Welcome to the VIGS database

Background

Virus-induced gene silencing (VIGS) has become a powerful tool for understanding plant gene function. Tobacco rattle virus-based VIGS vector has been used to silence large number of genes in Nicotiana benthamiana and other dicot species. This database compiles a large number of phenotypic information of gene silenced plants. This can serve as a platform for researchers to quickly know (without doing an experiment) the expected visible developmental changes upon silencing a plant gene.

Currently, the sequences and respective silencing phenotypes for ESTs/genes derived from two cDNA libraries are accessible in this database. N. benthamiana mixed elicitor (NbME) library was constructed using RNA from various biotic and abiotic stress inducing elicitors treated plants. Another library was constructed using RNA from both uninoculated and Tobacco mosaic virus-induced (TI) leaves. More genomic and phenomic information will be added in future as this database will continue to be updated.

About this Database

This database describes phenotypic information for a large number of gene silenced N. benthamiana plants. It has sequence information for ~4,500 N. benthamiana ESTs (inserts in the TRV2 vector) and also the phenotypic description and/or photographs for ~1,300 gene silenced plants. In addition, it provides user friendly search engine for any particular phenotype of interest using key words. It also has a built-in BLAST search to identify sequences and their silencing phenotypes by using a query sequence.

Acknowledgements

This website and the resources described therein were generated through various projects at Molecular Plant Microbe Lab and were funded by Noble Research Institute.

Collaborators

Gregory Martin (https://btiscience.org/greg-martin/)

S. P. Dinesh-Kumar (http://dinesh-kumarlab.genomecenter.ucdavis.edu/)

Citation(s):

Related references

1. Kaundal, A., Ramu, V., Oh, S., Lee, S., Pant, B.D., Lee, H.-K., Rojas, C., Senthil-Kumar, M. and Mysore, K.S. (2017) General control non-repressible-4 (GCN4) degrades 14-3-3 and RIN4 complex to regulate stomatal aperture with implications on nonhost resistance and drought tolerance. The Plant Cell 29(9):2233-2248.
2. Fernandez-Pozo, N., Rosli, Hernan G., Martin, Gregory B. and Mueller, Lukas A. (2015) The SGN VIGS tool: user-friendly software to design virus-induced gene silencing (VIGS) constructs for functional genomics. Molecular Plant, 8, 486-488.
3. Senthil-Kumar M and Mysore KS. 2014. Tobacco rattle virus-based virus-induced gene silencing in Nicotiana benthamiana. Nature Protocols 9, 1549-1562
4. Gilbert, B.M. & Wolpert, T.J. 2013. Characterization of the LOV1-mediated, Victorin-induced cell death response with Virus-Induced Gene Silencing. Mol. Plant Microbe Interact, 26(8):903-17
5. Ramegowda, V., Senthil-kumar, M., Udayakumar, M. & Mysore, K.S. 2013. A high-throughput virus-induced gene silencing protocol identifies genes involved in multi-stress tolerance. BMC Plant Biology, 13 (193)
6. Senthil-Kumar, M., Lee, H.K., Mysore, K.S. 2013. VIGS-mediated forward genetics screening for identification of genes involved in nonhost resistance. Journal of Visualized Experiments, 78, e51033
7. Rojas CM, Senthil-Kumar M, Wang K, Ryu CM, Kaundal A, Mysore KS. 2012. Glycolate oxidase plays a major role during nonhost resistance responses by modulating reactive oxygen species mediated signal transduction pathways. The Plant Cell 24:336-52
8. Wang K, Senthil-Kumar M, Ryu C-M, Kang L, Mysore KS. 2012. Phytosterols play a key role in plant innate immunity against bacterial pathogens by regulating nutrient efflux into the apoplast. Plant Physiology 158:1789-802
9. Senthil-Kumar M, Mysore KS. 2011. New dimensions for VIGS in plant functional genomics. Trends in Plant Science, 16(12):656-665
10. Chakravarthy S, Velasquez AC, Ekengren SK, Collmer A, Martin GB. 2010. Identification of Nicotiana benthamianagenes involved in pathogen-associated molecular pattern-triggered immunity. Mol Plant Microbe Interact 23:715-726
11. Wangdi T, Uppalapati SR, Nagaraj S, Ryu C-M, Bender CL, Mysore KS. 2010. A Virus-Induced Gene Silencing Screen Identifies a Role for Thylakoid Formation1 in Pseudomonas syringae pv tomato Symptom Development in Tomato and Arabidopsis. Plant Physiology 152:281-92
12. Velásquez, A. C., Chakravarthy, S., Martin, G. B. 2009. Virus-induced Gene Silencing (VIGS) in Nicotiana benthamiana and Tomato J. Vis. Exp. (28), e1292, doi:10.3791/1292.
13. Anand A, Vaghchhipawala Z, Ryu C-M, Kang L, Wang K, et al. 2007. Identification and characterization of plant genes involved in Agrobacterium-mediated plant transformation by virus-induced gene silencing. Molecular Plant-Microbe Interactions 20:41-52
14. Senthil-Kumar M, Govind G, Kang L, Mysore K, Udayakumar M. 2007. Functional characterization of Nicotiana benthamiana homologs of peanut water deficit-induced genes by virus-induced gene silencing. Planta 225:523-39
15. Senthil-Kumar M, Hema R, Anand A, Kang L, Udayakumar M, Mysore KS. 2007. A systematic study to determine the extent of gene silencing in Nicotiana benthamiana and other Solanaceae species when heterologous gene sequences are used for virus-induced gene silencing. New Phytologist 176:782-91
16. Burch-Smith, T.M., Anderson, J.C., Martin, G.B., and Dinesh-Kumar, S.P. (2004). Applications and advantages of virus induced gene silencing (VIGS) for gene function studies in plants. Plant J. 39:734-746
17. Liu, Y., Schiff, M., Marathe, R., and Dinesh-Kumar, S.P. (2002). Tobacco Rar1, EDS1, NPR1/NIM1 like genes are required for N-mediated resistance to tobacco mosaic virus. Plant J. 30: 415-429.

Related resources

- VIGS tool and other resources at BTI.
- siRNA scan and pSSRNAit: off-target gene silencing prediction resources at NRI.

Contact us

If you have any questions or suggestions regarding this web page please contact site administrator. For questions regarding VIGS, please contact Dr. Senthil-Kumar Muthappa (skmuthappa@nipgr.ac.in) or Dr. Kiran Mysore (ksmysore@noble.org).