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. Download this table (xlsx format)

SRR Tissue Description Reference
0 SRR1251567 Root Root sample 1 which was collected at 2 hours after the start of the mock treatment [1]
1 SRR1251568 Leaf Leaf sample 1 which was collected at 2 hours after the start of the mock treatment [1]
2 SRR1251569 Root Root sample 1 which was collected at 2 days after the start of the mock treatment [1]
3 SRR1251570 Leaf Leaf sample 1 which was collected at 2 days after the start of the mock treatment [1]
4 SRR1251571 Root Root sample 1 which was collected at 7 days after the start of the mock treatment [1]
5 SRR1251572 Leaf Leaf sample 1 which was collected at 7 days after the start of the mock treatment [1]
6 SRR1251957 Root Root sample 1 which was collected at 2 hours after the start of the salt treatment [1]
7 SRR1251958 Leaf Leaf sample 1 which was collected at 2 hours after the start of the salt treatment [1]
8 SRR1251959 Root Root sample 1 which was collected at 2 days after the start of the salt treatment [1]
9 SRR1251960 Leaf Leaf sample 1 which was collected at 2 days after the start of the salt treatment [1]
10 SRR1251961 Root Root sample 1 which was collected at 7 days after the start of the salt treatment [1]
11 SRR1251962 Leaf Leaf sample 1 which was collected at 7 days after the start of the salt treatment [1]
12 SRR1251963 Leaf Leaf sample 2 which was collected at 2 hours after the start of the mock treatment [1]
13 SRR1251964 Root Root sample 2 which was collected at 2 hours after the start of the mock treatment [1]
14 SRR1251965 Leaf Leaf sample 2 which was collected at 2 days after the start of the mock treatment [1]
15 SRR1251966 Root Root sample 2 which was collected at 2 days after the start of the mock treatment [1]
16 SRR1251967 Leaf Leaf sample 2 which was collected at 7 days after the start of the mock treatment [1]
17 SRR1251968 Root Root sample 2 which was collected at 7 days after the start of the mock treatment [1]
18 SRR1251969 Leaf Leaf sample 2 which was collected at 2 hours after the start of the salt treatment [1]
19 SRR1251970 Root Root sample 2 which was collected at 2 hours after the start of the salt treatment [1]
20 SRR1251971 Leaf Leaf sample 2 which was collected at 2 days after the start of the salt treatment [1]
21 SRR1251972 Root Root sample 2 which was collected at 2 days after the start of the salt treatment [1]
22 SRR1251973 Leaf Leaf sample 2 which was collected at 7 days after the start of the salt treatment [1]
23 SRR1251974 Root Root sample 2 which was collected at 7 days after the start of the salttreatment [1]
24 SRR1275402 roots Whole roots were collected at 24 hours after the start of the mock treatment [2]
25 SRR1275403 roots Whole roots were collected at 24 hours after the start of the mock treatment [2]
26 SRR1275404 roots Whole roots were collected at 24 hours after the start of the waterlogging stress treatment [2]
27 SRR1275405 roots Whole roots were collected at 24 hours after the start of the waterlogging stress treatment [2]
28 SRR1542235 Root Whole roots were collected at 24 hours after the start of the waterlogging stress treatment [3]
29 SRR1542239 Root Root sample 1 which was collected at 4 days after the seedlings were irrigated daily with Hoagland nutrient solution [3]
30 SRR1542240 Root Root sample 1 which was collected at 7 days after the seedlings were irrigated daily with Hoagland nutrient solution [3]
31 SRR1542241 Leaf Leaf sample 1 which was collected at 1 days after the seedlings were irrigated daily with Hoagland nutrient solution [3]
32 SRR1542242 Leaf Leaf sample 1 which was collected at 4 days after the seedlings were irrigated daily with Hoagland nutrient solution [3]
33 SRR1542243 Leaf Leaf sample 1 which was collected at 7 days after the seedlings were irrigated daily with Hoagland nutrient solution [3]
34 SRR1542244 Root Root sample 1 which was collected at 1 days after the seedlings were unirrigated with Hoagland nutrient solution [3]
35 SRR1542245 Root Root sample 1 which was collected at 4 days after the seedlings were unirrigated with Hoagland nutrient solution [3]
36 SRR1542246 Root Root sample 1 which was collected at 7 days after the seedlings were unirrigated with Hoagland nutrient solution [3]
37 SRR1542247 Leaf Leaf sample 1 which was collected at 1 days after the seedlings were unirrigated with Hoagland nutrient solution [3]
38 SRR1542248 Leaf Leaf sample 1 which was collected at 4 days after the seedlings were unirrigated with Hoagland nutrient solution [3]
39 SRR1542249 Leaf Leaf sample 1 which was collected at 7 days after the seedlings were unirrigated with Hoagland nutrient solution [3]
40 SRR1542250 Root Root sample 2 which was collected at 1 days after the seedlings were irrigated daily with Hoagland nutrient solution [3]
41 SRR1542251 Root Root sample 2 which was collected at 4 days after the seedlings were irrigated daily with Hoagland nutrient solution [3]
42 SRR1542252 Root Root sample 2 which was collected at 7 days after the seedlings were irrigated daily with Hoagland nutrient solution [3]
43 SRR1542253 Leaf Leaf sample 2 which was collected at 1 days after the seedlings were irrigated daily with Hoagland nutrient solution [3]
44 SRR1542254 Leaf Leaf sample 2 which was collected at 4 days after the seedlings were irrigated daily with Hoagland nutrient solution [3]
45 SRR1542255 Root Leaf sample 2 which was collected at 7 days after the seedlings were irrigated daily with Hoagland nutrient solution [3]
46 SRR1542256 Root Root sample 2 which was collected at 1 days after the seedlings were unirrigated with Hoagland nutrient solution [3]
47 SRR1542257 Root Root sample 2 which was collected at 4 days after the seedlings were unirrigated with Hoagland nutrient solution [3]
48 SRR1542258 Root Root sample 2 which was collected at 7 days after the seedlings were unirrigated with Hoagland nutrient solution [3]
49 SRR1542259 Leaf Leaf sample 2 which was collected at 1 days after the seedlings were unirrigated with Hoagland nutrient solution [3]
50 SRR1542260 Leaf Leaf sample 2 which was collected at 4 days after the seedlings were unirrigated with Hoagland nutrient solution [3]
51 SRR1542261 Leaf Leaf sample 2 which was collected at 7 days after the seedlings were unirrigated with Hoagland nutrient solution [3]
52 SRR1539206 Leaf Jatropha genotypes 9-1 showing tolerance to Colletotrichum gloeosporioides were uninfected with pure isolate of Colletotrichum gloeosporioides.The uninfected tissue of tolerant line collected after 2, 24, 96 and 144 hours of infection were pooled as A_9-1_Control. [4]
53 SRR1560722 Leaf Jatropha genotypes RJ127 showing Colletotrichum gloeosporioides susceptible were uninfected with pure isolate of Colletotrichum gloeosporioides.The uninfected tissue of susceptible line collected after 2, 24, 96 and 144 hours of infection were pooled as C_ RJ127_control. [4]
54 SRR1560723 Leaf Jatropha genotypes RJ127 showing Colletotrichum gloeosporioides susceptible were infected with pure isolate of Colletotrichum gloeosporioides.The induced tissue of susceptible line collected after 2, 24, 96 and 144 hours of infection were pooled as C_ RJ127_control. [4]
55 SRR1560724 Leaf Jatropha genotypes 9-1 showing tolerance to Colletotrichum gloeosporioides were artificially infected with pure isolate of Colletotrichum gloeosporioides.The induced tissue of tolerant line collected after 2, 24, 96 and 144 hours of infection were pooled as B_9-1_Cg induced. [4]
56 SRR1565783 Leaf Leaves of Jatropha curcas (ind_br1) under well-watered conditions (Control) were collected at day 0. [5]
57 SRR1565784 Leaf Leaves of Jatropha curcas (cvi_br2) under well-watered conditions (Control) were collected at day 0. [5]
58 SRR1565785 Leaf Leaves of Jatropha curcas (ind_br1) under well-watered conditions (Control) were collected at day 13. [5]
59 SRR1565786 Leaf Leaves of Jatropha curcas (cvi_br2) under well-watered conditions (Control) were collected at day 13. [5]
60 SRR1565787 Leaf Leaves of Jatropha curcas (ind_br1) were collected at moderate drought (day 13). [5]
61 SRR1565788 Leaf Leaves of Jatropha curcas (cvi_br2) were collected at moderate drought (day 13). [5]
62 SRR1565789 Root Roots of Jatropha curcas (ind_br1) under well-watered conditions (Control) were collected at day 13. [5]
63 SRR1565790 Root Roots of Jatropha curcas (cvi_br2) under well-watered conditions (Control) were collected at day 13. [5]
64 SRR1565791 Root Roots of Jatropha curcas (ind_br1) were collected at moderate drought (day 13). [5]
65 SRR1565792 Root Roots of Jatropha curcas (cvi_br2) were collected at moderate drought (day 13). [5]
66 SRR1565793 Leaf Leaves of Jatropha curcas (ind_br1) were collected at maximum stress (day 49). [5]
67 SRR1565794 Leaf Leaves of Jatropha curcas (cvi_br2) were collected at maximum stress (day 49). [5]
68 SRR1565795 Root Roots of Jatropha curcas (ind_br1) were collected at maximum stress (day 49). [5]
69 SRR1565796 Root Roots of Jatropha curcas (cvi_br2) were collected at maximum stress (day 49). [5]
70 SRR1565797 Leaf Leaves of Jatropha curcas (ind_br1) under well-watered conditions (Control) were collected at day 49-52. [5]
71 SRR1565798 Leaf Leaves of Jatropha curcas (cvi_br2) under well-watered conditions (Control) ere collected at day 49-52. [5]
72 SRR1565799 Root Roots of Jatropha curcas (ind_br1) under well-watered conditions (Control) were collected at day 49-52. [5]
73 SRR1565800 Root Roots of Jatropha curcas (cvi_br2) under well-watered conditions (Control) were collected at day 49-52. [5]
74 SRR1565801 Leaf Leaves of Jatropha curcas (ind_br1) were collected at day 52 (rewatering). [5]
75 SRR1565802 Leaf Leaves of Jatropha curcas (cvi_br2) were collected at day 52 (rewatering) 0. [5]
76 SRR1565803 Root Roots of Jatropha curcas (ind_br1) were collected at day 52 (rewatering). [5]
77 SRR1565804 Root Roots of Jatropha curcas (cvi_br2) were collected at day 52 (rewatering). [5]
78 SRR1596307 stem tissue The nodal stem at node 1 was collected after 24 hours of mock treatment as sample C1. [6]
79 SRR1596308 stem tissue The nodal stem at node 1 was collected after 24 hours of mock treatment as sample C2. [6]
80 SRR1596309 stem tissue The nodal stem at node 1 was collected after 24 hours of mock treatment as sample C3. [6]
81 SRR1596310 stem tissue The nodal stem at node 1 was collected after 24 hours of GA3 treatment as sample G1. [6]
82 SRR1596311 stem tissue The nodal stem at node 1 was collected after 24 hours of GA3 treatment as sample G2. [6]
83 SRR1596312 stem tissue The nodal stem at node 1 was collected after 24 hours of GA3 treatment as sample G3. [6]
84 SRR1596313 stem tissue The nodal stem at node 1 was collected after 24 hours of BA treatment as sample B1. [6]
85 SRR1596314 stem tissue The nodal stem at node 1 was collected after 24 hours of BA treatment as sample B2. [6]
86 SRR1596315 stem tissue The nodal stem at node 1 was collected after 24 hours of BA treatment as sample B3. [6]
87 SRR1639661 seed [7]
88 SRR1663442 inflorescence meristems Inflorescence meristems were collected before BA treatment. [8]
89 SRR1663443 inflorescence meristems Inflorescence meristems were collected with 2 hours BA treatment. [8]
90 SRR1663444 inflorescence meristems Inflorescence meristems were collected 4 hours after 2 hours BA treatment. [8]
91 SRR1663445 inflorescence meristems Inflorescence meristems were collected 22 hours after 2 hours BA treatment. [8]
92 SRR1712654 Seed Seeds were collected 14 days after pollination. [9]
93 SRR1712657 Seed Seeds were collected 19 days after pollination. [9]
94 SRR1712659 Seed Seeds were collected 25 days after pollination. [9]
95 SRR1712661 Seed Seeds were collected 29 days after pollination. [9]
96 SRR1712663 Seed Seeds were collected 35 days after pollination. [9]
97 SRR1712665 Seed Seeds were collected 41 days after pollination. [9]
98 SRR1712666 Seed Seeds were collected 45 days after pollination. [9]
99 SRR2039597 Mixed flower buds Flower buds of six development phases were mixed as a pool sample. [10]
100 SRR653198 seedlings Leaves from the control and three cold-treated (chilling at 12°C for 12, 24,and 48 h, respectively) Jatropha curcas seedlings were mixed as a pool sample. [11]
101 O1YL (unreleased data) Young leaf Young leave sample 1 of octoploid Jatropha curcas. [12]
102 O2YL (unreleased data) Young leaf Young leave sample 2 of octoploid Jatropha curcas. [12]
103 O3YL (unreleased data) Young leaf Young leave sample 3 of octoploid Jatropha curcas. [12]
104 O1SA (unreleased data) Shoot apex Shoot apex sample 1 of octoploid Jatropha curcas. [12]
105 O2SA (unreleased data) Shoot apex Shoot apex sample 2 of octoploid Jatropha curcas. [12]
106 O3SA (unreleased data) Shoot apex Shoot apex sample 3 of octoploid Jatropha curcas. [12]
107 O3SAA_l1 (unreleased data) Seedling shoot apex Seedling shoot apex of octoploid Jatropha curcas. [12]
108 D1SA (unreleased data) Shoot apex Shoot apex sample 1 of diploid Jatropha curcas. [12]
109 D2SA (unreleased data) Shoot apex Shoot apex sample 2 of diploid Jatropha curcas. [12]
110 D3SA (unreleased data) Shoot apex Shoot apex sample 3 of diploid Jatropha curcas. [12]
111 D1YL (unreleased data) Young leaf Young leave sample 1 of diploid Jatropha curcas. [12]
112 D2YL (unreleased data) Young leaf Young leave sample 2 of diploid Jatropha curcas. [12]
113 D3YL (unreleased data) Young leaf Young leave sample 3 of diploid Jatropha curcas. [12]

[1] Zhang, L., Zhang, C., Wu, P., Chen, Y., Li, M., Jiang, H., & Wu, G. (2014). Global analysis of gene expression profiles in physic nut (Jatropha curcas L.) seedlings exposed to salt stress. PLoS One 9(5), e97878.

[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.

[12] Longjian Niu, Yan-Bin Tao, Mao-Sheng Chen, Qiantang Fu, Yuling Dong, Huiying He & Zeng-Fu Xu (2016) Identification and characterization of tetraploid and octoploid Jatropha curcas induced by colchicine, Caryologia, 69:1, 58-66, DOI: 10.1080/00087114.2015.1110308.

(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.