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

Abstract

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 (Capsicum annuum L.). The recent release of the complete genome sequence of pepper allowed us to perform a genome-wide investigation of Capsicum annuum L. NAC (CaNAC) proteins. In the present study, a comprehensive analysis of the CaNAC gene family in pepper was performed, and a total of 104 CaNAC genes were identified. Genome mapping analysis revealed that CaNAC genes were enriched on four chromosomes (chromosomes 1, 2, 3, and 6). In addition, phylogenetic analysis of the NAC domains from pepper, potato, Arabidopsis, and rice showed that CaNAC genes could be clustered into three groups (I, II, and III). Group III, which contained 24 CaNAC genes, was exclusive to the Solanaceae plant family. Gene structure and protein motif analyses showed that these genes were relatively conserved within each subgroup. The number of introns in CaNAC genes varied from 0 to 8, with 83 (78.9%) of CaNAC genes containing two or less introns. Promoter analysis confirmed that CaNAC genes are involved in pepper growth, development, and biotic or abiotic stress responses. Further, the expression of 22 selected CaNAC genes in response to seven different biotic and abiotic stresses [salt, heat shock, drought, Phytophthora capsici, 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 CaNAC genes, including CaNAC72 and CaNAC27, which are orthologs of the known stress-responsive Arabidopsis gene ANAC055 and potato gene StNAC30, respectively, were highly regulated by treatment with different types of stress. Our results also showed that CaNAC36 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 CaNAC genes.

Genome-wide analysis of the NAC transcription factor family in broomcorn millet (Panicum miliaceum L.) and expression analysis under drought stress

“…A total of 180 NAC genes were identified in broomcorn millet. The number of NAC genes in broomcorn millet was higher than the 117 in A. thaliana [41], 151 in rice [60], 104 in pepper [51], 82 in melon [53], 96 in cassava [53], 152 in maize [45], 147 in foxtail millet [47], 152 in soybean [48], and 110 in potato [49], and lower than that of 288 in bread wheat [42] and 188 in Chinese cabbage [50]. There were extensive variations in gene length, predicted protein MW, and protein pI, whereas the gene structures and protein motifs were relatively conserved in the clades, which provided a valuable reference for their analysis and function.…”

“…All 180 PmNAC members were divided into 12 subgroups based on their sequence homology and classification from Arabidopsis [41]. Phylogenetic analysis divided tartary buckwheat, cassava and pepper NACs into 15, 16 and 14 subgroups, respectively [44,45,51]. These data indicated that NAC proteins showed diversity in different species.…”

“…The grains of broomcorn millet not only have high nutritional value, containing abundant proteins, starch, and a variety of vitamins and minerals, but also have medicinal value and are used in millet wine and other products. The NAC gene family has been widely studied in many species, such as A. thaliana [41], rice [41], wheat [42,43], tartary buckwheat [44], maize [45,46], foxtail millet [47], soybean [48], potato [49], Chinese cabbage [50], pepper [51], cassava [52], melon [53], physic nut [54], apple [55], and pigeon pea [56]. However, no systematic study of the NAC family in broomcorn millet is available.…”

Genome-Wide Identification, Characterization and Expression Analysis of Non-Arginine Aspartate Receptor like kinase gene family underColletotrichum truncatumstress conditions in Hot pepper

“…Consequently, non-synonymous (Ka) and synonymous substitution (Ks) among duplicated CaRLK gene pairs were calculated using PAL2NAL (http://www.bork.embl.de/pal2nal/). The divergence time of the duplicated gene pairs was calculated as described by Koch et al (2000) [21].…”

The Role of Major Transcription Factors in Solanaceous Food Crops under Different Stress Conditions: Current and Future Perspectives

“…The genome wide analyses of each transcription factor have been completed and "-"indicates the genome wide analysis was not done yet. Potato's WRKY [63] Dof [58], NAC [145]; ARF [192]; ERF [181] Pepper WRKY [193] ERF [194]; Dof [51] MYB [103]; ARF [190]; NAC [195] Tomato WRKY [62] Dof [53] MYB [88] HSF [120] ARF [196] ERF [171]; Eggplant's WRKY [197] Dof [52] MYB [84].…”