In silico genome-wide analysis of the growth-regulating factor gene family and their expression profiling in Vitis vinifera under biotic stress.

IF 1.8 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Cell Biochemistry and Biophysics Pub Date : 2024-11-01 DOI:10.1007/s12013-024-01554-9
Nimra Nazir, Azhar Iqbal, Hadia Hussain, Faisal Ali, Khalid S Almaary, Most Nazmin Aktar, Muhammad Sajid, Mohammed Bourhia, Ahmad Mohammad Salamatullah
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Abstract

Growth regulatory factors (GRFs) are transcription factors that encode the proteins involved in plant growth and development. However, no comprehensive analysis of Vitis vinifera GRF genes has yet been conducted. In the current study, we performed a genome-wide analysis of the GRF gene family to explore the VvGRF gene's role in Vitis vinifera. We identified 30 VvGRF genes in the Vitis vinifera genome, localized over 20 chromosomes. Based on evolutionary analysis, 49 GRF genes (nine AtGRF, ten FvGRF, and 30 VvGRF) were clustered into six groups. Many cis-elements involved in light control, defense, and plant growth have been identified in the promoter region of VvGRF genes, and multiple miRNAs have been predicted to be involved in regulating VvGRF gene expression. Protein-protein interaction analysis showed that nine VvGRF proteins formed a complex protein interaction network. Furthermore, the gene expression analysis of VvGRF revealed that VvGRF-5 and VvGRF-6 were highly upregulated suggesting that these genes are involved in biotic responses. This study provides comprehensive insights into the functional characteristics and occurrence of the VvGRF gene family in Vitis vinifera, which may be applied in breeding programs to enhance the growth of Vitis vinifera varieties under stress and growth changes.

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生物胁迫下葡萄藤生长调节因子基因家族的全基因组分析及其表达谱分析。
生长调节因子(GRFs)是一种转录因子,它编码参与植物生长和发育的蛋白质。然而,目前尚未对葡萄 GRF 基因进行全面分析。在本研究中,我们对 GRF 基因家族进行了全基因组分析,以探索 VvGRF 基因在葡萄中的作用。我们在葡萄基因组中发现了 30 个 VvGRF 基因,分布在 20 条染色体上。根据进化分析,49个GRF基因(9个AtGRF、10个FvGRF和30个VvGRF)被分为六组。在 VvGRF 基因的启动子区域发现了许多涉及光控、防御和植物生长的顺式元件,并预测多种 miRNA 参与调控 VvGRF 基因的表达。蛋白质相互作用分析表明,VvGRF 的九种蛋白质形成了一个复杂的蛋白质相互作用网络。此外,VvGRF的基因表达分析表明,VvGRF-5和VvGRF-6高度上调,表明这些基因参与了生物反应。本研究全面揭示了 VvGRF 基因家族在葡萄中的功能特点和发生规律,可应用于育种计划,以提高葡萄品种在胁迫和生长变化条件下的生长能力。
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来源期刊
Cell Biochemistry and Biophysics
Cell Biochemistry and Biophysics 生物-生化与分子生物学
CiteScore
4.40
自引率
0.00%
发文量
72
审稿时长
7.5 months
期刊介绍: Cell Biochemistry and Biophysics (CBB) aims to publish papers on the nature of the biochemical and biophysical mechanisms underlying the structure, control and function of cellular systems The reports should be within the framework of modern biochemistry and chemistry, biophysics and cell physiology, physics and engineering, molecular and structural biology. The relationship between molecular structure and function under investigation is emphasized. Examples of subject areas that CBB publishes are: · biochemical and biophysical aspects of cell structure and function; · interactions of cells and their molecular/macromolecular constituents; · innovative developments in genetic and biomolecular engineering; · computer-based analysis of tissues, cells, cell networks, organelles, and molecular/macromolecular assemblies; · photometric, spectroscopic, microscopic, mechanical, and electrical methodologies/techniques in analytical cytology, cytometry and innovative instrument design For articles that focus on computational aspects, authors should be clear about which docking and molecular dynamics algorithms or software packages are being used as well as details on the system parameterization, simulations conditions etc. In addition, docking calculations (virtual screening, QSAR, etc.) should be validated either by experimental studies or one or more reliable theoretical cross-validation methods.
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