National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China.
Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China.
Plant J. 2023 Nov;116(4):1018-1029. doi: 10.1111/tpj.16350. Epub 2023 Jun 22.
Horticultural plants contribute immensely to the quality of human's life. The rapid development of omics studies on horticultural plants has resulted in large volumes of valuable growth- and development-related data. Genes that are essential for growth and development are highly conserved in evolution. Cross-species data mining reduces the impact of species heterogeneity and has been extensively used for conserved gene identification. Owing to the lack of a comprehensive database for cross-species data mining using multi-omics data from all horticultural plant species, the current resources in this field are far from satisfactory. Here, we introduce GERDH (https://dphdatabase.com), a database platform for cross-species data mining among horticultural plants, based on 12 961 uniformly processed publicly available omics libraries from more than 150 horticultural plant accessions, including fruits, vegetables and ornamental plants. Important and conserved genes that are essential for a specific biological process can be obtained by cross-species analysis module with interactive web-based data analysis and visualization. Moreover, GERDH is equipped with seven online analysis tools, including gene expression, in-species analysis, epigenetic regulation, gene co-expression, enrichment/pathway and phylogenetic analysis. By interactive cross-species analysis, we identified key genes contributing to postharvest storage. By gene expression analysis, we explored new functions of CmEIN3 in flower development, which was validated by transgenic chrysanthemum analysis. We believe that GERDH will be a useful resource for key gene identification and will allow for omics big data to be more available and accessible to horticultural plant community members.
园艺植物极大地提高了人类的生活质量。园艺植物组学研究的快速发展产生了大量有价值的生长和发育相关数据。在进化过程中，与生长和发育相关的基因高度保守。跨物种数据挖掘减少了物种异质性的影响，并已被广泛用于保守基因鉴定。由于缺乏一个综合的数据库，用于使用来自所有园艺植物物种的多组学数据进行跨物种数据挖掘，目前该领域的资源远远不能令人满意。在这里，我们介绍了 GERDH（https://dphdatabase.com），这是一个基于 12961 个来自 150 多个园艺植物品系的统一处理的公共组学文库的园艺植物跨物种数据挖掘数据库平台，其中包括水果、蔬菜和观赏植物。通过具有交互式网络数据分析和可视化功能的跨物种分析模块，可以获得对特定生物过程至关重要的重要和保守基因。此外，GERDH 还配备了七个在线分析工具，包括基因表达、种内分析、表观遗传调控、基因共表达、富集/途径和系统发育分析。通过交互式跨物种分析，我们确定了对采后贮藏有贡献的关键基因。通过基因表达分析，我们探索了 CmEIN3 在花发育中的新功能，这通过转基因菊花分析得到了验证。我们相信 GERDH 将成为鉴定关键基因的有用资源，并使组学大数据更易于园艺植物研究人员获取和使用。
