Nicotiana benthamiana

Bioinformatics Tools

Nb Experimental Protocols and Resources

New Publications:

New, efficient method for VIGS design

Reporter genes for investigating Nb-Pseudomonas interactions

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

Virus-induced gene silencing in Nicotiana benthamiana

Virus-induced gene silencing – video

Virus-induced gene silencing – 1
(requires JoVE subscription)

PTI assay
(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
Agroinfiltration of Nicotiana benthamiana leaf

Agroinfiltration- 2

Phytophthora capsici infects N. benthamiana

Cover of "Molecular Plant-Microbe Interactions"

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.

Projects underway:

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.

Two Nicotiana benthamiana parents (outside; Nb-1 and Nb-DZ) were crossed to develop an F1 (middle) that was selfed to produce an F2 population for use in genotype-by-sequencing (GBS). Photo: Dave Zaitlin, U. of Kentucky.