Welcome to Jatropha curcas Database
Jatropha curcas L. also known as physic nut, is a perennial small tree or large shrub belonging to the family Euphorbiaceae ,which includes some of the most efficient biomass accumulators. With the gradual depletion and cost escalation of fossil energy resources, J. curcas is now attracting much attention as a plant with great potential for biofuel production, because of its unique characteristics like high seed oil content, easy propagation, and adaptation to wide agro-climatic conditions. J. curcas is also a potential model organism for functional genomics analysis, particularly in the Euphorbiaceae. The J. curcas genome has been sequenced by different groups worldwide. For the NCBI's representative genome (from Wu lab) , the assembled genome has a total length of 320.5 Mbp with a scaffold N50 of 0.746 Mbp. In addition, a linkage map containing 1208 markers has also been established, which covered about 80% of the assembled genome.
In recent years, there have emerged a mass of high-throughput transcriptome sequencing of J. curcas. How to availably integrate and analyze these high-throughput data is crucial for further functional genomics research on J. curcas. By establishing pipelines for processing high-throughput transcriptome sequencing data, gene function annotation, gene co-expression profiling and gene network construction, we systematically integrated and analyzed a series of J. curcas transcriptome data from SRA database. Based on all these data, we constructed the Jatropha curcas DataBase (JCDB) , which is freely accessible to the J. curcas research community. Compared with existing J. curcas databases, such as Jatropha Genome Database from Kazusa DNA Research Institute or NCBI Jatropha curcas Annotation Release, which mainly focused on J. curcas genome sequence and corresponding gene annotations, JCDB has several distinctive features:
a) JCDB is an integrated knowledge database, which include not only basic gene information, but also gene functional annotation, gene expression profiles and gene network information;
b) JCDB provides a user-friendly interface and a convenient search option, allowing efficient recovery of sequence, gene expression matrix, gene network and other information;
c) JCDB also provides the tools which focus on more specific purposes, such as online BLAST service, JBrowse genome browser, and JCDBTools -- a tool suite for genome sequence retrieving, gene ID conversion and gene network construction.
We believe JCDB will provide a valuable resource and also an important platform for further fundamental and applied research on the biofuel plant J. curcas and other related plants.
Browse all genes, transcripts and proteins.
Search keywords and gene network.
Find regions of similarity between your sequences.
- The BLAST database was updated. [03/15/2019]
- The search tools were updated. [01/15/2019]
- The gene co-expression profiles were updated. [12/5/2017]
- The gene network information was added to JCDB. [16/2/2017]
- The JTools online service was added to JCDB. [20/12/2016]
- The JCDB online BLAST service was updated. [9/9/2016]
- The first version of JCDB was publicly released. [23/4/2016]
Please send comments or questions about JCDB to
or call us at
Key Laboratory of Tropical Plant Resources and Sustainable Use,
Xishuangbanna Tropical Botanical Garden,
Chinese Academy of Sciences.
Zhang, X., Li, J., Pan, B.-Z., Chen, W., Chen, M., Tang, M., Xu, Z.-F.*, Liu, C.* (2021) Extended mining of the oil biosynthesis pathway in biofuel plant Jatropha curcas by combined analysis of transcriptome and gene interactome data. BMC Bioinformatics 22 (6): 409. https://doi.org/10.1186/s12859-021-04319-w
Zhang, X., Pan, B.-Z., Chen, M., Chen, W., Li, J., Xu, Z.-F.*, Liu, C.* (2019). JCDB: a comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants. BMC genomics, 20(Suppl 9), 958. https://doi.org/10.1186/s12864-019-6356-z