JCDB: a comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants

BMC Genomics

Changning Liu¹  Wen Chen¹  Bang-Zhen Pan²  Jing Li²  Maosheng Chen²  Zeng-Fu Xu²  Xuan Zhang³ 

[1] CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 666303, Yunnan, Menglun, Mengla, China;CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 666303, Yunnan, Menglun, Mengla, China;Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, 666303, Yunnan, Menglun, Mengla, China;CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 666303, Yunnan, Menglun, Mengla, China;College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China;

关键词: Jatropha curcas;    Woody energy plant;    Functional genomics;    Database;   

DOI  :  10.1186/s12864-019-6356-z

来源: Springer

【 摘 要 】

BackgroundJatropha curcas is an oil-bearing plant, and has seeds with high oil content (~ 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.ResultsBy 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.ConclusionsJCDB 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.liu-lab.com/.

【 授权许可】

CC BY