- BLAST tool
- VIGS Tool
- CRISPR-P Tool
- CCTop CRISPR tool
- Genome sequence
- Gene annotation
- Metabolic Pathways
- Proteomics Databases
- Genome Browser
- VIGS: genes to phenotypes database
Nb Experimental Protocols and Resources
Virus-induced gene silencing – 1
(requires JoVE subscription)
(requires JoVE subscription)
First papers to use agroinfiltration
Article 1: Tang, X., R. Frederick, D. Halterman, J. Zhou and G. B. Martin (1996). Initiation of plant disease resistance by physical interaction of AvrPto with Pto kinase. Science 274: 2060–2063.
Article 2: Scofield, S. R., C. M. Tobias, J. P. Rathjen, J. H. Chang, D. T. Lavelle, R. W. Michelmore and B. J. Staskawicz (1996). Molecular basis of gene-for-gene specificity in bacterial speck disease of tomato. Science 274: 2063–2065.
Cell-to-cell movement assay
A cell-to-cell macromolecular transport assay in planta utilizing biolistic bombardment.
Agroinfiltration of Nicotiana benthamiana leaf
TRV infection of N. benthamiana
Tobacco rattle virus (TRV) infection of Nicotiana benthamiana
Nb, Future Plans
Our current plan is to improve the assembly of the Nicotiana benthamiana genome sequence and link the sequence to the nineteen chromosomes. We are also working to improve the gene annotation.
- Sequence an additional lane of a 5-kb mate-pair library at the Cornell-Weill facility.
- Use an F2 population (~96 individuals) developed by Dave Zaitlin (University of Kentucky) for a genotype-by-sequencing (GBS) approach using the Cornell Institute for Genomic Diversity facility.
- Sequence a 15-kb mate-pair library (University of Illinois-Urbana/Champagne Sequencing Facility).
- Create a new assembly of the genome sequence based on the data in the preceding text.
- Improve annotation using with RNA-seq data from various researchers.
Gregory Martin, BTI: PAMP- and Effector-triggered immunity transcriptome
Zach Lippman, Cold Spring Harbor Laboratory: meristem tissue
Dave Zaitlin, University of Kentucky: leaves, roots, flowers, developing seed capsules
Peter Moffett, University of Sherbrooke: ribosome-IP-RNA-Seq (defense response)
Data from others is welcome—please contact us!
This project is supported by BTI Innovation Funds and by National Science Foundation grant IOS-1025642.
Nicotiana benthamiana News
This Nicotiana benthamiana web site shares papers, results, tools, protocols, and other materials from researchers using NB as a study plant. Read more »
The genome of an experimentally important relative of tobacco has been sequenced by US and Canadian researchers. Read more »
Scientists at the Boyce Thompson Institute for Plant Research (BTI) released a draft sequence of the Nicotiana benthamiana genome which is accessible through the SGN BLAST tool and can be downloaded from an ftp site (see: http://solgenomics.net/). The project was funded by BTI and National Science Foundation grants Read more »