CuGenDBv2: an updated database for cucurbit genomics Article Swipe
Jingyin Yu
,
Shan Wu
,
Honghe Sun
,
Xin Wang
,
Xuemei Tang
,
Shaogui Guo
,
Zhonghua Zhang
,
Sanwen Huang
,
Yong Xu
,
Yiqun Weng
,
Michael Mazourek
,
Cecilia McGregor
,
Susanne S. Renner
,
Sandra E. Branham
,
Chandrasekar S. Kousik
,
Patrick Wechter
,
Amnon Levi
,
Rebecca Grumet
,
Yi Zheng
,
Zhangjun Fei
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkac921
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkac921
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.
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Metadata
- Type
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- en
- Landing Page
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- OA Status
- gold
- Cited By
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- References
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- Related Works
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- OpenAlex ID
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All OpenAlex metadata
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https://openalex.org/W4307091543Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1093/nar/gkac921Digital Object Identifier
- Title
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CuGenDBv2: an updated database for cucurbit genomicsWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2022Year of publication
- Publication date
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2022-10-22Full publication date if available
- Authors
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Jingyin Yu, Shan Wu, Honghe Sun, Xin Wang, Xuemei Tang, Shaogui Guo, Zhonghua Zhang, Sanwen Huang, Yong Xu, Yiqun Weng, Michael Mazourek, Cecilia McGregor, Susanne S. Renner, Sandra E. Branham, Chandrasekar S. Kousik, Patrick Wechter, Amnon Levi, Rebecca Grumet, Yi Zheng, Zhangjun FeiList of authors in order
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https://doi.org/10.1093/nar/gkac921Publisher landing page
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https://academic.oup.com/nar/article-pdf/51/D1/D1457/48441438/gkac921.pdfDirect link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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Biology, Genomics, Database, Computational biology, Genetics, Genome, Gene, Computer scienceTop concepts (fields/topics) attached by OpenAlex
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107Total citation count in OpenAlex
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2025: 36, 2024: 45, 2023: 25Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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