Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops
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Author
Zheng, Yi
Wu, Shan
Bai, Yang
Sun, Honghe
Jiao, Chen
Guo, Shaogui
Zhao, Kun
Blanca, Jose
Zhang, Zhonghua
Huang, Sanwen
Xu, Yong
Weng, Yiqun
Mazourek, Michael
Reddy, Umesh K
Ando, Kaori
McCreight, James D
Schaffer, Arthur A
Burger, Joseph
Tadmor, Yaakov
Katzir, Nurit
Tang, Xuemei
Liu, Yang
Giovannoni, James J
Ling, Kai-Shu
Wechter, W Patrick
Levi, Amnon
Grumet, Rebecca
Fei, Zhangjun
Publication date
2018-10-13ISSN
0305-1048
Abstract
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.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
633 - Field crops and their production
Pages
9
Publisher
Oxford University Press
Is part of
Nucleic Acids Research
Citation
Zheng, Yi, Shan Wu, Yang Bai, Honghe Sun, Chen Jiao, Shaogui Guo, and Kun Zhao et al. 2018. "Cucurbit Genomics Database (Cugendb): A Central Portal For Comparative And Functional Genomics Of Cucurbit Crops". Nucleic Acids Research 47 (D1): D1128-D1136. Oxford University Press (OUP). doi:10.1093/nar/gky944.
Program
Genòmica i Biotecnologia
This item appears in the following Collection(s)
- ARTICLES CIENTÍFICS [2811]
Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by-nc/4.0/