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JCDB: a comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants
Zhang, Xuan1; Pan, Bang-Zhen; Chen, Maosheng; Chen, Wen; Li, Jing; Xu, Zeng-Fu; Liu, Changning
2019
Source PublicationBMC GENOMICS
ISSN1471-2164
Volume20Issue:xPages:-
Abstract

Background: Jatropha curcas is an oil-bearing plant, and has seeds with high oil content (similar to 40%). Several advantages, such as easy genetic transformation and short generation duration, have led to the emergence of J. curcas as a model for woody energy plants. With the development of high-throughput sequencing, the genome of Jatropha curcas has been sequenced by different groups and a mass of transcriptome data was released. How to integrate and analyze these omics data is crucial for functional genomics research on J. curcas. Results: By establishing pipelines for processing novel gene identification, gene function annotation, and gene network construction, we systematically integrated and analyzed a series of J. curcas transcriptome data. Based on these data, we constructed a J. curcas database (JCDB), which not only includes general gene information, gene functional annotation, gene interaction networks, and gene expression matrices but also provides tools for browsing, searching, and downloading data, as well as online BLAST, the JBrowse genome browser, ID conversion, heatmaps, and gene network analysis tools. Conclusions: JCDB is the most comprehensive and well annotated knowledge base for J. curcas. We believe it will make a valuable contribution to the functional genomics study of J. curcas. The database is accessible at http://jcdb.xtbg.ac.cn.

KeywordJatropha curcas Woody energy plant Functional genomics Database
Subject AreaBiotechnology & Applied Microbiology ; Genetics & Heredity
DOI10.1186/s12864-019-6356-z
Indexed BySCI
Language英语
WOS IDWOS:000505593700011
Citation statistics
Document Type期刊论文
Identifierhttp://ir.xtbg.org.cn/handle/353005/11589
Collection2012年后新成立研究组
Affiliation1.Chinese Acad Sci, Innovat Acad Seed Design, CAS Key Lab Trop Plant Resources & Sustainable Us, Xishuangbanna Trop Bot Garden, Mengla 666303, Yunnan, Peoples R China
2.Univ Chinese Acad Sci, Coll Life Sci, Beijing 100049, Peoples R China
3.Chinese Acad Sci, Ctr Econ Bot, Core Bot Gardens, Mengla 666303, Yunnan, Peoples R China
Recommended Citation
GB/T 7714
Zhang, Xuan,Pan, Bang-Zhen,Chen, Maosheng,et al. JCDB: a comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants[J]. BMC GENOMICS,2019,20(x):-.
APA Zhang, Xuan.,Pan, Bang-Zhen.,Chen, Maosheng.,Chen, Wen.,Li, Jing.,...&Liu, Changning.(2019).JCDB: a comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants.BMC GENOMICS,20(x),-.
MLA Zhang, Xuan,et al."JCDB: a comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants".BMC GENOMICS 20.x(2019):-.
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