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Article

Decoding G-Quadruplexes Sequence in Vitis vinifera: Regulatory Region Enrichment, Drought Stress Adaptation, and Sugar–Acid Metabolism Modulation

by
Jun Xie
1,2,†,
Kangkang Song
3,†,
Gaixia Qiao
2,
Rong Wang
2,
Hongyuan Wu
4,
Qiaoxia Jia
2,
Yujuan Liu
2,
Yi Li
1,* and
Meilong Xu
5,*
1
College of Forestry, Gansu Agriculture University, Lanzhou 730070, China
2
State Key Laboratory of Efficient Production of Forest Resources, Yinchuan 750004, China
3
College of Forestry, Shandong Agricultural University, Tai’an 271018, China
4
Beijing Anling Ecological Construction Co., Ltd., Beijing 102300, China
5
Horticulture Research Institute, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan 750012, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Plants 2025, 14(8), 1180; https://doi.org/10.3390/plants14081180
Submission received: 7 March 2025 / Revised: 4 April 2025 / Accepted: 8 April 2025 / Published: 10 April 2025
(This article belongs to the Special Issue Bioinformatics and Functional Genomics in Modern Plant Science)
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Abstract

G-quadruplexes play a crucial role in transcription, translation, and DNA replication in plant genomes. Here, we comprehensively examined the prevalence and functions of G-quadruplexes in Vitis vinifera. A total of 467,813 G-quadruplexes were identified in grapevine genome, with enrichment in the promoter (0.54/kbp) and near transcription start sites (TSSs, 1.00/kbp), and showed conservative strand preference. The G-quadruplex density in centromeres exhibited heterogeneity. The differentially expressed genes (DEGs) under two-day drought stress manifested high G-quadruplex density in the promoter and TSS regions. The upregulated DEGs showed template strand-biased G-quadruplex enrichment, while downregulated DEGs displayed coding strand dominance linked to metal ion homeostasis and sugar–acid metabolism pathways, respectively. G-quadruplexes were enriched in key sugar–acid metabolism genes, including pyruvate kinase and sucrose synthase. The number of G-quadruplexes in sucrose transferase VINV genes was higher than that in the CWINV and NINV genes. This study revealed G-quadruplexes as regulatory elements of stress response and berry development, providing abundant genetic targets for precision breeding and the quality improvement of grapevines.
Keywords: Vitis vinifera; G-quadruplex; transcriptional regulation; drought stress; sugar–acid metabolism Vitis vinifera; G-quadruplex; transcriptional regulation; drought stress; sugar–acid metabolism

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MDPI and ACS Style

Xie, J.; Song, K.; Qiao, G.; Wang, R.; Wu, H.; Jia, Q.; Liu, Y.; Li, Y.; Xu, M. Decoding G-Quadruplexes Sequence in Vitis vinifera: Regulatory Region Enrichment, Drought Stress Adaptation, and Sugar–Acid Metabolism Modulation. Plants 2025, 14, 1180. https://doi.org/10.3390/plants14081180

AMA Style

Xie J, Song K, Qiao G, Wang R, Wu H, Jia Q, Liu Y, Li Y, Xu M. Decoding G-Quadruplexes Sequence in Vitis vinifera: Regulatory Region Enrichment, Drought Stress Adaptation, and Sugar–Acid Metabolism Modulation. Plants. 2025; 14(8):1180. https://doi.org/10.3390/plants14081180

Chicago/Turabian Style

Xie, Jun, Kangkang Song, Gaixia Qiao, Rong Wang, Hongyuan Wu, Qiaoxia Jia, Yujuan Liu, Yi Li, and Meilong Xu. 2025. "Decoding G-Quadruplexes Sequence in Vitis vinifera: Regulatory Region Enrichment, Drought Stress Adaptation, and Sugar–Acid Metabolism Modulation" Plants 14, no. 8: 1180. https://doi.org/10.3390/plants14081180

APA Style

Xie, J., Song, K., Qiao, G., Wang, R., Wu, H., Jia, Q., Liu, Y., Li, Y., & Xu, M. (2025). Decoding G-Quadruplexes Sequence in Vitis vinifera: Regulatory Region Enrichment, Drought Stress Adaptation, and Sugar–Acid Metabolism Modulation. Plants, 14(8), 1180. https://doi.org/10.3390/plants14081180

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