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BMC Genomics. 2019 Dec 24;20(Suppl 9):958. doi: 10.1186/s12864-019-6356-z.

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

Zhang X1,2, Pan BZ1,3, Chen M1,3, Chen W1, Li J1,3, Xu ZF4,5, Liu C6.

Author information

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, Menglun, Mengla, Yunnan, 666303, China.
2
College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
3
Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China.
4
CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China. zfxu@xtbg.ac.cn.
5
Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China. zfxu@xtbg.ac.cn.
6
CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China. liuchangning@xtbg.ac.cn.

Abstract

BACKGROUND:

Jatropha curcas is an oil-bearing plant, and has seeds with high oil content (~‚ÄČ40%). 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.

KEYWORDS:

Database; Functional genomics; Jatropha curcas; Woody energy plant

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