Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.
National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China.
Nucleic Acids Res. 2019 Jan 8;47(D1):D1128-D1136. doi: 10.1093/nar/gky944.
The Cucurbitaceae family (cucurbit) includes several economically important crops, such as melon, cucumber, watermelon, pumpkin, squash and gourds. During the past several years, genomic and genetic data have been rapidly accumulated for cucurbits. To store, mine, analyze, integrate and disseminate these large-scale datasets and to provide a central portal for the cucurbit research and breeding community, we have developed the Cucurbit Genomics Database (CuGenDB; http://cucurbitgenomics.org) using the Tripal toolkit. The database currently contains all available genome and expressed sequence tag (EST) sequences, genetic maps, and transcriptome profiles for cucurbit species, as well as sequence annotations, biochemical pathways and comparative genomic analysis results such as synteny blocks and homologous gene pairs between different cucurbit species. A set of analysis and visualization tools and user-friendly query interfaces have been implemented in the database to facilitate the usage of these large-scale data by the community. In particular, two new tools have been developed in the database, a 'SyntenyViewer' to view genome synteny between different cucurbit species and an 'RNA-Seq' module to analyze and visualize gene expression profiles. Both tools have been packed as Tripal extension modules that can be adopted in other genomics databases developed using the Tripal system.
葫芦科（葫芦）包括几种经济上重要的作物，如甜瓜、黄瓜、西瓜、南瓜、葫芦和葫芦。在过去的几年中，葫芦科的基因组和遗传数据已经迅速积累。为了存储、挖掘、分析、整合和传播这些大规模数据集，并为葫芦科的研究和育种界提供一个中心门户，我们使用 Tripal 工具包开发了葫芦科基因组数据库（CuGenDB；http://cucurbitgenomics.org）。该数据库目前包含所有可用的基因组和表达序列标签（EST）序列、遗传图谱和转录组图谱，以及序列注释、生化途径和比较基因组分析结果，如不同葫芦科物种之间的同线性块和同源基因对。数据库中实现了一组分析和可视化工具以及用户友好的查询接口，以方便社区使用这些大规模数据。特别是，数据库中开发了两个新工具，一个是“同源基因对可视化工具（SyntenyViewer）”，用于查看不同葫芦科物种之间的基因组同线性，另一个是“RNA-Seq 模块”，用于分析和可视化基因表达谱。这两个工具都被打包为 Tripal 扩展模块，可以在使用 Tripal 系统开发的其他基因组数据库中采用。
