Gene expression data generated from multiple biological samples (mutant, double mutant, and wild-type) are often compared via Venn diagram tools. It is of great interest to know the expression pattern between overlapping genes and their associated gene pathways or gene ontology (GO) terms. We developed DiVenn (Dive into the Venn diagram and create a force directed graph)—a novel web-based tool that compares gene lists from multiple RNA-Seq experiments in a force-directed graph, which shows the gene regulation levels for each gene and integrated KEGG pathway and gene ontology knowledge for the data visualization. DiVenn has four key features: (1) informative force-directed graph with gene expression levels to compare multiple data sets; (2) interactive visualization with biological annotations and integrated pathway and GO databases, which can be used to subset or highlight gene nodes to pathway or GO terms of interest in the graph; (3) Pathway and GO enrichment analysis of all or selected genes in the graph; and (4) high resolution image and gene-associated information export. DiVenn is freely available at http://divenn.noble.org/.

Nudix hydrolases comprise a large gene family of twenty nine members in Arabidopsis, each containing a conserved motif capable of hydrolyzing specific substrates like ADP-glucose and NADH. Until now only two members of this family, AtNUDX6 and AtNUDX7, have been shown to be involved in plant immunity. RPP4 is a resistance gene from a multigene family that confers resistance to downy mildew. A time course expression profiling after Hyaloperonospora arabidopsidis inoculation in both wild-type (WT) and the rpp4 mutant was carried out to identify differentially expressed genes in RPP4-mediated resistance. AtNUDX8 was one of several differentially expressed, downregulated genes identified. A T-DNA knockout mutant (KO-nudx8) was obtained from a Salk T-DNA insertion collection, which exhibited abolished AtNUDX8 expression. The KO-nudx8 mutant was infected separately from the oomycete pathogen Hpa and the bacterial pathogen Pseudomonas syringae pv. maculicola ES4326. The mutant displayed a significantly enhanced disease susceptibility to both pathogens when compared with the WT control. We observed a small, stunted phenotype for KO-nudx8 mutant plants when grown over a 12/12 hour photoperiod but not over a 16/8 hour photoperiod. AtNUDX8 expression peaked at 8 hours after the lights were turned on and this expression was significantly repressed four-fold by salicylic acid (SA). The expression of three pathogen-responsive thioredoxins (TRX-h2, TRX-h3 and TRX-h5) were downregulated at specific time points in the KO-nudx8 mutant when compared with the WT. Furthermore, KO-nudx8 plants like the npr1 mutant, displayed SA hypersensitivity. Expression of a key SA biosynthetic gene ICS1 was repressed at specific time points in the KO-nudx8 mutant suggesting that AtNUDX8 is involved in SA signaling in plants. Similarly, NPR1 and PR1 transcript levels were also downregulated at specific time points in the KO-nudx8 mutant. This study shows that AtNUDX8 is involved in plant immunity as a positive regulator of defense in Arabidopsis.

Iron–sulfur cluster proteins play a role in plant innate immunity by regulating plant defense-related genes.