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.

As a large plant-specific gene family, the NAC (NAM, ATAF1/2, and CUC2) transcription factor is related to plant growth, development, and response to abiotic stresses. Although the draft genome of garden asparagus (Asparagus officinalis) has been released, the genome-wide investigation of the NAC gene family is still unavailable. In this study, a total of 85 A. officinalis NAC genes were identified, and a comprehensive analysis of the gene family was performed, including physicochemical properties, phylogenetic relationship, chromosome localization, gene structure, conserved motifs, intron/exon, cis-acting elements, gene duplication, syntenic analysis, and differential gene expression analysis. The phylogenetic analysis demonstrated that there were 14 subgroups in both A. officinalis and Arabidopsis thaliana, and the genes with a similar gene structure and motif distribution were clustered in the same group. The cis-acting regulatory analysis of AoNAC genes indicated four types of cis-acting elements were present in the promoter regions, including light-responsive, hormone-responsive, plant-growth-and-development-related, and stress-responsive elements. The chromosomal localization analysis found that 81 NAC genes in A. officinalis were unevenly distributed on nine chromosomes, and the gene duplication analysis showed three pairs of tandem duplicated genes and five pairs of segmental duplications, suggesting that gene duplication is possibly associated with the amplification of the A. officinalis NAC gene family. The differential gene expression analysis revealed one and three AoNAC genes that were upregulated and downregulated under different types of salinity stress, respectively. This study provides insight into the evolution, diversity, and characterization of NAC genes in garden asparagus and will be helpful for future understanding of their biological roles and molecular mechanisms in plants.

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.

In recent years, the related research of the WRKY gene family has been gradually promoted, which is mainly reflected in the aspects of environmental stress and hormone response. However, to make the study of the WRKY gene family more complete, we also need to focus on the whole-genome analysis and identification of the family. In previous studies, the whole WRKY gene family of Arabidopsis, legumes and other plants has been thoroughly studied. However, since the publication of Asparagus officinalis genome-wide data, there has never been an analysis of the whole WRKY gene family. To understand more broadly the function of the WRKY gene family, the whole genome and salt stress transcriptome data of asparagus were used for comprehensive analysis in this study, including WRKY gene family identification, phylogenetic tree construction, analysis of conserved mods and gene domains, extraction of cis-acting elements, intron/exon analysis, species collinearity analysis, and WRKY expression analysis under salt stress. The results showed that a total of 70 genes were selected and randomly distributed on 10 chromosomes and one undefined chromosome. According to the functional classification of Arabidopsis thaliana, the WRKY family of asparagus was divided into 11 subgroups (C1–C9, U1, U2). It is worth considering that the distribution rules of gene-conserved motifs, gene domains and introns/exons in the same subfamily are similar, which suggests that genes in the same subfamily may regulate similar physiological processes. In this study, 11 cis-acting elements of WRKY family were selected, among which auxin, gibberellin, abscisic acid, salicylic acid and other hormone-regulated induction elements were involved. In addition, environmental stress (such as drought stress and low-temperature response) also accounted for a large proportion. Interestingly, we analyzed a total of two tandem duplicate genes and 13 segmental duplication genes, suggesting that this is related to the amplification of the WRKY gene family. Transcriptome data analysis showed that WRKY family genes could regulate plant growth and development by up-regulating and down-regulating gene expression under salt stress. Volcanic maps showed that 3 and 15 AoWRKY genes were significantly up-regulated or down-regulated in NI&NI+S and AMF&AMF+S, respectively. These results provide a new way to analyze the evolution and function of the WRKY gene family, and can provide a reference for the production and research of asparagus.

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.

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.