JCDB (Jatropha curcas DataBase) is an integrated database to provide a comprehensive resource of Jatropha curcas, which include general gene information, gene functional annotation, gene expression and gene network information. In addition, JCDB also provided the tools for browsing, searching and download against all data, as well as online BLAST service, JBrowse genome browser and JTools to help the users more efficiently using JCDB. JCDB is publicly available and we believe that it will offer an important platform for further study on Jatropha curcas.

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All the public transcritpome datasets are collected from NCBI SRA dataset. The deadline for data collection was Jun. 15th, 2017.

SRR Abbreviation Tissue Condition PMID
0 SRR1251567 C2hR-1 Root Control 2 hour root 1 [1]
1 SRR1251568 C2hL-1 Leaf Control 2 hour leaf 1 [1]
2 SRR1251569 C2dR-1 Root Control 2 day root 1 [1]
3 SRR1251570 C2dL-1 Leaf Control 2 day leaf 1 [1]
4 SRR1251571 C7dR-1 Root Control 7 day root 1 [1]
5 SRR1251572 C7dL-1 Leaf Control 7 day leaf 1 [1]
6 SRR1251957 S2hR-1 Root Salt 2 hour root 1 [1]
7 SRR1251958 S2hL-1 Leaf Salt 2 hour leaf 1 [1]
8 SRR1251959 S2dR-1 Root Salt 2 day root 1 [1]
9 SRR1251960 S2dL-1 Leaf Salt 2 day leaf 1 [1]
10 SRR1251961 S7dR-1 Root Salt 7 day root 1 [1]
11 SRR1251962 S7dL-1 Leaf Salt 7 day leaf 1 [1]
12 SRR1251963 C2hL-2 Leaf Control 2 hour leaf 2 [1]
13 SRR1251964 C2hR-2 Root Control 2 hour root 2 [1]
14 SRR1251965 C2dL-2 Leaf Control 2 day leaf 2 [1]
15 SRR1251966 C2dR-2 Root Control 2 day root 2 [1]
16 SRR1251967 C7dL-2 Leaf Control 7 day leaf 2 [1]
17 SRR1251968 C7dR-2 Root Control 7 day root 2 [1]
18 SRR1251969 S2hL-2 Leaf Salt 2 hour leaf 2 [1]
19 SRR1251970 S2hR-2 Root Salt 2 hour root 2 [1]
20 SRR1251971 S2dL-2 Leaf Salt 2 day leaf 2 [1]
21 SRR1251972 S2dR-2 Root Salt 2 day root 2 [1]
22 SRR1251973 S7dL-2 Leaf Salt 7 day leaf 2 [1]
23 SRR1251974 S7dR-2 Root Salt 7 day root 2 [1]
24 SRR1275402 GSM1382421 roots Whole roots, 24 h nonstress [2]
25 SRR1275403 GSM1382422 roots Whole roots, 24 h nonstress [2]
26 SRR1275404 GSM1382423 roots Whole roots, 24 h waterlogging stress [2]
27 SRR1275405 GSM1382424 roots Whole roots, 24 h waterlogging stress [2]
28 SRR1542235 C1dR-1 Root Control 1 day root 1 [3]
29 SRR1542239 C4dR-1 Root Control 4 day root 1 [3]
30 SRR1542240 C7dR-11 Root Control 7 day root 1 [3]
31 SRR1542241 C1dL-1 Leaf Control 1 day leaf 1 [3]
32 SRR1542242 C4dL-1 Leaf Control 4 day leaf 1 [3]
33 SRR1542243 C7dL-11 Leaf Control 7 day leaf 1 [3]
34 SRR1542244 D1dR-1 Root Drought 1 day root 1 [3]
35 SRR1542245 D4dR-1 Root Drought 4 day root 1 [3]
36 SRR1542246 D7dR-1 Root Drought 7 day root 1 [3]
37 SRR1542247 D1dL-1 Leaf Drought 1 day leaf 1 [3]
38 SRR1542248 D4dL-1 Leaf Drought 4 day leaf 1 [3]
39 SRR1542249 D7dL-1 Leaf Drought 7 day leaf 1 [3]
40 SRR1542250 C1dR-2 Root Control 1 day root 2 [3]
41 SRR1542251 C4dR-2 Root Control 4 day root 2 [3]
42 SRR1542252 C7dR-21 Root Control 7 day root 2 [3]
43 SRR1542253 C1dL-2 Leaf Control 1 day leaf 2 [3]
44 SRR1542254 C4dL-2 Leaf Control 4 day leaf 2 [3]
45 SRR1542255 C7dR-21 Root Control 7 day root 2 [3]
46 SRR1542256 D1dR-2 Root Drought 1 day root 2 [3]
47 SRR1542257 D4dR-2 Root Drought 4 day root 2 [3]
48 SRR1542258 D7dR-2 Root Drought 7 day root 2 [3]
49 SRR1542259 D1dL-2 Leaf Drought 1 day leaf 2 [3]
50 SRR1542260 D4dL-2 Leaf Drought 4 day leaf 2 [3]
51 SRR1542261 D7dL-2 Leaf Drought 7 day leaf 2 [3]
52 SRR1539206 A_9-1_Control [4]
53 SRR1560722 C_ RJ127_control [4]
54 SRR1560723 D_ RJ127_CG induced [4]
55 SRR1560724 B_9-1_Cg induced [4]
56 SRR1565783 GSM1496861 Leaf 0d_leaf_control_ind_br1 [5]
57 SRR1565784 GSM1496862 Leaf 0d_leaf_control_cvi_br2 [5]
58 SRR1565785 GSM1496863 Leaf 13d_leaf_control_ind_br1 [5]
59 SRR1565786 GSM1496864 Leaf 13d_leaf_control_cvi_br2 [5]
60 SRR1565787 GSM1496865 Leaf 13d_leaf_stress_ind_br1 [5]
61 SRR1565788 GSM1496866 Leaf 13d_leaf_stress_cvi_br2 [5]
62 SRR1565789 GSM1496867 Root 13d_root_control_ind_br1 [5]
63 SRR1565790 GSM1496868 Root 13d_root_control_cvi_br2 [5]
64 SRR1565791 GSM1496869 Root 13d_root_stress_ind_br1 [5]
65 SRR1565792 GSM1496870 Root 13d_root_stress_cvi_br2 [5]
66 SRR1565793 GSM1496871 Leaf 49d_leaf_stress_ind_br1 [5]
67 SRR1565794 GSM1496872 Leaf 49d_leaf_stress_cvi_br2 [5]
68 SRR1565795 GSM1496873 Root 49d_root_stress_ind_br1 [5]
69 SRR1565796 GSM1496874 Root 49d_root_stress_cvi_br2 [5]
70 SRR1565797 GSM1496875 Leaf 49-52d_leaf_control_ind_br1 [5]
71 SRR1565798 GSM1496876 Leaf 49-52d_leaf_control_cvi_br2 [5]
72 SRR1565799 GSM1496877 Root 49-52d_root_control_ind_br1 [5]
73 SRR1565800 GSM1496878 Root 49-52d_root_control_cvi_br2 [5]
74 SRR1565801 GSM1496879 Leaf 52d_leaf_stress_ind_br1 [5]
75 SRR1565802 GSM1496880 Leaf 52d_leaf_stress_cvi_br2 [5]
76 SRR1565803 GSM1496881 Root 52d_root_stress_ind_br1 [5]
77 SRR1565804 GSM1496882 Root 52d_root_stress_cvi_br2 [5]
78 SRR1596307 C2 stem tissue Mock-2 [6]
79 SRR1596308 C1 stem tissue Mock-1 [6]
80 SRR1596309 C3 stem tissue Mock-3 [6]
81 SRR1596310 G1 stem tissue GA3-1 [6]
82 SRR1596311 G2 stem tissue GA3-2 [6]
83 SRR1596312 G3 stem tissue GA3-3 [6]
84 SRR1596313 B1 stem tissue BA-1 [6]
85 SRR1596314 B2 stem tissue BA-2 [6]
86 SRR1596315 B3 stem tissue BA-3 [6]
87 SRR1639661 [7]
88 SRR1663442 inflorescence meristems before treatment [8]
89 SRR1663443 inflorescence meristems treated with cytokinin 2hrs [8]
90 SRR1663444 inflorescence meristems treated with cytokinin 2hrs, waited for 4hrs [8]
91 SRR1663445 inflorescence meristems treated with cytokinin 2hrs, waited for 22hrs [8]
92 SRR1712654 Seed 14 DAP [9]
93 SRR1712657 Seed 19 DAP [9]
94 SRR1712659 Seed 25 DAP [9]
95 SRR1712661 Seed 29 DAP [9]
96 SRR1712663 Seed 35 DAP [9]
97 SRR1712665 Seed 41 DAP [9]
98 SRR1712666 Seed 45 DAP [9]
99 SRR2039597 Mixed flower buds [10]
100 SRR653198 seedlings cold: 12, 24, and 48 h [11]
101 private data O1YL our unpublished data
102 private data O2YL our unpublished data
103 private data O3YL our unpublished data
104 private data O1SA our unpublished data
105 private data O2SA our unpublished data
106 private data O3SA our unpublished data
107 private data O3SAA_l1 our unpublished data
108 private data D1SA our unpublished data
109 private data D2SA our unpublished data
110 private data D3SA our unpublished data
111 private data D1YL our unpublished data
112 private data D2YL our unpublished data
113 private data D3YL our unpublished data

[1] Zhang, C., Zhang, L., Zhang, S., Zhu, S., Wu, P., Chen, Y., et al. (2015) Global analysis of gene expression profiles in physic nut (Jatropha curcas L.) seedlings exposed to drought stress. BMC Plant Biol 15: 17.

[2] Juntawong, P., Sirikhachornkit, A., Pimjan, R., Sonthirod, C., Sangsrakru, D., Yoocha, T., et al. (2014) Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling. Front Plant Sci 5: 658.

[3] Zhang, C., Zhang, L., Zhang, S., Zhu, S., Wu, P., Chen, Y., et al. (2015) Global analysis of gene expression profiles in physic nut (Jatropha curcas L.) seedlings exposed to drought stress. BMC Plant Biol 15: 17.

[4] https://www.ncbi.nlm.nih.gov/bioproject/PRJNA254929

[5] Sapeta, H., Lourenco, T., Lorenz, S., Grumaz, C., Kirstahler, P., Barros, P.M., et al. (2016) Transcriptomics and physiological analyses reveal co-ordinated alteration of metabolic pathways in Jatropha curcas drought tolerance. J Exp Bot 67: 845-860.

[6] Ni, J., Gao, C., Chen, M.S., Pan, B.Z., Ye, K. and Xu, Z.F. (2015) Gibberellin Promotes Shoot Branching in the Perennial Woody Plant Jatropha curcas. Plant Cell Physiol 56: 1655-1666.

[7] https://www.ncbi.nlm.nih.gov/biosample/SAMN03160711

[8] Pan, B.Z., Chen, M.S., Ni, J. and Xu, Z.F. (2014) Transcriptome of the inflorescence meristems of the biofuel plant Jatropha curcas treated with cytokinin. BMC Genomics 15: 974.

[9] Jiang, H., Wu, P., Zhang, S., Song, C., Chen, Y., Li, M., et al. (2012) Global analysis of gene expression profiles in developing physic nut (Jatropha curcas L.) seeds. PLoS One 7: e36522.

[10] Xu, G., Huang, J., Yang, Y. and Yao, Y.A. (2016) Transcriptome Analysis of Flower Sex Differentiation in Jatropha curcas L. Using RNA Sequencing. PLoS One 11: e0145613.

[11] Wang, H., Zou, Z., Wang, S. and Gong, M. (2013) Global analysis of transcriptome responses and gene expression profiles to cold stress of Jatropha curcas L. PLoS One 8: e82817.

(a) Novel gene discovery pipeline. (b) Coding and non-coding gene annotation pipeline. (c) Gene co-expression and PPI (protein-protein interaction) network construction pipeline.

JCDB's gene network include two parts: protein interaction network and gene co-expression network. The protein interaction network was constructed based on the inference of ortholog-based protein-protein interactions from Arabidopsis thaliana protein interactions by using InParanoid with the default settings. The gene co-expression network was constructed on the basis of the Jatroph curcas transcritpome datasets in JCDB by using the Spearman's rank correlation coefficient for calculating the correlation of each gene pair across the samples (cutoff: correlation_value>0.6 & top100).

JCDB's BLAST service is based on the ViroBLAST standalone package , which is developed by the Mullins Lab at the University of Washington. For more details about BLAST programs and parameters, please visit here.

JCDB's genome browser service is based on the JBrowse, which is a fast and embeddable genome browser built completely with JavaScript and HTML5 (http://jbrowse.org/). For more details about Jbrowse, please visit here: https://youtu.be/NE8TBTbvDfM (JBrowse Overview Screencast).

For all JCDB genes, we first filtered out some very-low-variance ones (filter_sd=0.01), and then checked whether their co-expression profiles with other genes are significant enough (method: Spearman's rank correlation coefficient; adjusted P-value< 0.01). So, not all genes have their co-expression matrixs/heatmaps.