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Research Project: Trait Discovery, Genetics, and Enhancement of Allium, Cucumis, and Daucus Germplasm

Location: Vegetable Crops Research

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

Author
item Zheng, Yi - Boyce Thompson Institute
item Wu, Shan - Boyce Thompson Institute
item Bai, Yang - Boyce Thompson Institute
item Sun, Honghe - Boyce Thompson Institute
item Jiao, Chen - Boyce Thompson Institute
item Guo, Shaogui - Boyce Thompson Institute
item Zhao, Kun - Boyce Thompson Institute
item Blanca, Jose - University Of Spain
item Zhang, Zhonghua - Chinese Academy Of Agricultural Sciences
item Huang, Sanwen - Chinese Academy Of Agricultural Sciences
item Xu, Yong - Beijing Academy Of Agricultural Sciences
item Weng, Yiqun
item Mazourek, Michael - Cornell University - New York
item Reddy, Umesh - West Virginia State University
item Ando, Kaori
item Mccreight, James - Jim
item Schaffer, Arthur - Agricultural Research Organization Of Israel
item Burger, Joseph - Agricultural Research Organization Of Israel
item Tadmor, Yaakov - Agricultural Research Organization Of Israel
item Katzir, Nurit - Agricultural Research Organization Of Israel
item Tang, Xuemei - Boyce Thompson Institute
item Liu, Yang - Boyce Thompson Institute
item Giovannoni, James
item Ling, Kai-shu
item Wechter, William - Pat
item Levi, Amnon
item Garcia-mas, Jordi - Center For Agricultural Research And Training, Cantabria Government (CIFA)
item Grumet, Rebecca - Michigan State University
item Fei, Zhangjun - Cornell University - New York

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/26/2018
Publication Date: 10/13/2018
Citation: Zheng, Y., Wu, S., Bai, Y., Sun, H., Jiao, C., Guo, S., Zhao, K., Blanca, J., Zhang, Z., Huang, S., Xu, Y., Weng, Y., Mazourek, M., Reddy, U., Ando, K., Mccreight, J.D., Schaffer, A.A., Burger, J., Tadmor, Y., Katzir, N., Tang, X., Liu, Y., Giovannoni, J.J., Ling, K., Wechter, W.P., Levi, A., Garcia-Mas, J., Grumet, R., Fei, Z. 2018. Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. Nucleic Acids Research. 47(D1):1128-1136. https://doi.org/10.1093/nar/gky944.
DOI: https://doi.org/10.1093/nar/gky944

Interpretive Summary: Cucurbits such as cucumber, melon, cucumber, watermelon, and pumpkin/squash are economically important crops. Technology advancements in the last decade has allowed accumulation of vast genetic and genomic data which play important roles for cucurbit improvement. 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). The database contains all available genome and expressed gene sequences, and genetic maps for all four major cucurbit crops species. In addition, sequence functions, biochemical pathways and comparative genomic analysis results among these cucurbit crops are also provided in this database. To facilitate the usage of these large-scale data by the community, a set of analysis and visualization tools and user-friendly query interfaces have been implemented in the database. This database is being actively curated and updated. This database will be a very important tool tool for both cucurbit researchers and breeders to make full use the genetic and genomic resources to expedite cucurbit improvement.

Technical Abstract: The Cucurbitaceae family (cucurbit) includes several economically important crops, such as melon, cucumber, watermelon, pumpkin, and squash. 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.