCBI Sequence Read Archive under project number PRJNA1158437 and the National Genomics Data Center (NGDC) Genome Sequence Archive (GSA) (https://ngdc.cncb.ac.cn/gsa/), with BioProject number PRJCA029988. The assembly and annotation have been deposited in zenodo: https://doi.org/10.5281/zenodo.13732355.

Conflicts of interest statement

The authors declare no competing interests.

Supplementary material

Supplementary material is available at Horticulture Research online.

References

[1] Banilas G, Korkas E, Kaldis P. et al. Olive and grapevine bio-diversity in greece and cyprus—a review. In: Lichtfouse E, Intercropping,ed. Climate Change, Pest Control and Beneficial Microorganisms. Springer: Dordrecht, 2009,401-28

[2] This P, Lacombe T, Thomas MR. Historical origins and genetic diversity of wine grapes. Trends Genet. 2006; 22:511-9

[3] Jun W, Changqing D. Advance in research on domestication and taxonomy of Eurasian grape (Vitis vinifera L.). Front Plant Sci. 2010; 11:572

[4] Dong Y, Duan S, Xia Q. et al. Dual domestications and origin of traits in grapevine evolution. Science. 2023; 379:892-901

[5] Manen JF, Bouby L, Dalnoki O. et al. Microsatellites from archaeological Vitis vinifera seeds allow a tentative assignment of the geographical origin of ancient cultivars. J Archaeol Sci. 2003; 30:721-9

[6] Arroyo-García R, Ruiz-García L, Bolling L. et al. Multiple ori-gins of cultivated grapevine ( sativa) based on chloroplast DNA polymorphisms. Mol Ecol. 2006; 15: 3707-14

[7] Grassi F, Mattia FD, Zecca G. et al. Historical isolation and quaternary range expansion of divergent lineages in wild grapevine. Biol J Linn Soc. 2008; 95:611-9

[8] Maghradze D, Melyan G, Salimov V. et al. Wild grapevine (Vitis sylvestris C.C.Gmel.) wines from the Southern Caucasus region. OENO One. 2020; 54:809-22

[9] Liu X. Viticulture and Viniculture in the Turfan Region.

[10] Laufer B. SINO-IRANICA: chinese contributions to the history of civilization in ancient Iran. Publ Field Mus Nat Hist Anthropol Ser. 1919;15:i-630

[11] Zhao M, Jiang H, Grassa CJ. Archaeobotanical studies of the Yanghai cemetery in Turpan, Xinjiang, China. Archaeol Anthro-pol Sci. 2018; 11:1143-53

[12] Jiang H, Zhang YB, Li X. et al. Evidence for early viticulture in China: proof of a grapevine (Vitis vinifera L., Vitaceae) in the Yanghai Tombs, Xinjiang. J Archaeol Sci. 2009; 36:1458-65

[13] Uchibayashi M. Introduction of grapes and alfalfa into China: a reflection on the role of Zhang Qian. Yakugaku Zasshi. 2005; 125:895-8

[14] Li S. Grapevine breeding and genetics in china: history, cur-rent status and the future. Acta Hortic. 2025; 1082:165-76

[15] Zhang F, Zhong H, Zhou X. et al. Grafting with rootstocks promotes phenolic compound accumulation in grape berry skin during development based on integrative multi-omics analysis. Hortic Res. 2022;9:uhac055

[16] Liu S, Zhong H, Zhang F. et al. Genetic diversity and core germplasm research of 144 munake grape resources using 22 pairs of SSR markers. Horticulturae. 2023; 9:917

[17] Mou Z, Yuan Y, Wei W. et al. Integrative metabolomic and tran-scriptomic analysis provides novel insights into the effects of SO2 on the postharvest quality of ‘munage’ table grapes. Foods. 2024; 13:3494

[18] Zhang Z, Xing S, Yuan Y. et al. Sulfur dioxide fumigation pro-motes GABA accumulation and energy metabolism to delay quality deterioration in postharvest table grapes. Postharvest Biol Technol. 2024; 215:113022

[19] Yin X, Liu B, Maimaitiyiming R. et al. The effect of non-Saccharomyces cerevisiae Torulaspora delbrueckii on the aroma composition of munage grape base-wine and the mechanism of the effect. Fermentation. 2024; 10:266

[20] Wang Y, Lv Y, Han T. et al. Post-harvest quality changes and molecular responses of epidermal wax in ‘munage’ grapes with Botrytis cinerea Infection. Int J Mol Sci. 2025; 26:3468

[21] Huang J, Zhang G, Li Y. et al. Integrative genomic and tran-scriptomic analyses of a bud sport mutant ‘Jinzao Wuhe’ with the phenotype of large berries in grapevines. PeerJ. 2023; 11:e14617

[22] Wang X, Liu Z, Zhang F. et al. Integrative genomics reveals the polygenic basis of seedlessness in grapevine. Curr Biol. 2023; 34:3763-3777.e5

[23] Guo D-L, Zhang G-H. A new early-ripening grape cultivar -‘fengzao’. Acta Hortic. 2015; 1082:153-56

[24] Wei L, Cao Y, Cheng J. et al. Comparative transcriptome anal-yses of a table grape ‘Summer Black’ and its early-ripening mutant ‘Tiangong Moyu’ identify candidate genes potentially involved in berry development and ripening. J Plant Interact. 2020; 15:213-22

[25] Leng F, Ye Y, Zhu X. et al. Comparative transcriptomic analysis between ‘Summer Black’ and its bud sport ‘Nantaihutezao’ during developmental stages. Planta. 2021; 253:23

[26] Azuma A, Kobayashi S, Goto-Yamamoto N. et al. Color recovery in berries of grape (Vitis vinifera L.) ‘Benitaka’, a bud sport of ‘Italia’, is caused by a novel allele at the VvmybA1 locus. Plant Sci. 2009; 176:470-8

[27] Pan Q, Chen F, Zhu BQ. et al. Molecular cloning and expres-sion of gene encoding aromatic amino acid decarboxy-lase in ‘Vidal blanc’ grape berries. Mol Biol Rep. 2012; 39: 4319-25

[28] Negri AS, Prinsi B, Failla O. et al. Proteomic and metabolic traits of grape exocarp to explain different anthocyanin con-centrations of the cultivars. Front Plant Sci. 2015; 6:603

[29] Calderón L, Carbonell-Bejerano P, Muñoz C. et al. Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation. Hortic Res. 2024;11: uhae080

[30] Zhang K, du M, Zhang H. et al. The haplotype-resolved T2T genome of teinturier cultivar Yan73 reveals the genetic basis of anthocyanin biosynthesis in grapes. Hortic Res. 2023;10:uhad205

[31] Shirasawa K, Hirakawa H, Azuma A. et al. De novo whole-genome assembly in an interspecific hybrid table grape, ‘Shine Muscat’. DNA Res. 2022;29:dsac040

[32] Shi X, Cao S, Wang X. et al. The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding. Hortic Res. 2023;10:uhad061

[33] Boyes DC, Nam J, Dangl JL. The Arabidopsis thaliana RPM1 disease resistance gene product is a peripheral plasma membrane protein that is degraded coincident with the hypersensitive response. Proc Natl Acad Sci USA. 1998; 95: 15849-54

[34] Gil P, Dewey E, Friml J. et al. BIG: a calossin-like protein required for polar auxin transport in Arabidopsis. Genes Dev. 2001; 15:1985-97

[35] Cramer WA, Hasan SS. Structure-Function of the Cytochrome b6f Lipoprotein Complex. Dordrecht: Springer Netherlands; 2016; 84:1349-58

[36] Yadeta KA, Elmore JM, Creer AY. et al. A cysteine-rich protein kinase associates with a membrane immune complex and the cysteine residues are required for cell death. Plant Physiol. 2016; 173:771-87

[37] Gao C. Genome engineering for crop improvement and future agriculture. Cell. 2021; 184:1621-35

[38] Yu, Ying-hui L, Qing-wen Y. et al. Genomics-based crop germplasm research: advances and perspectives. 2015; 48: 3333-53

[39] Liu Z, Wang N, Su Y. et al. Grapevine pangenome facil-itates trait genetics and genomic breeding. Nat Genet. 2024; 56:2804-14

[40] Zhang Z, Liu W, Zhang T. et al. Population genomics of Vitis pseudoreticulata reveals the genetic basis of fungal resistance in grapevine. Hortic Plant J. 2025

[41] Liu Y, Dong Y, Fang X. et al. Pangenomics and single-cell tran-scriptomics uncover the genetic basis of continuous bearing trait in grapevine. Hortic Res. 2025;uhaf228

[42] Zhou Y, Minio A, Massonnet M. et al. The population genetics of structural variants in grapevine domestication. Nat Plants. 2019; 5:965-79

[43] Zhou Y, Massonnet M, Sanjak JS. et al. Cantu D. & Gaut B.S. Wild grapevine (Vitis sylvestris C.C.Gmel.) wines from the Southern Caucasus region. Proc Natl Acad Sci USA. 2017; 114:11715-20

[44] Zhang T, Peng W, Xiao H. et al. Population genomics high-lights structural variations in local adaptation to saline coastal environments in woolly grape. J Integr Plant Biol. 2024; 66: 1408-26

[45] Gaut BS, Seymour DK, Liu Q. et al. Demography and its effects on genomic variation in crop domestication. Nat Plants. 2018; 4:512-20

[46] Xiao H, Liu Z, Wang N. et al. Adaptive and maladaptive intro-gression in grapevine domestication. Proc Natl Acad Sci USA. 2023; 120:e2222041120

[47] Djari A, Madignier G, di Valentin O. et al. Haplotype-resolved genome assembly and implementation of VitExpress, an open interactive transcriptomic platform for grapevine. Proc Natl Acad Sci USA. 2024; 121:e2403750121

[48] Wang Y, Ding K, Li H. et al. Biography of Vitis genomics: recent advances and prospective. Hortic Res. 2024;11:uhae128

[49] Li Y. Agriculture and palaeoeconomy in prehistoric Xinjiang, China (3000-200 bc). Veg Hist Archaeobotany. 2020; 30:287-303

[50] Lamoureux D, et al.Bernole A, le Clainche I. Anchoring of a large set of markers onto a BAC library for the development of a draft physical map of the grapevine genome. Theor Appl Genet. 2006; 113:344-56

[51] Kui L, Tang M, Duan S. et al. Identification of selective sweeps in the domesticated table and wine grape (Vitis vinifera L.). Front Plant Sci. 2020; 11:572

[52] Zhang M, Xu X, Zhang T. et al. The dynamics of wild Vitis species in response to climate change facilitate the breeding of grapevine and its rootstocks with climate resilience. Hortic Res. 2025;12:uhaf104

[53] Hou T, Xu Y, Dong Y. et al. The cytonuclear interactions during grapevine domestication. J Integr Plant Biol. 2025; 67:13968

[54] Miller AJ, Gross BL. From forest to field: perennial fruit crop domestication. Am J Bot. 2011; 98:1389-414

[55] Forneck A, Benjak A, Rühl EH. Grapevine (Vitis ssp.): example of clonal reproduction in agricultural important plants. In: Schon I, Martens K, Dijk P,eds. Lost Sex. Heidelberg, Germany: Springer, 2009

[56] Peng Y, Wang Y, Liu Y. et al. The genomic and epige-nomic landscapes of hemizygous genes across crops with contrasting reproductive systems. Proc Natl Acad Sci USA. 2025; 122:e2422487122

[57] Xiao H, Wang Y, Liu W. et al. Impacts of reproductive sys-tems on grapevine genome and breeding. Nat Commun. 2025; 16:2031

[58] Jaillon O, Aury J-M, Noel B. et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007; 449:463-7

[59] Kobayashi S, Goto-Yamamoto N, Hirochika H. Retrotransposon-induced mutations in grape skin color. Science. 2004; 304:982-2

[60] Ranallo-Benavidez TR, Jaron KS, Jaron KS. et al. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nat Commun. 2020; 11: 1432

[61] Durand NC, Shamim MS, Machol I. et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 2016; 3:95-8

[62] Dudchenko O, Batra SS, Omer AD. et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science. 2016; 356:92-5

[63] Simão FA, Waterhouse RM, Ioannidis P. et al. BUSCO: assess-ing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015; 31:3210-2

[64] Kim D, Paggi JM, Park C. et al. Graph-based genome align-ment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019; 37:907-15

[65] Stanke M, Keller O, Gunduz I. et al. AUGUSTUS: ab ini-tio prediction of alternative transcripts. Nucleic Acids Res. 2006;34:W435-9

[66] Flynn JM, Hubley R, Goubert C. et al. RepeatModeler2 for auto-mated genomic discovery of transposable element families. Proc Natl Acad Sci. 2020; 117:9451-7

[67] Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2017; 34:3094-100

[68] Danecek P, Bonfield JK, Liddle J. et al. Twelve years of SAM-tools and BCFtools. GigaScience. 2020;10:giab008

[69] Goel M, Sun H, Jiao W-B. et al. SyRI: finding genomic rear-rangements and local sequence differences from whole-genome assemblies. Genome Biol. 2019; 20:277

[70] Goel M, Schneeberger K. plotsr: visualizing structural similar-ities and rearrangements between multiple genomes. Bioin-formatics. 2022; 38:2922-6

[71] Chen S. Ultrafast one-pass FASTQ data preprocessing, qual-ity control, and deduplication using fastp. iMeta. 2023; 2: e107

[72] Danecek P, Auton A, Abecasis G. et al. The variant call format and VCFtools. Bioinformatics. 2011; 27:2156-8

[73] Huerta-Cepas J, Szklarczyk D, Heller D. et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 2018;47:D309-14

[74] Chen C, Chen H, Zhang Y. et al. TBtools—an integrative toolkit developed for interactive analyses of big biological data. Mol Plant. 2020; 13:1194-202

[75] Purcell SM, Neale B, Todd-Brown K. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007; 81:559-75

[76] Piñeiro C, Abuín JM, Pichel JC. Very Fast Tree: speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies. Bioinformatics. 2020; 36:4658-9

[77] Alexander DH, Novembre J, Lange KL. Fast model-based esti-mation of ancestry in unrelated individuals. Genome Res. 2009; 19:1655-64

[78] Pavlidis P, Zivkovic D, Stamatakis A. et al. SweeD: likelihood-based detection of selective sweeps in thousands of genomes. Mol Biol Evol. 2013; 30: 2224-34

[79] Hämälä T, Savolainen O. Genomic patterns of local adap- tation under gene flow in Arabidopsis lyrata. Mol Biol Evol. 2019; 36:2557-71

[80] Pertea G, Pert,ea M. GFF Utilities: GffRead and GffCompare. F1000 Res. 2020;9:ISCB Comm J-304

[81] Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2013; 30:923-30

[82] Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014; 15:550