Genome-Wide Analyses of the NAC Transcription Factor Gene Family in Pepper (Capsicum annuum L.): Chromosome Location, Phylogeny, Structure, Expression Patterns, Cis-Elements in the Promoter, and Interaction Network

The NAM, ATAF1/2, and CUC2 (NAC) transcription factors form a large plant-specific gene family, which is involved in the regulation of tissue development in response to biotic and abiotic stress. To date, there have been no comprehensive studies investigating chromosomal location, gene structure, gene phylogeny, conserved motifs, or gene expression of NAC in pepper (<i>Capsicum annuum</i> L.). The recent release of the complete genome sequence of pepper allowed us to perform a genome-wide investigation of <i>Capsicum annuum</i> L. NAC (<i>CaNAC</i>) proteins. In the present study, a comprehensive analysis of the <i>CaNAC</i> gene family in pepper was performed, and a total of 104 <i>CaNAC</i> genes were identified. Genome mapping analysis revealed that <i>CaNAC</i> genes were enriched on four chromosomes (chromosomes 1, 2, 3, and 6). In addition, phylogenetic analysis of the NAC domains from pepper, potato, <i>Arabidopsis</i>, and rice showed that <i>CaNAC</i> genes could be clustered into three groups (I, II, and III). Group III, which contained 24 <i>CaNAC</i> genes, was exclusive to the <i>Solanaceae</i> plant family. Gene structure and protein motif analyses showed that these genes were relatively conserved within each subgroup. The number of introns in <i>CaNAC</i> genes varied from 0 to 8, with 83 (78.9%) of <i>CaNAC</i> genes containing two or less introns. Promoter analysis confirmed that <i>CaNAC</i> genes are involved in pepper growth, development, and biotic or abiotic stress responses. Further, the expression of 22 selected <i>CaNAC</i> genes in response to seven different biotic and abiotic stresses [salt, heat shock, drought, <i>Phytophthora capsici</i>, abscisic acid, salicylic acid (SA), and methyl jasmonate (MeJA)] was evaluated by quantitative RT-PCR to determine their stress-related expression patterns. Several putative stress-responsive <i>CaNAC</i> genes, including <i>CaNAC</i>72 and <i>CaNAC</i>27, which are orthologs of the known stress-responsive <i>Arabidopsis</i> gene <i>ANAC</i>055 and potato gene <i>StNAC</i>30, respectively, were highly regulated by treatment with different types of stress. Our results also showed that <i>CaNAC</i>36 plays an important role in the interaction network, interacting with 48 genes. Most of these genes are in the mitogen-activated protein kinase (MAPK) family. Taken together, our results provide a platform for further studies to identify the biological functions of <i>CaNAC</i> genes.