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

Authors: ZHENG, YI - Cornell University; WU, SHAN - Cornell University; BAI, YANG - Cornell University; SUN, HONGHE - Cornell University; JIAO, CHEN - Cornell University; GUO, SHAOGUI - Beijing Academy Of Agricultural Sciences; ZHAO, KUN - Cornell University; BLANCA, JOSE - Polytechnical University Of Valencia; ZHANG, ZHONGHUA - Beijing Academy Of Agricultural Sciences; HUANG, SANWEN - Beijing 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 - US Department Of Agriculture (USDA); MCCREIGHT, JAMES - US Department Of Agriculture (USDA); SCHAFFER, ARTHUR - Volcani Center (ARO); BURGER, JOSEPH - Newe Ya'Ar Research Center; TADMOR, YAAKOV - Newe Ya'Ar Research Center; KATZIR, NURIT - Newe Ya'Ar Research Center; TANG, ZUEMEI - Cornell University; LIU, YANG - Cornell University; GIOVANNONI, JAMES - Cornell University; LING, KAI-SHU - US Department Of Agriculture (USDA); WECHTER, PATRICK - US Department Of Agriculture (USDA); LEVI, AMNON - US Department Of Agriculture (USDA); GARCIA-MAS, JORDI - Agricultural Institute Of Spain; GRUMET, REBECCA - Michigan State University; FEI, ZHANGJUN - Cornell University

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/4/2018
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.K., Ando, K., Mccreight, J.D., Schaffer, A., Burger, J., Tadmor, Y., Katzir, N., Tang, Z., Liu, Y., Giovannoni, J.J., Ling, K., Wechter, P.W., 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. (2019): Vol. 4747(D1):D1128-D1136.. https://doi.org/10.1093/nar/gky944.
DOI: https://doi.org/10.1093/nar/gky944

Interpretive Summary: The gourd family contains many economically important and popular fruit and vegetable crops (gourds). In the past decade, reference genomes have been generated for more than 20 cucurbit species. Data for genetic variations and from gene expression studies are accumulating rapidly for these cucurbit crops. For efficient use, analysis and dissemination of these large-scale datasets, we have developed an updated version of Cucurbit Genomics Database. The updated database, CuGenDBv2 (http://cucurbitgenomics.org/v2), currently hosts 33 reference genomes from 26 cucurbit species/subspecies in ten different genera. Protein-coding genes from these genomes have been comprehensively annotated by comparing their protein sequences to various public protein and domain databases. A novel “Genotype” module has been developed to facilitate mining and analysis of the functionally annotated genome sequence variants including SNPs and small indels from large-scale genome sequencing projects. An updated “Expression” module has been developed to provide a comprehensive gene expression atlas for cucurbits. Furthermore, synteny blocks between any two and within each of the 33 genomes, representing a total of 561 pair-wise genome comparisons, have been identified and can be explored and visualized in the database. This updated database constitutes a very important genetic/genomic resources for the cucurbit research community worldwide, which has been extensively and heavily accessed since it’s establishment.

Technical Abstract: The Cucurbitaceae (cucurbit) family consists of about 965 species across around 100 genera, including many economically important and popular fruit and vegetable crops. During the past several years, reference genomes have been generated for more than 20 cucurbit species, and variome and transcriptome profiling data have been rapidly accumulated for cucurbits. To efficiently mine, analyze and disseminate these large-scale datasets, we have developed an updated version of Cucurbit Genomics Database. The updated database, CuGenDBv2 (http://cucurbitgenomics.org/v2), currently hosts 33 reference genomes from 26 cucurbit species/subspecies belonging to 10 different genera. Protein-coding genes from these genomes have been comprehensively annotated by comparing their protein sequences to various public protein and domain databases. A novel “Genotype” module has been developed to facilitate mining and analysis of the functionally annotated variome data including SNPs and small indels from large-scale genome sequencing projects. An updated “Expression” module has been developed to provide a comprehensive gene expression atlas for cucurbits. Furthermore, synteny blocks between any two and within each of the 33 genomes, representing a total of 561 pair-wise genome comparisons, have been identified and can be explored and visualized in the database.