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

Authors: ZHENG, YI - Boyce Thompson Institute; WU, SHAN - Boyce Thompson Institute; BAI, YANG - Boyce Thompson Institute; SUN, HONGHE - Boyce Thompson Institute; JIAO, CHEN - Boyce Thompson Institute; GUO, SHAOGUI - Boyce Thompson Institute; ZHAO, KUN - Boyce Thompson Institute; BLANCA, JOSE - University Of Spain; ZHANG, ZHONGHUA - Chinese Academy Of Agricultural Sciences; HUANG, SANWEN - Chinese Academy Of Agricultural Sciences; XU, YONG - Beijing Academy Of Agricultural Sciences; Weng, Yiqun; MAZOUREK, MICHAEL - Cornell University; REDDY, UMESH - West Virginia State University; Ando, Kaori; McCreight, James - Jim; SCHAFFER, ARTHUR - Agricultural Research Organization Of Israel; BURGER, JOSEPH - Agricultural Research Organization Of Israel; TADMOR, YAAKOV - Agricultural Research Organization Of Israel; KATZIR, NURIT - Agricultural Research Organization Of Israel; TANG, XUEMEI - Boyce Thompson Institute; LIU, YANG - Boyce Thompson Institute; Giovannoni, James; Ling, Kai-Shu; Wechter, William - Pat; Levi, Amnon; GARCIA-MAS, JORDI - Center For Agricultural Research And Training, Cantabria Government (CIFA); GRUMET, REBECCA - Michigan State University; FEI, ZHANGJUN - Cornell University

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.