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Virus-induced gene silencing database for phenomics and functional genomics in Nicotiana benthamiana

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Title Virus-induced gene silencing database for phenomics and functional genomics in Nicotiana benthamiana
 
Creator Senthil-Kumar, Muthappa
Wang, Mingyi
Chang, Junil
Ramegowda, Venkategowda
Pozo, Olga del
Liu, Yule
Doraiswamy, Vanthana
Lee, Hee-Kyung
Ryu, Choong-Min
Wang, Keri
Xu, Ping
Eck, Joyce Van
Chakravarthy, Suma
Dinesh-Kumar, Savithramma P.
Martin, Gregory B.
Mysore, Kirankumar S.
 
Subject functional genomics
gene silencing
Nicotiana benthamiana
tomato
Virus-induced gene silencing
 
Description Accepted date: 24 March 2018
Virus-induced gene silencing (VIGS) is an important forward and reverse genetics
method for the study of gene function in many plant species, especially Nicotiana
benthamiana. However, despite the widespread use of VIGS, a searchable database
compiling the phenotypes observed with this method is lacking. Such a database
would allow researchers to know the phenotype associated with the silencing of a
large number of individual genes without experimentation. We have developed a
VIGS phenomics and functional genomics database (VPGD) that has DNA sequence
information derived from over 4,000 N. benthamiana VIGS clones along with the
associated silencing phenotype for approximately 1,300 genes. The VPGD has a
built-in BLAST search feature that provides silencing phenotype information of
specific genes. In addition, a keyword-based search function could be used to find a
specific phenotype of interest with the corresponding gene, including its Gene
Ontology descriptions. Query gene sequences from other plant species that have
not been used for VIGS can also be searched for their homologs and silencing phenotype
in N. benthamiana. VPGD is useful for identifying gene function not only in
N. benthamiana but also in related Solanaceae plants such as tomato and potato.
The database is accessible at http://vigs.noble.org.
This work was supported by Noble Research
Institute and NSF grant IOS-1025642 to
GBM.
 
Date 2018-04-27T09:14:30Z
2018-04-27T09:14:30Z
2018
 
Type Article
 
Identifier Plant Direct, 2(4): e00055
2475-4455
http://223.31.159.10:8080/jspui/handle/123456789/853
https://onlinelibrary.wiley.com/doi/full/10.1002/pld3.55
https://doi.org/10.1002/pld3.55
 
Language en_US
 
Format application/pdf
 
Publisher American Society of Plant Biologists, John Wiley & Sons