Cucurbit Genomics Database (CuGenDB) : A central portal for comparative and functional genomics of cucurbit crops
Zheng, Yi (Cornell University. Boyce Thompson Institute)
Wu, Shan (Cornell University. Boyce Thompson Institute)
Bai, Yang (Cornell University. Boyce Thompson Institute)
Sun, Honghe (Beijing Academy of Agriculture and Forestry Sciences. National Engineering Research Center for Vegetables)
Jiao, Chen (Cornell University. Boyce Thompson Institute)
Guo, Shaogui (Beijing Academy of Agriculture and Forestry Sciences. National Engineering Research Center for Vegetables)
Zhao, Kun (Cornell University. Boyce Thompson Institute)
Blanca, José (Universitat Politècnica de València. Institut Universitari de Conservació i Millora de l'Agrodiversitat Valenciana)
Zhang, Zhonghua (Chinese Academy of Agricultural Sciences. Institute of Vegetables and Flowers)
Huang, Sanwen (Chinese Academy of Agricultural Sciences. Agricultural Genomics Institute at Shenzhen)
Xu, Yong (Beijing Academy of Agriculture and Forestry Sciences. National Engineering Research Center for Vegetables)
Weng, Yiqun (University of Wisconsin. Department of Horticulture)
Mazourek, Michael (Cornell University. Plant Breeding and Genetics Section)
Reddy, Umesh K. (West Virginia State University. Department of Biology)
Ando, Kaori (U.S. Crop Improvement and Protection Research Unit. Department of Agriculture-Agricultural Research Service)
McCreight, James D. (Crop Improvement and Protection Research Unit. Department of Agriculture-Agricultural Research Service)
Schaffer, Arthur A. (Volcani Center. Plant Science Institute)
Burger, Joseph (Newe Yaar Research Center. Plant Science Institute)
Tadmor, Yaakov (Newe Yaar Research Center. Plant Science Institute)
Katzir, Nurit (Newe Yaar Research Center. Plant Science Institute)
Tang, Xuemei (Cornell University. Boyce Thompson Institute)
Liu, Yang (Cornell University. Horticulture Section)
Giovannoni, James J. (U.S. Robert W. Holley Center for Agriculture and Health. Department of Agriculture-Agricultural Research Service)
Ling, Kai-Shu (U.S. Vegetable Laboratory. Department of Agriculture-Agricultural Research Service)
Wechter, William P. (U.S. Vegetable Laboratory. Department of Agriculture-Agricultural Research Service)
Levi, Amnon (U.S. Vegetable Laboratory. Department of Agriculture-Agricultural Research Service)
Garcia-Mas, Jordi (Centre de Recerca en Agrigenòmica)
Grumet, Rebecca (Michigan State University. Department of Horticulture)
Fei, Zhangjun (U.S. Robert W. Holley Center for Agriculture and Health. Department of Agriculture-Agricultural Research Service)

Fecha:	2019
Resumen:	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.
Derechos:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original.
Lengua:	Anglès
Documento:	Article ; recerca ; Versió publicada
Publicado en:	Nucleic acids research, Vol. 47, Issue D1 (January 2019) , p. D1128-D1136, ISSN 1362-4962

DOI: 10.1093/nar/gky944
PMID: 30321383

9 p, 4.9 MB

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