Comprehensive Analysis of Genes Reveals Differential Expression Patterns in Response to DC3000 and Their Overlapping Expression Pattern during PTI and ETI in Tomato.

NAC (NAM/ATAF/CUC) transcription factors belong to a unique gene family in plants, which play vital roles in regulating diverse biological processes, including growth, development, senescence, and in response to biotic and abiotic stresses. Tomato (), as the most highly valued vegetable and fruit crop worldwide, is constantly attacked by pv. DC3000 ( DC3000), causing huge losses in production. Thus, it is essential to conduct a comprehensive identification of the genes involved in response to DC3000 in tomato. In this study, a complete overview of this gene family in tomato is presented, including genome localization, protein domain architectures, physical and chemical features, and nuclear location score. Phylogenetic analysis identified 20 genes as putative stress-responsive genes, named -. Expression profiles analysis revealed that 18 of these 20 genes were significantly induced in defense response to DC3000 stress. Furthermore, the RNA-seq data were mined and analyzed, and the results revealed the expression pattern of the 20 genes in response to DC3000 during the PTI and ETI. Among them, , , , , , , and were up-regulated against DC3000 during PTI and ETI, which suggested that these genes may participate in both the PTI and ETI pathway during the interaction between tomato and DC3000. In addition, genes induced by exogenous hormones, including indole-3-acetic acid (IAA), abscisic acid (ABA), salicylic acid (SA), and methyl jasmonic acid (MeJA), were also recovered. These results implied that genes may participate in the DC3000 stress response by multiple regulatory pathways of the phytohormones. In all, this study provides important clues for further functional analysis and of the regulatory mechanism of genes under DC3000 stress.