New Website Is Portal for Nicotiana benthamiana Experimental Resources
BTI and collaborators launch Nicotiana benthamiana web site for researchers.
Scientists from BTI and seven other institutions are collaborating on a project to improve the genome sequence of Nicotiana benthamiana and develop software tools for its analysis. As part of this effort, a website has been developed that serves as a portal for bioinformatics and experimental resources for this plant species (https://bti.cornell.edu/nicotiana-benthamiana/).
Nicotiana benthamiana is widely used for experimentation because it is particularly amenable to virus-induced gene silencing (VIGS) which enables functional characterization of genes and for transient expression of proteins using Agrobacterium infiltration of its large leaves.
“The website was a natural extension of the N. benthamiana genome project,” said project leader Greg Martin, the Boyce Schulze Downey Scientist at Boyce Thompson Institute and a Cornell professor. “It provides a way to share the databases and tools with the broader community of researchers.”
The website provides various bioinformatics resources including a link for accessing the draft genome sequence of N. benthamiana which was published in 2012. The genome sequence can be searched using a BLAST Tool provided on the website and ftp links allow downloading of the sequence, its gene annotation and a database of its predicted proteome.
A ‘VIGS Tool’, developed by Dr. Noe Fernandez (BTI) and available on the website, enables the rapid identification of a DNA sequence that allows effective gene silencing and avoids silencing of non-target genes. A complementary tool for the design of artificial microRNAs is available from the University of Sydney and a link is provided to that website.
Other links on the website provide publications related to the history, taxonomy and use of N. benthamiana and protocols for performing VIGS, Agrobacterium-infiltration, and assays of the plant immune system.
Several efforts are underway to improve the assembly of the N. benthamiana genome sequence and the gene annotation. These include additional sequencing of a 5-kb mate-pair library, use of an F2 population (~96 individuals) developed by Dr. Dave Zaitlin (U. Kentucky) for a genotype-by-sequencing (GBS) approach, development and sequencing of a 15-kb mate-pair library, and generation of a new assembly of the genome sequence and improved gene annotation based on the data above. In addition, a genome-to-phenome database is under development that will provide information about unusual plant phenotypes that are observed due to silencing of specific genes.
Researchers who would like to contribute RNA-seq data or genome sequences to the N. benthamiana genome project or would like to have their protocols or other materials highlighted on the website should contact Greg Martin at email@example.com or Lukas Mueller at firstname.lastname@example.org.
The N. benthamiana genome project and website are the result of a collaboration between scientists from BTI, USDA-ARS, Cold Spring Harbor Laboratory, National Institute of Plant Genome Research (India), Samuel Roberts Noble Foundation, University of Kentucky, and Université de Sherbrooke (Canada).
The N. benthamiana genome project and the website are supported by BTI Innovation Funds and by National Science Foundation grant IOS-1025642.
Visit the Nicotiana benthamiana website now