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

## TL;DR

This study explores G-quadruplexes in grapevines, showing their role in stress response and metabolism, offering targets for improving grape quality.

## Contribution

The study identifies G-quadruplexes as regulatory elements in grapevine stress adaptation and sugar–acid metabolism.

## Key findings

- G-quadruplexes are enriched in promoter and TSS regions, showing strand preference and heterogeneity in centromeres.
- Drought stress DEGs show G-quadruplex enrichment linked to metal ion homeostasis and sugar–acid metabolism.
- G-quadruplexes are enriched in key metabolism genes like pyruvate kinase and sucrose synthase.

## 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.