Release information
Release 4
In the forth version,circRNAs from 16 organisms Arabidopsis thaliana, Camellia sinensis, Gossypium arboreum, Gossypium hirsutum, Glycine max, Gossypium raimondii, Hordeum vulgare, Nicotiana benthamiana, Oryza sativa, Oryza sativa ssp. indica, Pyrus betulifolia, Poncirus trifoliata, Solanum lycopersicum, Solanum tuberosum, Triticum aestivum, and Zea mays, have been collected by PlantcircBase. Totally, the number of circRNA entries has been increased to 115,171.
Four new species (Camellia sinensis, Nicotiana benthamiana, Oryza sativa ssp. indica, Pyrus betulifolia) have been added to PlantcircBase, and novel circRNAs have been added to five species (Gossypium hirsutum, Glycine max, Solanum lycopersicum, Triticum aestivum, and Zea mays).
Detailed statistic data could be found here.
Release 3
In the third version,circRNAs from 12 organisms Arabidopsis thaliana, Gossypium arboreum, Gossypium hirsutum, Glycine max, Gossypium raimondii, Hordeum vulgare, Oryza sativa, Poncirus trifoliata, Solanum lycopersicum, Solanum tuberosum, Triticum aestivum, and Zea mays, have been collected by PlantcircBase. Totally, the number of circRNA entries has been increased to 95,143.
Release 2
In the second version, apart from the five organisms (Arabidopsis thaliana, Hordeum vulgare, Oryza sativa, Solanum lycopersicum, Zea mays), circRNA information from another three organisms, including Gossypium hirsutum, Glycine max and Triticum aestivum, have been added based on the published papers. Totally, the number of circRNA entries collected by PlantcircBase has been increased to 89,997. Detail statistics were shown in tables as following.
Table 1 The number of circRNAs in PlantcircBase (Release 2)
| Organisms | Number of circRNAs | Full-length sequence of circRNAs | Acting as miRNA sponge* | Networks of circRNA-miRNA-mRNA* | Tissues | References | ||
|---|---|---|---|---|---|---|---|---|
| Total | BS valided* | Total | FL valided* | |||||
| Oryza sativa | 12,037 | 10 | 0 | 0 | 405 | 251 | Roots, shoots | Ye et al., 2015 |
| 2,354 | 30 | 0 | 0 | 73 | 49 | Leaves | Lu et al., 2015 | |
| 2,824 | 0 | 2,824 | 61 | 14 | 10 | Roots | Ye et al., 2016 | |
| 26,160 | 37 | 0 | 9 | 585 | 343 | Leaves, anthers, pistils, seeds, shoots, roots | Chu et al., 2017 | |
| Arabidopsis thaliana | 6 | 6 | 0 | 0 | 0 | 0 | Roots | Wang et al., 2014 |
| 6,012 | 0 | 0 | 0 | 292 | 237 | Leaves | Ye et al., 2015 | |
| 165 | 0 | 0 | 0 | 5 | 4 | Siliques, seeds | Lu et al., 2015 | |
| 974 | 6 | 0 | 0 | 21 | 17 | NA | Sun et al., 2016 | |
| 30,534 | 13 | 0 | 0 | 2,411 | 2,206 | Inflorescences, roots, leaves, aerial | Chu et al., 2017 | |
| 2,165 | 19 | 0 | 0 | 46 | 35 | Seedlings | Pan et al., 2017 | |
| 5,861 | 10 | 0 | 0 | 173 | 141 | Whole plants | Chen et al., 2017 | |
| 168 | 4 | 0 | 0 | 7 | 6 | Leaves | Liu et al., 2017 | |
| 164 | 4 | 0 | 0 | 3 | 2 | Leaves | Dou et al., 2017 | |
| Zea mays | 496 | 0 | 0 | 0 | 1 | 1 | Shoots | Lu et al., 2015 |
| 2,771 | 37 | 0 | 0 | 39 | 36 | Seedling leaves | Chen et al., 2017 | |
| Hordeum vulgare | 47 | 16 | 0 | 0 | 0 | 0 | Leaves and seeds | Darbani et al. 2016 |
| Solanum lycopersicum | 854 | 0 | 0 | 0 | 6 | 5 | Fruit | Zuo et al. 2016 |
| 783 | 2 | 0 | 0 | 10 | 7 | Fruit | Tan et al., 2017 | |
| Triticum aestivum | 88 | 16 | 0 | 0 | 7 | 5 | Seedling leaves | Wang et al. 2016 |
| Glycine max | 5,372 | 7 | 0 | 0 | 61 | 56 | Leaves, roots, stems | Zhao et al. 2016 |
| Gossypium hirsutum | 499 | 7 | 0 | 0 | 7 | 0 | Leaves, ovules | Zhao et al. 2016 |
* miRNA sponges were predicted using eTM_finder (Ye et al., 2014);
miRNA targets were predicted using psRNATarget (Dai and Zhao, 2011) (http://plantgrn.noble.org/psRNATarget/);
BS valided means the back-splicing site has of circRNA been experimentally valided by Sanger sequencing;
FL valided means the full-length of circRNA has been experimentally valided by Sanger sequencing.
Table 2 Summary of circRNA entries in PlantcircBase (Release 2)
| Organisms | Total circRNAs | Back-splicing site validated | Full length sequence validated | Acting as miRNA sponge | Networks of circRNA-miRNA-mRNA |
|---|---|---|---|---|---|
| Oryza sativa | 40,314 | 137 | 70 | 901 | 539 |
| Arabidopsis thaliana | 38,938 | 61 | 0 | 2,641 | 2,392 |
| Zea mays | 3,267 | 37 | 0 | 40 | 37 |
| Hordeum vulgare | 47 | 16 | 0 | 0 | 0 |
| Solanum lycopersicum | 1,472 | 2 | 0 | 15 | 12 |
| Triticum aestivum | 88 | 16 | 0 | 7 | 5 |
| Glycine max | 5,372 | 7 | 0 | 61 | 56 |
| Gossypium hirsutum | 499 | 7 | 0 | 7 | 0 |
Release 1
In the first version of PlantcircBase, circRNA information from five organisms (Arabidopsis thaliana, Hordeum vulgare, Oryza sativa, Solanum lycopersicum, Zea mays), were included. And the total number of circRNA entries is 77,595. Detail statistics were shown in tables as following.
Table 1 The number of circRNAs in PlantcircBase (Release 1)
| Organisms | Number of circRNAs | Full-length sequence of circRNAs | Acting as miRNA sponge* | Networks of circRNA-miRNA-mRNA* | Tissues | References | ||
|---|---|---|---|---|---|---|---|---|
| Total | Back-splicing site valided | Total | Sanger sequencing valided | |||||
| Oryza sativa | 12,037 | 10 | 0 | 0 | 405 | 251 | Roots, shoots | Ye et al., 2015 |
| 2,354 | 30 | 0 | 0 | 73 | 49 | Leaves | Lu et al., 2015 | |
| 2,824 | 0 | 2,824 | 61 | 14 | 10 | Roots | Ye et al., 2016 | |
| 26,160 | 37 | 0 | 9 | 585 | 343 | Leaves, anthers, pistils, seeds, shoots, roots | This study | |
| Arabidopsis thaliana | 6 | 6 | 0 | 0 | 0 | 0 | Roots | Wang et al., 2014 |
| 6,012 | 0 | 0 | 0 | 231 | 188 | Leaves | Ye et al., 2015 | |
| 165 | 0 | 0 | 0 | 5 | 4 | Siliques, seeds | Lu et al., 2015 | |
| 970 | 6 | 0 | 0 | 10 | 6 | NA | Sun et al., 2016 | |
| 31,079 | 13 | 0 | 0 | 822 | 691 | Inflorescences, roots, leaves, aerial | This study | |
| Zea mays | 496 | 0 | 0 | 0 | 1 | 1 | Shoots | Lu et al., 2015 |
| Hordeum vulgare | 47 | 16 | 0 | 0 | 0 | 0 | Leaves and seeds | Darbani et al. 2016 |
| Solanum lycopersicum | 854 | 0 | 0 | 0 | 4 | 3 | Fruit | Zuo et al. 2016 |
*miRNA sponges were predicted using eTM_finder (Ye et al., 2014); miRNA targets were predicted using psRNATarget (Dai and Zhao 2011) in our lab.
Table 2 Summary of circRNA entries in PlantcircBase (Release 1)
| Organisms | Total circRNAs | Back-splicing site validated | Full length sequence validated | Acting as miRNA sponge | Networks of circRNA-miRNA-mRNA |
|---|---|---|---|---|---|
| Oryza sativa | 40,314 | 137 | 70 | 901 | 539 |
| Arabidopsis thaliana | 35,884 | 25 | 0 | 955 | 792 |
| Zea mays | 496 | 0 | 0 | 1 | 1 |
| Hordeum vulgare | 47 | 16 | 0 | 0 | 0 |
| Solanum lycopersicum | 854 | 0 | 0 | 4 | 3 |
References (for collecting circRNAs):
Chen G, Cui J, Wang L, Zhu Y, Lu Z, and Jin B. 2017. Genome-Wide Identification of Circular RNAs in Arabidopsis thaliana. Front Plant Sci 8, 1678. [Full text]
Chen L, Zhang P, Fan Y, Lu Q, Li Q, Yan J, Muehlbauer GJ, Schnable PS, Dai M and Li L. 2017. Circular RNAs mediated by transposons are associated with transcriptomic and phenotypic variation in maize. New Phytol. doi: 10.1111/nph.14901. [Full text]
Chu Q, Zhang X, Zhu X, Liu C, Mao L, Ye C, Zhu Q, Fan L. 2017. PlantcircBase: a database for plant circular RNAs. Molecular Plant [Full text]
Dai X, Zhao PX. 2011. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39(Web Server issue): W155-159. [PubMed]
Darbani B, Noeparvar S, Borg S. 2016. Identification of circular RNAs from the parental genes involved in multiple aspects of cellular metabolism in barley. Front Plant Sci 7: 776. [PMC free article]
Dou Y, Li S, Yang W, Liu K, Du Q, Ren G, Yu B, and Zhang C. 2017. Genome-wide Discovery of Circular RNAs in the Leaf and Seedling Tissues of Arabidopsis Thaliana. Curr Genomics 18, 360-365. [Full text]
Liu T, Zhang L, Chen G, and Shi T. 2017. Identifying and Characterizing the Circular RNAs during the Lifespan of Arabidopsis Leaves. Front Plant Sci 8, 1278. [Full text]
Lu T, Cui L, Zhou Y, Zhu C, Fan D, Gong H, Zhao Q, Zhou C, Zhao Y, Lu D, et al. 2015. Transcriptome-wide investigation of circular RNAs in rice. RNA 21(12): 2076-2087. [PubMed]
Pan T, Sun X, Liu Y, et al. 2017. Heat stress alters genome-wide profiles of circular RNAs in Arabidopsis. Plant Mol Biol. doi: 10.1007/s11103-017-0684-7. [Full text]
Sun X, Wang L, Ding J, Wang Y, Wang J, Zhang X, Che Y, Liu Z, Zhang X, Ye J, et al. 2016. Integrative analysis of Arabidopsis thaliana transcriptomics reveals intuitive splicing mechanism for circular RNA. FEBS Lett 590(20): 3510-3516. [PubMed]
Tan J, Zhou Z, Niu Y, Sun X, and Deng Z. 2017. Identification and Functional Characterization of Tomato CircRNAs Derived from Genes Involved in Fruit Pigment Accumulation. Sci Rep 7, 8594. [Full text]
Wang PL, Bao Y, Yee MC, Barrett SP, Hogan GJ, Olsen MN, Dinneny JR, Brown PO, Salzman J. 2014. Circular RNA is expressed across the eukaryotic tree of life. PLoS One 9(6): e90859. [PubMed]
Wang Y, Yang M, Wei S, Qin F, Zhao H, and Suo B. 2017. Identification of Circular RNAs and Their Targets in Leaves of Triticum aestivum L. under Dehydration Stress. Front Plant Sci 7, 2024. [Full text]
Ye CY, Chen L, Liu C, Zhu QH, Fan L. 2015. Widespread noncoding circular RNAs in plants. New Phytol 208(1): 88-95. [PubMed]
Ye CY, Zhang X, Chu Q, Liu C, Yu Y, Jiang W, Zhu QH, Fan L, Guo L. 2016. Full-length sequence assembly reveals circular RNAs with diverse non-GT/AG splicing signals in rice. RNA Biol DOI: 10.1080/15476286.2016.1245268 [Full text]
Zhao T, Wang L, Li S, Xu M, Guan X, and Zhou B. 2017. Characterization of conserved circular RNA in polyploid Gossypium species and their ancestors. FEBS Lett 591(21), 3660-3669. [Full text]
Zhao W, Cheng Y, Zhang C, You Q, Shen X, Guo W, and Jiao Y. 2017. Genome-wide identification and characterization of circular RNAs by high throughput sequencing in soybean. Sci Rep 7，5636. [Full text]
Zuo J, Wang Q, Zhu B, Luo Y, Gao L. 2016. Deciphering the roles of circRNAs on chilling injury in tomato. Biochem Biophys Res Commun 479(2): 132-138. [Full Text]
Copyright©2017-2018 Institute of Crop Sciences / Institute of Bioinformatics, Zhejiang University.
Any questions or suggestions, please contact the Fan's lab, bioinplant@zju.edu.cn
For submittion, please click here. Last modified at 2019-03-01.
