Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops
文献类型： 外文期刊
作者： Zheng, Yi 1 ; Wu, Shan 1 ; Bai, Yang 1 ; Sun, Honghe 1 ; Jiao, Chen 1 ; Guo, Shaogui 1 ; Zhao, Kun 1 ; Blanca, Jose 3 ; Zhan 1 ;
作者机构： 1.Cornell Univ, Boyce Thompson Inst, Ithaca, NY 14853 USA
2.Beijing Acad Agr & Forestry Sci, Natl Engn Res Ctr Vegetables, Key Lab Biol & Genet Improvement Hort Crops North, Beijing Key Lab Vegetable Germplasm Improvement, Beijing 100097, Peoples R China
3.Univ Politecn Valencia, Inst Conservat & Breeding Agr Biodivers COMAV UPV, E-46022 Valencia, Spain
4.Chinese Acad Agr Sci, Inst Vegetables & Flowers, Key Lab Biol & Genet Improvement Hort Crops, Minist Agr,Sino Dutch Joint Lab Hort Genom, Beijing 100081, Peoples R China
5.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Minist Agr, Genome Anal Lab, Shenzhen 518124, Guangdong, Peoples R China
6.USDA ARS, Vegetable Crops Res Unit, Madison, WI 53706 USA
7.Univ Wisconsin, Dept Hort, Madison, WI 53706 USA
8.Cornell Univ, Sch Integrat Plant Sci, Plant Breeding & Genet Sect, Ithaca, NY 14853 USA
9.West Virginia State Univ, Dept Biol, Institute, WV 25112 USA
10.USDA ARS, Crop Improvement & Protect Res Unit, Salinas, CA 93905 USA
11.Volcani Ctr, Agr Res Org, Plant Sci Inst, POB 6, IL-50250 Bet Dagan, Israel
12.Newe Yaar Res Ctr, Agr Res Org, Plant Sci Inst, IL-30095 Ramat Yishai, Israel
13.Cornell Univ, Sch Integrat Plant Sci, Hort Sect, Ithaca, NY 14853 USA
14.USDA ARS, Robert W Holley Ctr Agr & Hlth, Ithaca, NY 14853 USA
15.USDA ARS, US Vegetable Lab, 2700 Savannah Highway, Charleston, SC 29414 USA
16.UAB, CSIC, IRTA, Ctr Res Agr Genom,UB, Barcelona 08193, Spain
17.Inst Recerca & Tecnol Agroalimentaries, Barcelona 08193, Spain
18.Michigan State Univ, Dept Hort, E Lansing, MI 48824 USA
期刊名称：NUCLEIC ACIDS RESEARCH （ 影响因子：16.971； 五年影响因子：15.542 ）
ISSN： 0305-1048
年卷期： 2019 年 47 卷 D1 期
页码：
收录情况： SCI
摘要： 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.
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