As a plant-specific transcription factor, the NAC (NAM, ATAF1/2 and CUC2) domain protein plays an important role in plant growth and development, as well as stress resistance. Based on the genomic data of the cacao tree, this study identified 102 cacao NAC genes and named them according to their location within the genome. The phylogeny of the protein sequence of the cacao tree NAC family was analyzed using various bioinformatic methods, and then divided into 12 subfamilies. Then, the amino-acid composition, physicochemical properties, genomic location, gene structure, conserved domains, and promoter cis-acting elements were analyzed. This study provides information on the evolution of the TcNAC gene and its possible functions, laying the foundation for further research on the NAC family. Genes 2020, 11, 35 2 of 11 hormone signaling [23,24]. In total, 166 species with NAC genes were identified. For example, there are 105 in Arabidopsis [25], 151 in Oryza sativa [26], 142 in Vitis vinifera [27], 163 in Populus trichocarpa [28], 113 in Prunus mume [29], 63 in Coffea canephora [30], and 152 in the soybean genome [31]. However, NAC genes were not studied in Theobroma cacao.Theobroma cacao, also known as the cacao tree, belongs to the Malvaceae family and is one of the world s three major beverage crops. Cocoa beans are the seeds of cacao trees and are the main raw material for chocolate. Globally, 3.7 million tons of cocoa beans are produced per year; however, diseases and pests cause harvest losses of about 30%. Determining the genes associated with cacao tree resistance is a key issue in its genetic breeding. Cacao trees also have high economic value because the cacao flavanols provide health benefits, which can be used in nutritional products [32][33][34], and cocoa polyphenols such as catechin and epicatechin have significant antioxidant properties and free radical-scavenging ability. To date, most studies of cacao trees focused on their active components; there were few studies at the genome level. The genome of the cacao tree was completed and published in 2011 [35], providing a powerful tool for studying the cacao tree at the gene level.Many studies showed that, after plant stress, the NAC transcription factor family is involved in the regulation of responses to environmental stress [36]. Overexpression of TsNAC1 in Thellungiella salsuginea can increase abiotic stress resistance [37], especially salt stress resistance. Tomato JUN-GBRUNNEN1 directly binds to the promoters of SlDREB1, SlDREB2, and SlDELLA, increasing the drought tolerance of tomato [38]. PtrNAC72 is a repressor of putrescine biosynthesis in Poncirus trifoliata and may negatively regulate drought stress responses by regulating putrescine-related reactive oxygen homeostasis [39]. Since the NAC gene family plays a crucial role in many developmental processes and responses to abiotic stresses, it is of great significance to study the NAC gene family in Theobroma cacao. In this study, we analyze the genetic structure, conserved motifs, chromosome loc...

The MADS-box family gene is a class of transcription factors that have been extensively studied and involved in several plant growth and development processes, especially in floral organ specificity, flowering time and initiation and fruit development. In this study, we identified 69 candidate MADS-box genes and clustered these genes into five subgroups (Mα: 11; Mβ: 2; Mγ: 14; Mδ: 9; MIKC: 32) based on their phylogenetical relationships with Arabidopsis. Most TcMADS genes within the same subgroup showed a similar gene structure and highly conserved motifs. Chromosomal distribution analysis revealed that all the TcMADS genes were evenly distributed in 10 chromosomes. Additionally, the cis-acting elements of promoter, physicochemical properties and subcellular localization were also analyzed. This study provides a comprehensive analysis of MADS-box genes in Theobroma cacao and lays the foundation for further functional research.

The MYB gene family is involved in the regulation of plant growth, development and stress responses. In this paper, to identify Theobroma cacao R2R3-MYB (TcMYB) genes involved in environmental stress and phytohormones, we conducted a genome-wide analysis of the R2R3-MYB gene family in Theobroma cacao (cacao). A total of 116 TcMYB genes were identified, and they were divided into 23 subgroups according to the phylogenetic analysis. Meanwhile, the conserved motifs, gene structures and cis-acting elements of promoters were analyzed. Moreover, these TcMYB genes were distributed on 10 chromosomes. We conducted a synteny analysis to understand the evolution of the cacao R2R3-MYB gene family. A total of 37 gene pairs of TcMYB genes were identified through tandem or segmental duplication events. Additionally, we also predicted the subcellular localization and physicochemical properties. All the studies showed that TcMYB genes have multiple functions, including responding to environmental stresses. The results provide an understanding of R2R3-MYB in Theobroma cacao and lay the foundation for a further functional analysis of TcMYB genes in the growth of cacao.

GRAS genes exist widely and play vital roles in various physiological processes in plants. In this study, to identify Theobroma cacao (T. cacao) GRAS genes involved in environmental stress and phytohormones, we conducted a genome-wide analysis of the GRAS gene family in T. cacao. A total of 46 GRAS genes of T. cacao were identified. Chromosomal distribution analysis showed that all the TcGRAS genes were evenly distributed on ten chromosomes. Phylogenetic relationships revealed that GRAS proteins could be divided into twelve subfamilies (HAM: 6, LISCL: 10, LAS: 1, SCL4/7: 1, SCR: 4, DLT: 1, SCL3: 3, DELLA: 4, SHR: 5, PAT1: 6, UN1: 1, UN2: 4). Of the T. cacao GRAS genes, all contained the GRAS domain or GRAS superfamily domain. Subcellular localization analysis predicted that TcGRAS proteins were located in the nucleus, chloroplast, and endomembrane system. Gene duplication analysis showed that there were two pairs of tandem repeats and six pairs of fragment duplications, which may account for the rapid expansion in T. cacao. In addition, we also predicted the physicochemical properties and cis-acting elements. The analysis of GO annotation predicted that the TcGRAS genes were involved in many biological processes. This study highlights the evolution, diversity, and characterization of the GRAS genes in T. cacao and provides the first comprehensive analysis of this gene family in the cacao genome.