{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T07:03:04Z","timestamp":1776063784396,"version":"3.50.1"},"reference-count":56,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,10,22]],"date-time":"2022-10-22T00:00:00Z","timestamp":1666396800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["2015-51181-24285"],"award-info":[{"award-number":["2015-51181-24285"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["2020-51181-32139"],"award-info":[{"award-number":["2020-51181-32139"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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 &amp;gt;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 \u2018Genotype\u2019 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 \u2018Expression\u2019 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.<\/jats:p>","DOI":"10.1093\/nar\/gkac921","type":"journal-article","created":{"date-parts":[[2022,10,22]],"date-time":"2022-10-22T09:57:47Z","timestamp":1666432667000},"page":"D1457-D1464","source":"Crossref","is-referenced-by-count":122,"title":["CuGenDBv2: an updated database for cucurbit genomics"],"prefix":"10.1093","volume":"51","author":[{"given":"Jingyin","family":"Yu","sequence":"first","affiliation":[{"name":"Boyce Thompson Institute , Ithaca , NY 14853 , USA"}]},{"given":"Shan","family":"Wu","sequence":"additional","affiliation":[{"name":"Boyce Thompson Institute , Ithaca , NY 14853 , USA"}]},{"given":"Honghe","family":"Sun","sequence":"additional","affiliation":[{"name":"Boyce Thompson Institute , Ithaca , NY 14853 , USA"},{"name":"Plant Biology Section, School of Integrative Plant Science, Cornell University , Ithaca , NY 14853 , USA"}]},{"given":"Xin","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Horticulture and Forestry Sciences, Huazhong Agricultural University , Wuhan 430070 , China"}]},{"given":"Xuemei","family":"Tang","sequence":"additional","affiliation":[{"name":"Boyce Thompson Institute , Ithaca , NY 14853 , USA"}]},{"given":"Shaogui","family":"Guo","sequence":"additional","affiliation":[{"name":"National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement , Beijing 100097 , China"}]},{"given":"Zhonghua","family":"Zhang","sequence":"additional","affiliation":[{"name":"Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University , Qingdao 266109 , China"}]},{"given":"Sanwen","family":"Huang","sequence":"additional","affiliation":[{"name":"Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen , Guangdong 518124 , China"}]},{"given":"Yong","family":"Xu","sequence":"additional","affiliation":[{"name":"National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement , Beijing 100097 , China"}]},{"given":"Yiqun","family":"Weng","sequence":"additional","affiliation":[{"name":"U.S. Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit , Madison , WI 53706 , USA"},{"name":"Department of Horticulture, University of Wisconsin , Madison , WI 53706 , USA"}]},{"given":"Michael","family":"Mazourek","sequence":"additional","affiliation":[{"name":"Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University , Ithaca , NY 14853 , USA"}]},{"given":"Cecilia","family":"McGregor","sequence":"additional","affiliation":[{"name":"Department of Horticulture, University of Georgia , Athens , GA 30602 , USA"}]},{"given":"Susanne S","family":"Renner","sequence":"additional","affiliation":[{"name":"Faculty of Biology, Systematic Botany and Mycology, University of Munich (LMU) , 80638 Munich , Germany"},{"name":"Department of Biology, Washington University , Saint Louis , MO 63130 , USA"}]},{"given":"Sandra","family":"Branham","sequence":"additional","affiliation":[{"name":"Coastal Research and Educational Center, Clemson University , Charleston , SC 29414 , USA"}]},{"given":"Chandrasekar","family":"Kousik","sequence":"additional","affiliation":[{"name":"U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory , 2700 Savannah Highway , Charleston , SC 29414 , USA"}]},{"given":"W\u00a0Patrick","family":"Wechter","sequence":"additional","affiliation":[{"name":"U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory , 2700 Savannah Highway , Charleston , SC 29414 , USA"}]},{"given":"Amnon","family":"Levi","sequence":"additional","affiliation":[{"name":"U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory , 2700 Savannah Highway , Charleston , SC 29414 , USA"}]},{"given":"Rebecca","family":"Grumet","sequence":"additional","affiliation":[{"name":"Department of Horticulture, Michigan State University , East Lansing , MI 48824 , USA"}]},{"given":"Yi","family":"Zheng","sequence":"additional","affiliation":[{"name":"Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture , Beijing 102206,\u00a0 China"},{"name":"Bioinformatics Center, Beijing University of Agriculture , Beijing 102206,\u00a0 China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9684-1450","authenticated-orcid":false,"given":"Zhangjun","family":"Fei","sequence":"additional","affiliation":[{"name":"Boyce Thompson Institute , Ithaca , NY 14853 , USA"},{"name":"U.S. Department of Agriculture-Agricultural Research Service, Robert W. 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