文献类型： 外文期刊

作者： Yu, Jingyin ¹ ; Wu, Shan ¹ ; Sun, Honghe ¹ ; Wang, Xin ³ ; Tang, Xuemei ¹ ; Guo, Shaogui ⁴ ; Zhang, Zhonghua ⁵ ; Huang, Sanwen ⁶ ; Xu, Yong ⁴ ; Weng, Yiqun ⁷ ; Mazourek, Michael ⁹ ; McGregor, Cecilia ¹⁰ ; Renner, Susanne S. ¹¹ ; Branham, Sandra ¹³ ; Kousik, Chandrasekar ¹⁴ ; Wechter, W. Patrick ¹⁴ ; Levi, Amnon ¹⁴ ; Grumet, Rebecca ¹⁵ ; Zheng, Yi ¹⁶ ; Fei, Zhangjun ¹ ;

作者机构： 1.Boyce Thompson Inst Plant Res, Ithaca, NY 14853 USA

2.Cornell Univ, Sch Integrat Plant Sci, Plant Biol Sect, Ithaca, NY 14853 USA

3.Huazhong Agr Univ, Coll Hort & Forestry Sci, Wuhan 430070, Peoples R China

4.Beijing Acad Agr & Forestry Sci, Natl Watermelon & Melon Improvement Ctr, Key Lab Biol & Genet Improvement Hort Crops North, Beijing Key Lab Vegetable Germplasm Improvement, Beijing 100097, Peoples R China

5.Qingdao Agr Univ, Coll Hort, Engn Lab Genet Improvement Hort Crops Shandong Pr, Qingdao 266109, Peoples R China

6.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Minist Agr, Genome Anal Lab, Shenzhen 518124, Guangdong, Peoples R China

7.ARS, USDA, Vegetable Crops Res Unit, Madison, WI 53706 USA

8.Univ Wisconsin, Dept Hort, 1575 Linden Dr, Madison, WI 53706 USA

9.Cornell Univ, Sch Integrat Plant Sci, Plant Breeding & Genet Sect, Ithaca, NY 14853 USA

10.Univ Georgia, Dept Hort, Athens, GA 30602 USA

11.Univ Munich LMU, Fac Biol Systemat Bot & Mycol, D-80638 Munich, Germany

12.Washington Univ, Dept Biol, Campus Box 1137, St Louis, MO 63130 USA

13.Clemson Univ, Coastal Res & Educ Ctr, Charleston, SC 29414 USA

14.Michigan State Univ, Dept Hort, 2700 Savannah Highway, Charleston, SC 29414 USA

15.Michigan State Univ, Dept Hort, E Lansing, MI 48824 USA

16.Beijing Univ Agr, Coll Plant Sci & Technol, Beijing Key Lab Agr Applicat & New Tech, Beijing 102206, Peoples R China

17.Beijing Univ Agr, Bioinformat Ctr, Beijing 102206, Peoples R China

18.ARS, USDA, Robert W Holley Ctr Agr & Hlth, Ithaca, NY 14853 USA

期刊名称：NUCLEIC ACIDS RESEARCH （ 影响因子：19.16； 五年影响因子：17.21 ）

ISSN： 0305-1048

年卷期：

页码：

收录情况： SCI

摘要： The Cucurbitaceae (cucurbit) family consists of about 1,000 species in 95 genera, including many economically important and popular fruit and vegetable crops. During the past several years, reference genomes have been generated for >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 34 reference genomes from 27 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 implemented 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 34 genomes, representing a total of 595 pair-wise genome comparisons, have been identified and can be explored and visualized in the database.