Decoding G-Quadruplexes Sequence in <i>Vitis vinifera</i>: Regulatory Region Enrichment, Drought Stress Adaptation, and Sugar–Acid Metabolism Modulation
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 <i>Vitis vinifera</i>. A total of 467,813 G-quadruplexes were identified in grapevine genome, with e...
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2025-04-01
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| author | Jun Xie Kangkang Song Gaixia Qiao Rong Wang Hongyuan Wu Qiaoxia Jia Yujuan Liu Yi Li Meilong Xu |
| author_facet | Jun Xie Kangkang Song Gaixia Qiao Rong Wang Hongyuan Wu Qiaoxia Jia Yujuan Liu Yi Li Meilong Xu |
| author_sort | Jun Xie |
| collection | DOAJ |
| description | 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 <i>Vitis vinifera</i>. 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. |
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| language | English |
| publishDate | 2025-04-01 |
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| spelling | doaj-art-64f2e3f3cbc743309a2faef5cddf35ca2025-08-20T02:18:10ZengMDPI AGPlants2223-77472025-04-01148118010.3390/plants14081180Decoding G-Quadruplexes Sequence in <i>Vitis vinifera</i>: Regulatory Region Enrichment, Drought Stress Adaptation, and Sugar–Acid Metabolism ModulationJun Xie0Kangkang Song1Gaixia Qiao2Rong Wang3Hongyuan Wu4Qiaoxia Jia5Yujuan Liu6Yi Li7Meilong Xu8College of Forestry, Gansu Agriculture University, Lanzhou 730070, ChinaCollege of Forestry, Shandong Agricultural University, Tai’an 271018, ChinaState Key Laboratory of Efficient Production of Forest Resources, Yinchuan 750004, ChinaState Key Laboratory of Efficient Production of Forest Resources, Yinchuan 750004, ChinaBeijing Anling Ecological Construction Co., Ltd., Beijing 102300, ChinaState Key Laboratory of Efficient Production of Forest Resources, Yinchuan 750004, ChinaState Key Laboratory of Efficient Production of Forest Resources, Yinchuan 750004, ChinaCollege of Forestry, Gansu Agriculture University, Lanzhou 730070, ChinaHorticulture Research Institute, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan 750012, ChinaG-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 <i>Vitis vinifera</i>. 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.https://www.mdpi.com/2223-7747/14/8/1180<i>Vitis vinifera</i>G-quadruplextranscriptional regulationdrought stresssugar–acid metabolism |
| spellingShingle | Jun Xie Kangkang Song Gaixia Qiao Rong Wang Hongyuan Wu Qiaoxia Jia Yujuan Liu Yi Li Meilong Xu Decoding G-Quadruplexes Sequence in <i>Vitis vinifera</i>: Regulatory Region Enrichment, Drought Stress Adaptation, and Sugar–Acid Metabolism Modulation Plants <i>Vitis vinifera</i> G-quadruplex transcriptional regulation drought stress sugar–acid metabolism |
| title | Decoding G-Quadruplexes Sequence in <i>Vitis vinifera</i>: Regulatory Region Enrichment, Drought Stress Adaptation, and Sugar–Acid Metabolism Modulation |
| title_full | Decoding G-Quadruplexes Sequence in <i>Vitis vinifera</i>: Regulatory Region Enrichment, Drought Stress Adaptation, and Sugar–Acid Metabolism Modulation |
| title_fullStr | Decoding G-Quadruplexes Sequence in <i>Vitis vinifera</i>: Regulatory Region Enrichment, Drought Stress Adaptation, and Sugar–Acid Metabolism Modulation |
| title_full_unstemmed | Decoding G-Quadruplexes Sequence in <i>Vitis vinifera</i>: Regulatory Region Enrichment, Drought Stress Adaptation, and Sugar–Acid Metabolism Modulation |
| title_short | Decoding G-Quadruplexes Sequence in <i>Vitis vinifera</i>: Regulatory Region Enrichment, Drought Stress Adaptation, and Sugar–Acid Metabolism Modulation |
| title_sort | decoding g quadruplexes sequence in i vitis vinifera i regulatory region enrichment drought stress adaptation and sugar acid metabolism modulation |
| topic | <i>Vitis vinifera</i> G-quadruplex transcriptional regulation drought stress sugar–acid metabolism |
| url | https://www.mdpi.com/2223-7747/14/8/1180 |
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