Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops

文献类型： 外文期刊

第一作者： Zheng, Yi

作者： Zheng, Yi;Wu, Shan;Bai, Yang;Sun, Honghe;Jiao, Chen;Guo, Shaogui;Zhao, Kun;Tang, Xuemei;Liu, Yang;Giovannoni, James J.;Fei, Zhangjun;Sun, Honghe;Guo, Shaogui;Xu, Yong;Blanca, Jose;Zhang, Zhonghua;Huang, Sanwen;Huang, Sanwen;Weng, Yiqun;Weng, Yiqun;Mazourek, Michael;Reddy, Umesh K.;Ando, Kaori;McCreight, James D.;Schaffer, Arthur A.;Burger, Joseph;Tadmor, Yaakov;Katzir, Nurit;Liu, Yang;Giovannoni, James J.;Fei, Zhangjun;Ling, Kai-Shu;Wechter, W. Patrick;Levi, Amnon;Garcia-Mas, Jordi;Garcia-Mas, Jordi;Grumet, Rebecca

作者机构：

期刊名称：NUCLEIC ACIDS RESEARCH （ 影响因子：16.971； 五年影响因子：15.542 ）

ISSN： 0305-1048

年卷期： 2019 年 47 卷 D1 期

页码：

收录情况： SCI

摘要： 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.

分类号：

  • 相关文献
作者其他论文 更多>>

微信小程序