期刊
NUCLEIC ACIDS RESEARCH
卷 47, 期 D1, 页码 D1128-D1136出版社
OXFORD UNIV PRESS
DOI: 10.1093/nar/gky944
关键词
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资金
- USDA National Institute of Food and Agriculture Specialty Crop Research Initiative [2015-51181-24285]
- US-Israel Binational Agricultural Research and Development Fund [IS-3333-02, IS-3877-06CR, IS-4223-09C]
- USDA Agricultural Research Service
- SNC Laboratoire ASL
- de Ruiter Seeds B.V.
- Enza Zaden B.V.
- Gautier Semences S.A.
- Nunhems B.V.
- Rijk Zwaan B.V.
- Sakata Seed Inc
- Semillas Fito S.A.
- Seminis Vegetable Seeds Inc
- Syngenta Seeds B.V.
- Takii and Company Ltd
- Vilmorin and Cie S.A.
- Zeraim Gedera Ltd
- USDA National Institute of Food and Agriculture
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.
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