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

Muthappa Senthil‐Kumar,Yule Liu,Olga Del Pozo,Suma Chakravarthy,Mingyi Wang,Ping Xu,Keri Wang,Vanthana Doraiswamy,Joyce Van Eck,Junil Chang,Savithramma P Dinesh‐Kumar,Gregory B Martin,Venkategowda Ramegowda,Choong‐Min Ryu,Hee‐Kyung Lee,Kirankumar S Mysore

doi:10.1002/pld3.55

Abstract

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.

Highlights

We have developed a Virus-induced gene silencing (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
As a first step toward integrating these data, we developed a “VIGS phenomics and functional genomics database” (VPGD) that compiles data from the silencing of 4,117 N. benthamiana genes
Nucleotide sequences used for VIGS are provided in the database and can be bioinformatically analyzed for their silencing efficiency and for off-target gene silencing using the VIGS tool (FernandezPozo, Rosli, Martin, & Mueller, 2015), siRNA scan, or pSSRNAit options integrated into the web site (Figure 5)

Summary

| INTRODUCTION

A member of the Solanaceae family, is a model plant species that is widely used for studying host–pathogen interactions and for transient protein expression to examine protein function, subcellular protein localization, and protein–protein interactions (Anand et al, 2007; Chakravarthy, Velasquez, Ekengren, Collmer, & Martin, 2010; Gilbert & Wolpert, 2013; Goodin, Zaitlin, Naidu, & Lommel, 2008; Kaundal et al, 2017; Lee et al, 2017; Liu et al, 2004; Rojas et al, 2012; Wang et al, 2012). The TRV-VIGS-based fast-forward genetics approach has been widely used in N. benthamiana to identify plant genes involved in disease resistance, Agrobacteriummediated transformation, flower development, and coronatine/victorin-induced cell death (Anand et al, 2007; Chakravarthy et al, 2010; del Pozo, Pedley, & Martin, 2004; Gilbert & Wolpert, 2013; Kaundal et al, 2017; Lee et al, 2017; Lu et al, 2003; Rojas et al, 2012; Senthil-Kumar et al, 2013; Wangdi et al, 2010) These studies have generated phenotypic data for a large number of genesilenced plants. We expect that the VPGD will be a useful resource for a wide range of researchers working with N. benthamiana and other economically important solanaceous plants such as tomato, potato, and pepper

| EXPERIMENTAL PROCEDURES

| RESULTS

| DISCUSSION

Findings

| CONCLUSIONS

CONFLICT OF INTERESTS