Next Article in Journal
The Effect of Mice Adaptation Process on the Pathogenicity of Influenza A/South Africa/3626/2013 (H1N1)pdm09 Model Strain
Next Article in Special Issue
Transcriptomic and Proteomic Analyses Unveil the Role of Nitrogen Metabolism in the Formation of Chinese Cabbage Petiole Spot
Previous Article in Journal
Myeloproliferative Neoplasms: Contemporary Review and Molecular Landscape
Previous Article in Special Issue
Molecular Regulatory Mechanism of Exogenous Hydrogen Sulfide in Alleviating Low-Temperature Stress in Pepper Seedlings
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
IJMS
Volume 24
Issue 24
10.3390/ijms242417384
ijms-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles thumb_up
...
Endorse textsms
...
Comment
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Comprehensive Analysis of NAC Transcription Factors Reveals Their Evolution in Malvales and Functional Characterization of AsNAC019 and AsNAC098 in Aquilaria sinensis

by
Zhuo Yang
1,†,
Wenli Mei
1,2,3,†,
Hao Wang
1,2,3,
Jun Zeng
1,2,3,
Haofu Dai
1,2,3,* and
Xupo Ding
1,2,3,*
1
Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
2
International Joint Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
3
Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Int. J. Mol. Sci. 2023, 24(24), 17384; https://doi.org/10.3390/ijms242417384
Submission received: 2 November 2023 / Revised: 5 December 2023 / Accepted: 7 December 2023 / Published: 12 December 2023
(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research 2.0)
Browse Figures
Versions Notes

Abstract

:
NAC is a class of plant-specific transcription factors that are widely involved in the growth, development and (a)biotic stress response of plants. However, their molecular evolution has not been extensively studied in Malvales, especially in Aquilaria sinensis, a commercial and horticultural crop that produces an aromatic resin named agarwood. In this study, 1502 members of the NAC gene family were identified from the genomes of nine species from Malvales and three model plants. The macroevolutionary analysis revealed that whole genome duplication (WGD) and dispersed duplication (DSD) have shaped the current architectural structure of NAC gene families in Malvales plants. Then, 111 NAC genes were systemically characterized in A. sinensis. The phylogenetic analysis suggests that NAC genes in A. sinensis can be classified into 16 known clusters and four new subfamilies, with each subfamily presenting similar gene structures and conserved motifs. RNA-seq analysis showed that AsNACs presents a broad transcriptional response to the agarwood inducer. The expression patterns of 15 AsNACs in A. sinensis after injury treatment indicated that AsNAC019 and AsNAC098 were positively correlated with the expression patterns of four polyketide synthase (PKS) genes. Additionally, AsNAC019 and AsNAC098 were also found to bind with the AsPKS07 promoter and activate its transcription. This comprehensive analysis provides valuable insights into the molecular evolution of the NAC gene family in Malvales plants and highlights the potential mechanisms of AsNACs for regulating secondary metabolite biosynthesis in A. sinensis, especially for the biosynthesis of 2-(2-phenyl) chromones in agarwood.

1. Introduction

Transcription factors (TFs) are the most important cofactors in transcriptional regulation and post-transcriptional modification. These genes bind to specific sequences upstream of the 5′ end of the transcriptional start site of a gene, thereby regulating the expression of the target gene [1]. NAC (NAM, ATAF1/ATAF2 and CUC2) is a gene family of plant-specific TFs that is widely found in plants. NACs were originally characterized in Arabidopsis thaliana and petunias, which both contain a highly differentiated transcriptional activation domain at the C-terminal and a conserved DNA-binding domain at the N-terminal [2,3,4,5].
The TF family of NAC has been widely studied for its important roles in plant growth and development, especially for apical meristem formation, flower morphogenesis, leaf senescence, the regulation of hormone signaling, cell division, secondary cell wall biosynthesis, lateral root formation, seed germination, fruit ripening and wood formation [6,7,8,9,10]. For example, GmNAC109 is involved in lateral root formation in soybean [11]. SlNAC1 controls the biosynthesis of lycopene and ethylene in tomato [12]. CmNAC-NOR directly activates the genes that are involved in the biosynthesis of carotenoids, ethylene and abscisic acid, thereby promoting fruit coloration and ripening in melons [13]. In addition, NAC plays an important role in the response to (a)biotic stresses [14,15,16]. For instance, environmental stimuli, such as high temperature, drought, salinity, pathogens and viral infections, can induce NAC expression, which participates in the regulation of plant stress resistance [17,18]. Previous studies have indicated that overexpression of ATAF1, a TF of NAC, can enhance resistance against powdery mildew in barley [19] and that OsNAC17 can enhance drought tolerance in rice [20]. Further, the LpNAC9 and LpNAC17 genes in lily (Lilium pumilum) were significantly expressed under abiotic stresses, such as drought, low temperatures, and salt stresses [21]. Additionally, NAC13, cloned from poplar (Populus L.), enhanced drought and salt tolerance in the plants [22]. Similarly, BpNACs mediated the low-temperature stress response of Betula plants [23].
NACs also contribute to leaf senescence. NtNAC080 in tobacco is a positive regulator of leaf senescence, as its overexpression leads to early senescence in Arabidopsis leaves [24]. AtNAP, NTL4 [25] and MtNAC96 [26] in Arabidopsis also exhibit a similar regulatory effect. Thus, the NAC family plays pivotal roles in various processes of plant growth and development and in response to environmental stresses. In recent years, NACs have been elaborately studied in medicinal plants. Twelve SbNACs are involved in regulating the synthesis of flavonoids in the flowers of Scutellaria baicalensis [27]. PgNAC41-2 positively regulates the biosynthesis of saponins in Panax ginseng [28] and the NAC family acts as a regulatory effector in the synthesis of a variety of metabolites under salt stress in Isatis indigotica [29]. However, a systematic study on the NAC gene family has not yet been clearly defined in Malvales, especially in Aquilaria sinensis.
Aquilaria species are aromatic and ornamental plants in south China and Southeast Asia. However, what make this species highly valuable is its production of agarwood, a dark-brown resin formed in the stem of Aquilaria species after injury or (a)biotic stresses [30,31]. Since antiquity, agarwood has been widely used as a natural spice, due to its favored smell and in traditional medicine, practices documented in the Holy Bible [32]. Agarwood is also a valuable medicinal herb and is used to treat ailments such as pain, stomach problems and vomiting [33,34]. Modern natural chemistry and pharmacology studies have revealed that 2-(2-phenyl) chromones (PECs) and sesquiterpenes are the main representative components in agarwood, whereas PECs are usually considered to be related to the quality of agarwood [35,36,37], but their biosynthesis mechanisms remain unclear. Recent studies have demonstrated that the plant type III PKS in Aquilaria sinensis is involved in the biosynthesis of diarylpentanoid, which is a ring-opening precursor of PECs. In previous research, plant type III PKS, chalcone synthase (CHS), has been found to catalyze the first rate-limiting step in the biosynthesis of flavonoids that are highly similar to those structures of PECs [38]. However, the remaining steps of PEC biosynthesis after the formation of the precursor of the C6–C5–C6 scaffold also remain mysterious, let alone type III PKS transcriptional regulation. The formation of agarwood is usually accompanied by the response of Aquilaria trees to (a)biotic stresses, and previous studies have indicated that many structural domain proteins of NAC are involved in the (a)biotic stress responses in plants, such as against bacteria, fungi, insects, drought, cold, salinity and mechanical damage [39]. These findings suggest that NAC might also be involved in agarwood formation, or in the regulation of PEC biosynthesis. Therefore, the characterization and functional analysis of NAC genes in A. sinensis are crucial for understanding their response to inducer treatment and injury stress and improving understanding of their roles in PEC biosynthesis and agarwood formation.
In this study, 1502 NAC genes were identified from the genomes of nine Malvales and three representative model plants. Our evolutionary analysis provides some evidence for an NAC gene family expansion occurring during the divergence of Malvales species. A total of 111 AsNAC transcription factors were characterized to explore their phylogenetic relationship, chromosome loci, gene structure, conserved motif, duplication types, intraspecific and interspecific synteny between A. sinensis and other species, and the transcriptional expression profiles in A. sinensis under inducer treatment and injury stresses. Finally, AsNAC019 and AsNAC098 were identified as potential candidates for the activation and regulation of PEC biosynthesis during agarwood formation. These systematic results will improve our understanding of the evolution and function of the NAC gene family in A. sinensis and Aquilaria trees’ response to various environmental stresses.

2. Results

2.1. Identification of the NAC Gene in A. sinensis and Eleven Other Species

To identify NAC gene sequences from A. sinensis and eleven other plant species (eight Malvales plants and three representative model species), BLAST and HMM searches were performed to identify their candidate genes. A total of 113 NAC protein sequences from Arabidopsis and seed sequences of PF01849 from PFAM, were used as query terms. In addition, the authenticity of the NAC structural domains in the candidate genes was further verified by searching the Pfam, CDD, MEME and eggNOG-mapper databases. Finally, a total of 111 NAC genes were identified in the A. sinensis genome (Table S1). Similarly, a total of 1278 NAC genes were identified from other species, including 86 from Corchorus capsularis, 81 from Corchorus olitorius, 126 from Dipterocarpus turbinatus, 229 from Durio zibethinus, 153 from Gossypium raimondii, 243 from Hibiscus cannabinus, 127 from Hopea hainanensis and 105 from Theobroma cacao, respectively. Overall, 44 NAC genes were identified in the Amborella trichopoda genome and 84 NAC genes were identified in the Vitis vinifera genome. NAC genes in the genomes of H. cannabinus and D. zibethinus were significantly more numerous compared to other Malvales species, whereas C. olitorius genome had the fewest NAC genes. The numbers presented in Table 1 were not corrected by BUSCO values, and the total number of genes of a gene family might be influenced by the quality of the genome assembly [40]. Therefore, the total numbers of NAC genes might need to be updated when better genome assemblies are available in the future.

2.2. Comparative Evolutionary Analysis of the NAC Family in Malvales

The expansion and contraction of NAC families were examined by reconstructing two phylogenetic trees: a phylogenetic tree of 12 plant species with 302 single-copy genes [41] and an evolutionary tree of all 1502 NAC genes. The results showed that a total of 84 ancestral genes were duplicated in the lineages that led to the common ancestor of A. trichopoda, A. thaliana, V. vinifera and Malvales plants. Later, 3 ancestral genes were lost and 97 ancestral genes were further duplicated in the lineages that were common ancestors of Malvales plants, A. thaliana, and V. vinifera (Figure 1). These events laid the foundation for the NAC gene family status in Arabidopsis, grape and A. sinensis. After two segregations, A. sinensis was separated from the other eight Malvales species and the ancestral genes began to expand. The earlier completion of differentiation of AsNAC among the Malvales plants suggests that NAC genes in A. sinensis are relatively conserved in the evolutionary process. Subsequently, the NAC ancestral genes of the remaining eight species of Malvales underwent different degrees of expansion before contractions, such as the number of ancestral genes in H. haianensis, D. turbinatus, C. capsularis, C. olitorius, G. raimondii or H. cannabinus (Figure 1).
It is well documented that gene families evolve through whole-genome duplications (WGD), segmental duplications and tandem duplications, which are accompanied by post-duplication diversification [42]. In this study, the duplication types of NAC genes in 12 species were examined (Table 1). The proportion of dispersed duplication and WGD-type NAC duplication were higher in A. sinensis. Regarding gene duplication events in other Malvales, C. capsularis, C. olitorius, T. cacao, and A. sinensis exhibited the same trends, while NAC genes in D. turbinatus, D. zibethinus, G. raimondii, H. cannabinus, and H. hainanensis were mainly retained as WGD events. This points to a different trend of replicative expansion of the NAC gene in A. sinensis compared to what is observed in other species. In particular, the number of NAC genes in D. zibethinus (229) and H. cannabinus (243) was almost double that in A. sinensis. In these two species, the recent WGD driven expansion accounted for 136 (59%) and 161 (66%) NAC genes, respectively. Our results suggest that the duplication types of WGD and dispersion may be the main driving forces for the NAC gene family expansion in Malvales plants.

2.3. Interspecific Synteny Analysis of AsNAC and NAC from Ten Other Species

To further explore the potential evolutionary events involving the NAC gene family across various species, we constructed the interspecific syntenic maps of A. sinensis with the two representative species (A. thaliana and grapevine) and eight Malvales plants (Figure 2). A total of 150 NAC gene pairs in D. zibethinus present the collinearity relationship with those in A. sinensis, followed by 130 in G. raimondii, 70 in T. cacao, 159 in H. cannabinus, 63 in C. capsularis, 64 in C. olitorius, 72 in V. vinifera, 76 in A. thaliana, 75 in H. hainanensis and 78 in D. turbinatu. Specifically, 20 AsNAC genes presented in a collinear manner in all of the other 10 species, while 37 AsNAC genes were not collinear with any of the other 10 species (Figure S1), which suggest that these genes may have been assigned a specific function in A. sinensis.
To understand the divergence time and positive selection of orthologous gene pairs, the nonsynonymous substitution rate (Ka), synonymous substitution rate (Ks), and Ka/Ks were calculated (Figure 3; Table S3). The Ka and Ks values of orthologous gene pairs ranged from 0.078 to 0.914 (Figure 3A) and 0.867 to 4.776 (Figure 3B), respectively. All the Ka/Ks ratios were below 1, indicating the NAC gene family from Malvales species is evolving under purifying selection (Figure 3C). Then, the divergence times of orthologous gene pairs between A. sinensis and ten other plants were estimated on the basis of the Ks values, and we found that the gene pairs might have diverged around 28–159 Mya ago [43,44].

2.4. Characterization, Chromosomal Localization and Intraspecific Syntenic Analysis of the AsNAC Genes

The physical maps demonstrated that 107 (96%) AsNAC genes were localized on 8 chromosomes (Figure 4), and the other 4 AsNAC genes were distributed on the unanchored scaffolds, which occupied 3.7% of all AsNAC genes. The ORF lengths of AsNACs were distributed from 210 bp (AsNAC087) to 2286 bp (AsNAC003), the amino acid length of AsNAC proteins ranged from 69 (AsNAC087) to 761 (AsNAC003), and the theoretical isoelectric points were between 4.39 (AsNAC046) and 9.85 (AsNAC029). The molecular weights of AsNAC proteins ranged from 7911.14 Da (AsNAC087) to 87,390.79 Da (AsNAC003). The average isoelectric point and molecular weight of AsNACs were 6.30 and 39,002.71 Da, respectively. The subcellular localization results showed that most of the AsNAC genes were localized in the nucleus (Table S2). In addition, the intraspecific homology of the AsNAC gene was analyzed (Figure 4). Twenty-nine intraspecific gene pairs were identified, all of which were derived from WGD, except AsNAC35 (tandem), AsNAC37 (proximal) and AsNAC81 (tandem).

2.5. Phylogenetic Analysis of AsNAC and AtNAC

To investigate their evolutionary relationship and classify the AsNACs, an unrooted evolutionary tree of NAC proteins from A. thaliana and A. sinensis was generated by IQ-TREE using the best-fit model of VT + F + I + I + R9 with the parameter of MFP (Figure 5). This led to the identification of separate clades of diverse subclasses of NAC genes in A. sinensis. Then, according to the NAC gene family classification system in Oryza sativa or A. thaliana [2], the independent classification of NAC genes in various subgroups of A. sinensis was carried out. We found that the NAC genes of A. sinensis could be categorized into the following 16 types: ANAC001, ANAC011, ANAC63, ATAF, ATNAC3, NAC1, NAC2, NAM, NAP, OsNAC7, OsNAC8, ONAC022, ONAC003, SENU5, TIP and TERN. The ONAC003 subfamily (11) contained the most AsNACs, and the OsNAC8 subfamilies only had one (the lowest) member, AsNAC013. Remarkably, 34 AsNAC genes were not classified according to the A. thaliana subgroups, and consequently formed 4 new subgroups. This indicated a possibility that these AsNACs may have obtained certain specific functions during A. sinensis evolution. A total of 53 (48%) NAC genes in A. sinensis originated from dispersed duplication, 35 (32%) NAC genes were duplicated as WGD or segmental, and 2 (2%), 5 (5%) and 16 (14%) genes were derived from singletons, proximal duplication and tandem duplication types, respectively. Among the new subgroups (34 AsNAC), only AsNAC097, AsNAC080, AsNAC070 and AsNAC073 were from WGD duplication (12%), indicating that dispersed (44%), proximal (5%), singleton (2%), and tandem (35%) duplication provide greater possibilities for the functional diversity of AsNAC genes (Figure 5, Table 1).

2.6. Gene Structure and Conserved Motif Analysis of the AsNAC Gene Family

During the evolutionary course of a species, genetic diversity plays an essential role in shaping phenotype diversity, which enables the plants to adapt to adverse environmental conditions and better use nearby natural resources [6]. We constructed a phylogenetic tree of 111 AsNAC proteins (Figure 6A) and analyzed their conserved motifs, which were visualized by CFVisual software (Figure 6B). The results showed that conserved motifs 1, 2, 3, 4, 7, and 9 were widely distributed in AsNAC proteins. The motifs in the unclassified sequences were diverse and corresponded to the intron–exon boundaries of this subgroup. Specific motifs may be associated with a particular function in different subgroups. All members of the AsNACs, especially in subgroup ONAC003, contained motif 8. Interestingly, motif 10 exists only in the subgroups of the unclassified proteins. Generally, NAC proteins that shared similar motifs were clustered in the same subgroups, indicating functional similarities between these members from the same subgroup.
To investigate the genomic features of AsNAC, the gene structures of the AsNAC genes were plotted (Figure 6C). The length of the introns of the AsNACs ranged from 0 to 5720 bp. No introns were identified in 12 AsNACs, most of which (except AsNAC008 and AsNAC009) were in the new subgroups. On the other hand, AsNAC081 contains the maximum number of 11 introns, followed by AsNAC014, which contains nine introns. The large number of introns in these genes could be due to the complex evolutionary history of AsNACs in A. sinensis. Furthermore, the number of exons in AsNAC genes is generally fewer than 10.

2.7. Expression Pattern of AsNAC Genes under Agarwood Inducer Treatment

To explore the function of AsNAC transcription factors in agarwood formation, their expression profiles under inducer treatment were analyzed. A total of 109 AsNAC genes exhibited expression patterns and formed three clusters. Cluster 1 contained 35 members with abundant transcription, and these genes showed various expression profiles. Among them, AsNAC076, AsNAC019, AsNAC060 and AsNAC039 were significantly upregulated after the inducer treatment. Cluster 2 contained 45 members, and their expression profiles were significantly higher than the other two clusters. Cluster 3 contained 29 members, and the expression of these genes was significantly downregulated after the inducer treatment (Figure 7).

2.8. Expression of AsNAC Genes under Injury Stress

To explore whether AsNACs are involved in regulating PEC biosynthesis, we selected 15 genes that are distributed in each of the branches and evaluated them by using RT-qPCR. These 15 AsNAC genes showed variable expression patterns at different stages after injury treatment (Figure 8). This indicated a possibility that these genes may exhibit various functions in a time/stage-dependent manner after injury stress in the stem of A. sinensis plants. Eight genes (AsNAC019, AsNAC022, AsNAC057, AsNAC097, AsNAC098, AsNAC097, AsNAC109 and AsNAC110) were significantly upregulated at 1 day after injury treatment, and then they were downregulated. AsNAC025 and AsNAC029 showed a continuous decrease in expression at days 1, 3, 5 and 6 after treatment. AsNAC025 and AsNAC029 showed a continuous downward trend in expression at days 1, 3, 5, and 6. AsNAC048 and AsNAC101 showed a significant downregulation of expression followed by an upregulation of expression (Figure 8A). Meanwhile, AsPKS01, AsPKS07, AsPKS08 and AsPKS09 were also selected to verify by RT-PCR and their expression patterns were significantly upregulated at days of 1 and 3, and downregulated at day 6 (Figure 8B). A correlation analysis performed between AsNAC and AsPKS gene expressions suggested that the expressions of AsNAC019, AsNAC068, and AsNAC098 showed positive correlations with those of AsPKS genes (Figure 8C). These results indicated that AsNAC019, AsNAC068, and AsNAC098 might be involved in the regulation of PEC biosynthesis as transcriptional activators to promote the expression of AsPKS genes.

2.9. Subcellular Localization of AsNAC019, AsNAC068 and AsNAC098

To clarify the subcellular localization of AsNAC019, AsNAC068, and AsNAC098, each of them was fused with a GFP tag, transformed into Agrobacterium tumefaciens and transfected into onion epidermal cells, respectively. The green fluorescence signals of AsNAC019-GFP, AsNAC068-GFP and AsNAC098-GFP were restricted to the nucleus (Figure 9A), whereas the fluorescent signal carrying the GFP tag alone was distributed throughout the cell. This suggests that AsNAC019, AsNAC068 and AsNAC098 are nucleus-localized proteins that may provide function in the nucleus (Figure 9A).

2.10. Transcriptional Activation of AsPKS07 by Interaction with AsNAC019, AsNAC068 and AsNAC098

To investigate the mechanisms behind AsNAC-mediated regulation of AsPKS07, AsNAC019, AsNAC068 and AsNAC098 were further selected to analyze the interactive activation with the promoter of AsPKS07, which was abandoned in the functional analysis due to its intron in the previous studies [45], and we identified that it also promoted PEC biosynthesis recently. The assays indicated that AsNAC019 and AsNAC098 proteins were able to bind and interact with the AsPKS07 promoter, whereas AsNAC068 did not exhibit the same function (Figure 9B).
To verify whether the AsNAC019 and AsNAC098 proteins promote the transcription of AsPKS07, a dual-luciferase reporter gene assay was performed in N. benthamiana leaves. The results indicated that AsNAC019 and AsNAC098 significantly increased the initiation activity of the promoter of AsPKS07 by 9.77- and 5.92-fold, respectively (Figure 9C). These findings suggest that AsNAC019 and AsNAC098 might activate the expression of AsPKS07.

3. Discussion

3.1. Identification and Evolution of NAC Transcription Factors

NAC is a unique and slightly larger family of transcription factors in plants. Their numbers are fewer only than those for bHLH, ERF and MYB. For example, 183 PbNAC genes were identified in white pear, 180 in apple, 167 NAC in cassava; 85 in Dendrobium nobile, 90 NAC in Dendrobium catenatum, 152 in Glycine max, 151 in Oryza sativa, and 226 such genes were identified in Triticum aestivum [46,47,48,49,50]. Recent studies have shown that the genes of the NAC family participate widely in various biological processes [51,52,53,54]. However, most of the studies on the function of NAC genes have focused on model plants or crops [55], such as A. thaliana, O. sativa and G. max. However, a systematic study of the NAC family in Malvales has not been conducted, especially in A. sinensis. The following numbers of NAC transcription factors were identified from nine Malvales plants in this study (Figure 1), including C. Capsularis (86), C. Olitorius (81), D. Turbinatus (126), D. Zibethinus (226), G. raimondii (153), H. Cannabinus (243), H. haianensis (127) and T. cacao (103). In particular, 111 NAC transcription factors were identified from A. sinensis, which were named AsNAC001–AsNAC111 (Figure 4). Apparently, the number of members of AsNAC gene families is lower than those in species that have undergone the events of WGT and WGD, but more than those in species that have only undergone the WGT event.
Gene duplication is a major evolutionary force for gene family expansion, for example, in the Arabidopsis genome, four major duplication events have occurred [56,57]. The number of AsNAC and AtNAC genes is comparable, and it was hypothesized that similar duplication events might have impacted them during the evolution of A. sinensis [58]. Furthermore, the research showed that all the NAC transcription factors have evolved from a common ancestor (direct lineage) and underwent many repetitive events during divergent and species-forming (paraphyletic) events that gave rise to different gene functions during plant development and growth [58]. Our analyses suggest that NAC is an ancient gene family and that the main drivers of its expansion in Malvales are the recent WGD and dispersed duplication events. Intergenomic covariance analysis showed that a large number of homologous gene pairs existed in A. sinensis and other Malvales plants (Figure 2), indicating that the AsNAC family was highly conserved during the evolutionary process. The Ka/Ks values also demonstrated that the purifying selection shaped the landscape of the NAC gene family in both the evolution and formation of Malvales plants (Figure 3). Furthermore, the vast majority of homologous genes in the intraspecific homology analysis were derived from the WGD event, which further suggests that the AsNAC genes expanded in the recent WGD events. Gene duplications may lead to functional redundancy and similar expression profiles might contribute to the same biological processes, for example, AsNAC064 and AsNAC065 share a consistent expression pattern. On the other hand, many homologous genes display differential expression patterns. According to the current theories, this may be due to the fact that duplicated genes have five modes of mutational selection [59].

3.2. Potential Function of NAC Genes in A. sinensis

In the phylogenetic tree within multispecies, genes belonging to a single branch tend to have potentially similar function [18]. In our study, the phylogenetic tree constructed by using the NAC proteins of A. sinensis and A. thaliana showed that homologues of all known NAC genes from A. thaliana could be found in members of the AsNAC gene families (Figure 5). This suggests that the NAC gene family existed before the divergence of these two species and therefore the genes in the same subfamily may present similar functions. For instance, the ATAF, NAP, and ATNAC3 subfamilies responded to the stresses [17,60,61], suggesting that AsNAC genes in these subfamilies might also contribute to these biological processes. In particular, four new branches containing proteins of unknown function were found in the phylogenetic tree. This may be due to the different environments in which A. sinensis and A. thaliana evolved, which led to their genetic differentiation. Therefore, the AsNAC genes in these new subclades may be related to specific biological traits of A. sinensis (Figure 5).
NAC transcription factors have highly conserved NAM structural domains at the N-terminus, which are associated with transcriptional regulatory activity and DNA binding [62]. In our analysis, conserved motifs 1 to 6 are annotated as NAM structural domains (Figure 6). Thus, all AsNAC genes contain at least one or more of the conserved motifs (1 to 6). In the ONAC003 subfamily, conserved motif 8 was specifically assigned and labeled NAC domain-containing protein suppressor of gamma response 1 (SOG1)-like, which has a conserved role in processes involved in secondary cell wall formation and stress responses. AtNAC107 and AtNA082 in the ONAC003 subfamily have been indicated as transcriptional activators that stimulate the expression of the secondary cell wall formation-related transcription factor MYB46 [63]. Further, the plant-specific transcription factor SOG1 (AtNAC010) played a key role in the transmission of ATM and ATR kinase signals that regulate the repair of damaged DNA [64,65]. These results suggest that the AsNAC genes in the ONAC003 subfamily may be endowed with similar functions (Figure 6). In addition, a total of 10 AsNAC genes (AsNAC003, 006, 035, 036, 037, 041, 062, 070, 073 and 086) have a conserved motif 10, and all of them belong to unclassified subfamilies. Combined with covariance analysis, nine AsNAC genes, except AsNAC003, were not homologous to any NAC genes of the other ten species (Figure 6), which implied that these genes could have acquired unique functions during the evolution of A. sinensis.

3.3. Possible Role of NAC Genes in Secondary Metabolite Synthesis in A. sinensis

The patterns of expression of AsNAC genes could provide valuable insights for probing the role of AsNAC genes in specific physiological processes. Agarwood is typically produced due to injury in A. sinensis. The accumulation of PEC could be increased depending on the treatment of the agarwood inducer. In this study, many AsNAC genes showed differential expression under agarwood inducer treatment (Figure 7). Most of the AsNAC genes in clusters 1 and 2 exhibited high expression. AsNAC genes belonging to ATAF, ATNAC3 and NAP subfamilies appeared in cluster 1 and cluster 3, and exhibited significantly high expression. AtNAC002, in the same subfamily, was found to be upregulated under a variety of abiotic stresses and gray mold infection [66]; AtNAC110 plays a regulatory role in hypoxic stress in plant seedlings [67]. Similarly, AtNAC088 is thought to be involved in multiple defenses against pathogen infection and in response to injury stimuli [68]. Our results indicate that the AsNAC genes in these three subclades may be involved in abiotic stress and defense responses in A. sinensis.
The NAC family of transcription factors may also contribute to the regulation of the secondary metabolite biosynthesis of plants. Overexpression of the PaNAC03 transcription factor in Picea abies leads to an independent negative regulation of flavan-3-ol biosynthesis [69]. SmNAC2 promotes the accumulation of tanshinone I in medicinal ginseng [70], and the PpNAC transcription factor known as BLOOD (BL) was identified in peach (Prunus persica), which can form a heterodimer with PpNAC1 and activate the transcription of PpMYB10.1 to promote the accumulation of anthocyanins in peach fruits [71]. In addition, the LcNAC002 transcription factor co-activates the expression of LcSGR and LcMYB1 in lychee to help in chlorophyll degradation and anthocyanin biosynthesis [72]. Banana ripening-induced MaNAC1 is involved in the banana fruit cold response by interacting with MaCBF1 [73]. The greatest economic value of the A. sinensis plant comes from the formation of agarwood, in which PECs are characteristic components whose contents form the benchmark for high-quality agarwood [74]. However, the molecular regulatory mechanisms underlying the formation of PECs are poorly understood.
Biochemically, plant type III PKSs are considered vital and multifunctional enzymes in the secondary metabolite biosynthesis processes of plants in the form of alkaloids, flavonoids or stilbene [75]. Type III PKSs can generate the precursor of PECs by catalyzing malonyl-CoA and 4-hydroxyphenylpropionyl-CoA [45,76]. Our recent studies have demonstrated that the transcription factors in A. sinensis were also involved in the regulation of AsPKS expression, such as AsMYB054, which was the repressor in the transcripts of AsPKS02 and AsPKS09 [39]. It is interesting that a syntenic gene pair of AsbZIP14 and AsbZIP41 presents a different interaction with AsPKS from the same subtype of typical type III PKS, especially for AsbZIP14, which activated the expression of AsPKS08 and repressed the expression of AsPKS09 [41]. By combining bioinformatics analysis and gene expression data, we also identified two candidate genes that may be associated with the accumulation of PECs (Figure 8). Then, yeast one-hybrid and two-luciferase assays indicated that AsNAC019 and AsNAC098 were the activators to regulate the expression pattern of AsPKS by binding the specific sequences in the promoter of AsPKS07 (Figure 9). Taken together, our findings suggest that AsNACs may act as transcriptional regulators in AsPKS expression to contribute to PEC biosynthesis and agarwood formation, which should be further studied in future research.

4. Materials and Methods

4.1. Plant Material and Treatment

The samples of A. sinensis were collected from Wenchang Nursery Garden (19°54′ N, 110°77′ E). To eliminate physiological and environmental influences, three-year-old trees were selected, and the samples were collected from branches of similar length and age. Holes were drilled into the trunk, approximately 10 cm above the base, 5 mm in diameter and 1 cm deep. Stem segments within 3 cm of the hole were collected after the treatment at days of 0, 1, 3 and 6. Total RNA was immediately isolated with the Plant Total RNA Isolation Kit Plus (FOREGENE, Chengdu, China) according to the manufacturer’s instructions. Then, cDNA was synthesized with the Fastking RT kit (TIANGEN, Beijing, China). The seedlings of Nicotiana benthamiana were planted with a photoperiod of 12/12 h (day/night) at 24 °C in the greenhouse at the Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (19°98′ N, 110°33′). Each treatment contained three biological replicates [41]. The seeds of N. benthamiana were obtained from the lab of Dr. Yuan Yao in our institute.

4.2. Identification of NAC Gene Family in the Genomes of A. sinensis and 11 Other Plants

The protein sequence of NAC genes in A. thaliana were collected from the plant transcription factor database (TFDB) [77]. First, the protein sequences of AtNAC were used as a query to align the protein sequences of A. sinensis by using BlastP [78] with an E-value cutoff of less than 1 × 10−5. Meanwhile, the sequences of PF01849, from the PFAM database [79], were also used as seed NAC genes to scan the protein database of A. sinensis with an HMM search with E-value of 1 × 10−5. The results from BLAST and HMM searches were combined to generate the candidate genes of AsNAC. These candidates were then verified with CCD [80], MEME [81], InterPro [79], and eggNOG-mapper with default parameters [82].
The genome sequences and files of A. trichopoda, C. capsularis, C. olitorius, D. turbinatus, D. zibethinus, G. raimondii, H. cannabinus, H. hainanensis, T. cacao and V. vinifera were collected from NCBI, and the NAC transcription factor family in these plants was then identified with the same method as described above for AsNACs. ExPASy software (https://www.expasy.org/) was employed to evaluate the physiochemical properties of AsNACs, including the length of ORF and protein, the molecular weight (MW), aliphatic index and instability, and the grand average of hydropathicity (GRAVY) [83].

4.3. Expansion and Contraction of NAC Genes

Two evolutionary trees were constructed to illuminate the duplication and loss of the NAC gene family in Malvales. Firstly, a phylogenetic tree of species was constructed by using OrthoFinder v 2.5.4 based on the single-copy genes from the 12 species genomes. This tree is the same as that used in our previous study [40,84]. Secondly, a phylogenetic tree of all NAC protein sequences from the 12 species was aligned with MAFFT v.7.310 [85] before constructing an evolutionary tree of proteins using FastTree v 2.1.11 [86]. These two phylogenetic trees were finally analyzed with Notung v 2.9.13 to generate the events of duplications and losses concerning the NAC gene family in Malvales species evolution [87].

4.4. Identification of Syntenic Genes and Calculation of Ka, Ks and Ka/Ks Values

MCScanX was used to detect gene duplicate types on the basis of BLASTP results from the protein database of each of the species against itself with a cutoff of 1 × 10−5 [88]. The identification of potentially homologous gene pairs across multiple genomes was performed with BLASTP with a cutoff of 1 × 10−5 [78]. The syntenic gene pairs of NAC from A. sinensis and ten other species were also identified and visualized by using JCVI v 0.8.4 [89]. The values of Ka, Ks and Ka/Ks were calculated using the MA model in KaKs_calculator 3.0 by using the coding sequences of orthologous gene pairs of A. sinensis and the other ten species identified from WGDI v0.6.5 [90]. The divergence periods of each orthologous gene pair were calculated using the formula of T = Ks/2r, where Ks is the synonymous substitution rate per site as mentioned above, and the rate of divergence of the nuclear gene of r is set as 1.5 × 10−8, which is the synonymous substitutions per site per year of dicotyledonous plants [91].

4.5. Phylogenetic Analysis and Chromosomal Localization of the AsNAC Transcription Factors

The MUSCLE program was used to align NAC protein sequences from A. sinensis and A. thaliana [92,93]. Then, the best model, VT + F + I + I + R9, was selected to construct a phylogenetic tree using IQ-tree v 2.2.0 with the following parameters: -m MFP -B 1000 --bnni -T AUTO [94,95]. The phylogenetic tree was then visualized using iTOL [96]. The gene location of AsNACs on the chromosomes of the A. sinensis genome and their intraspecific synteny were analyzed with JCVI 0.84 and visualized with Circos v0.9 [97,98].

4.6. Gene Structure and Conserved Motif Analyses

The arrangement of exons/introns from AsNAC genes was illustrated with GSDS software (http://gsds.gao-lab.org/index.php) [99] using the sequences of genomic DNA and the corresponding CDS region. The 5′ untranslated regions (UTRs) were removed for better comparisons and visualization. The conserved motifs of AsNAC proteins were searched with MEME software (https://meme-suite.org/meme/tools/meme) [81], where the maximum numbers were set as 10 and the optimal motif width was between 30 and 50 amino acids. The conserved motifs were then visualized with the help of CFVisual V2.1.5 software [100].

4.7. Real-Time Quantitative PCR (RT-qPCR) Analysis

Fifteen NAC genes distributed in each branch were selected on the basis of their differential expression of log2-fold change ≥2 in our previous study for further analysis by RT-qPCR [41]. For RT-qPCR, a histone gene (His) was selected as the housekeeping gene [101] and the reaction was run on a CFX96 Real-Time System (Bio-Rad, Hercules, CA, USA). The reaction mixture of a total volume of 20 μL was set as follows: 10 μL 2 × RealUniversal PreMix(TIANGEN), 1 μL of cDNA(100 ng/μL), 0.25 μL primers (0.3 μM) for each of forward and reverse, and 8.5 μL of dd H2O. Three biological replicates and two technical replicates were used, and the results were analyzed using the 2−ΔΔCT method [40,102]. The primers used in RT-qPCR are listed in Table S4.

4.8. Gene Cloning and Subcellular Localization of AsNAC Genes

The primers for AsNAC19, AsNAC 68, and AsNAC 98 were designed and synthesized by Sangon Biotech, Shanghai, China (Table S5). According to the manufacturer’s instructions (MonAmpTM, Monad Biotech, Suzhou, China), the PCR reaction mixture included 25 μL of MonAmpTM 2 × Taq Mix (+Dye), 1 μL forward and reverse primers of each (10 μmol/L), and 1 μL of cDNA (100 ng/μL), and the final volume was 50 μL by dd H2O fixed. The reaction parameters were set as follows: pre-denaturation for 2 min at 95 °C, denaturation for 40 s at 95 °C, annealing for 40 s at 55° C, extension for 1 min at 72 °C, 35 cycles, and refolding for 5 min at 72 °C [39].
The sequences of three AsNAC plasmids, verified by the method of Sanger sequencing, were used to construct a recombinant vector of pNC-Green-SubN-AsNAC [103]. The recombinant vector was transferred into Agrobacterium tumefaciens GV3101 receptor cells, which was then infiltrated into the cells of the onion epidermis [39,41]. Transfected onion cells were cultured in the dark at 28 °C for 48 h and the fluorescence values of GFP were attained with a confocal laser scanning microscope (Olympus Corporation, Tokyo, Japan) at 488 nm.

4.9. Yeast One-Hybrid (Y1H) Assay

The Y1H assay was carried out using the Matchmaker Gold Y1H System (Clontech, Mountain View, CA, USA). The primers used to amplify the promoters of AsPKS07 (1351 bp) and AsPKS09 (1272 bp) were described in our previous study [39,40]. These amplified fragments were then integrated into the pHis2.1 vector to form the bait vector, referred to as AsPKSspro-His2.1. Simultaneously, the coding sequence of AsNACs was also transformed into the pNC-GADT7 vector via Nimble cloning, generating the prey vector named pNC-GADT7-AsNAC [103]. Then, both the prey and bait plasmids were co-transformed into yeast cells of strain Y187. The transformed yeast Y187 strain housed these bait and prey vectors, which were cultivated at 28 °C for 5 days. This cultivation occurred on a selective medium that lacked tryptophan (Trp), histidine (His), and leucine (Leu), while being added to a proper concentration (0.5 mM) of 3-amino-1,2,4-triazole (3AT). Notably, this medium did not contain Trp, Leu, or His (referred to as SD/-TLH + 3-AT).

4.10. Dual-Luciferase Assay

The promoter sequences of AsPKS07 and AsPKS09 were transformed into the pGreenII 0800-LUC vector to create reporter constructs and the coding sequences of AsNAC019 and AsNAC098 were integrated into the pGreenII 62-SK vector as the effector plasmids, also employing the Nimble Cloning system [103]. These dual-luciferase recombinant plasmids were subsequently introduced into the A. tumefaciens strain GV3101, which hosted both pGreenII 0800-LUCpAsPKSs and pGreenII 62SK-AsNAC mixed in a 1:2 volume ratio. This mixed culture was co-transiented into N. benthamiana leaves while the OD600 values reached 0.8 [39]. The luciferase activities were assessed after co-inoculation for 72 h using a dual-luciferase reporter assay kit (Promega, Madison, WI, USA). The ratio of luciferase activities to renilla luciferase activities was then calculated to estimate the transcriptional activity.

5. Conclusions

A total of 1502 NAC transcription factors were identified in 12 high-quality genomes from the species of Malvales or model plants. Recent WGD might be the driving force behind the current layout of NAC in Malvales according to the phylogenetic relationship between species and genes. However, as the basal species in Malvales, A. sinensis preserved the medium members of NAC, even though this species also experienced the recent WGD event. Therefore, the characterization of 111 AsNAC genes was systemically analyzed. The data from the transcriptome and RT-qPCR indicated that AsNAC genes may be extensively involved in agarwood formation and stress response. Finally, AsNAC019 and AsNAC098 were demonstrated to positively regulate the expression of AsPKS07 via binding to its promoter. These findings advance our knowledge of the functional and regulatory mechanisms of NAC transcription factors in the plant, especially by improving our understanding of their roles in secondary metabolite biosynthesis and environmental stress response.

Supplementary Materials

The following supporting information can be downloaded at https://www.mdpi.com/article/10.3390/ijms242417384/s1.

Author Contributions

Conceptualization, X.D., H.D. and W.M. methodology, X.D.; software, X.D. and Z.Y.; validation, Z.Y., W.M. and H.W. formal analysis, Z.Y.; investigation, X.D.; resources, Z.Y. and J.Z.; data curation, Z.Y. and X.D.; writing—original draft preparation, Z.Y. and X.D.; writing—review and editing, H.W., H.D. and W.M.; visualization, H.D. and W.M.; supervision, H.D.; project administration, W.M.; funding acquisition, X.D., W.M. and H.D. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the National Natural Science Foundation of China (31870668 and 32171824), the Central Public-interest Scientific Institution Basal Research Fund for Chinese Academy of Tropical Agricultural Sciences (1630052020003) and the Earmarked Fund of the China Agriculture Research System (CARS-21).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Data resulting from the database search are available in the Supplementary files.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Liu, X.; Wang, T.; Bartholomew, E.; Black, K.; Dong, M.; Zhang, Y.; Yang, S.; Cai, Y.; Xue, S.; Weng, Y.; et al. Comprehensive analysis of NAC transcription factors and their expression during fruit spine development in cucumber (Cucumis sativus L.). Hortic. Res. 2018, 5, 31. [Google Scholar] [CrossRef] [PubMed]
  2. Ooka, H.; Satoh, K.; Doi, K.; Nagata, T.; Otomo, Y.; Murakami, K.; Matsubara, K.; Osato, N.; Kawai, J.; Carninci, P.; et al. Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana. DNA Res. 2003, 10, 239–247. [Google Scholar] [CrossRef]
  3. Shen, S.Y.; Zhang, Q.R.; Shi, Y.; Sun, Z.M.; Zhang, Q.Q.; Hou, S.J.; Wu, R.L.; Jiang, L.B.; Zhao, X.Y.; Guo, Y.Q. Genome-wide analysis of the NAC domain transcription factor gene family in Theobroma cacao. Genes 2020, 11, 35. [Google Scholar] [CrossRef] [PubMed]
  4. Yue, Y.Z.; Li, L.; Li, Y.L.; Li, H.Y.; Ding, W.J.; Shi, T.T.; Chen, G.W.; Yang, X.L.; Wang, L.G. Genome-wide analysis of NAC transcription factors and characterization of the cold stress response in Sweet osmanthus. Plant Mol. Biol. Rep. 2020, 38, 314–330. [Google Scholar] [CrossRef]
  5. Munir, N.; Chen, Y.K.; Chen, X.H.; Nawaz, M.A.; Iftikhar, J.; Rizwan, H.M.; Xu, S.; Lin, Y.L.; Xu, X.H.; Lai, Z.X. Genome-wide identification and comprehensive analyses of NAC transcription factor gene family and expression patterns during somatic embryogenesis in Dimocarpus longan Lour. Plant Physiol. Bioch. 2020, 157, 169–184. [Google Scholar] [CrossRef] [PubMed]
  6. Liu, J.; Qiao, Y.; Li, C.; Hou, B. The NAC transcription factors play core roles in flowering and ripening fundamental to fruit yield and quality. Front. Plant Sci. 2023, 14, 1095967. [Google Scholar] [CrossRef]
  7. Han, K.J.; Zhao, Y.; Sun, Y.H.; Li, Y. NACs, generalist in plant life. Plant Bio. J. 2023, 21, 1–25. [Google Scholar] [CrossRef]
  8. Moyano, E.; Martinez-Rivas, F.J.; Blanco-Portales, R.; Molina-Hidalgo, F.J.; Ric-Varas, P.; Matas-Arroyo, A.J.; Caballero, J.L.; Munoz-Blanco, J.; Rodriguez-Franco, A. Genome-wide analysis of the NAC transcription factor family and their expression during the development and ripening of the Fragaria x ananassa fruits. PLoS ONE 2018, 13, e0196953. [Google Scholar] [CrossRef]
  9. Min, X.Y.; Jin, X.Y.; Zhang, Z.S.; Wei, X.Y.; Ndayambaza, B.; Wang, Y.R.; Liu, W.X. Genome-wide identification of NAC transcription factor family and functional analysis of the abiotic stress-responsive genes in Medicago sativa L. J. Plant Growth Regul. 2020, 39, 324–337. [Google Scholar] [CrossRef]
  10. Hussey, S.G.; Saidi, M.N.; Hefer, C.A.; Myburg, A.A.; Grima-Pettenati, J. Structural, evolutionary and functional analysis of the NAC domain protein family in Eucalyptus. New Phytol. 2015, 206, 1337–1350. [Google Scholar] [CrossRef]
  11. Yang, X.F.; Kim, M.Y.; Ha, J.; Lee, S.H. Overexpression of the soybean NAC gene GmNAC109 increases lateral root formation and abiotic stress tolerance in transgenic Arabidopsis plants. Front. Plant Sci. 2019, 10, 1036. [Google Scholar] [CrossRef]
  12. Ma, N.N.; Feng, H.L.; Meng, X.; Li, D.; Yang, D.Y.; Wu, C.G.; Meng, Q.W. Overexpression of tomato SlNAC1 transcription factor alters fruit pigmentation and softening. BMC Plant Biol. 2014, 14, 351. [Google Scholar] [CrossRef] [PubMed]
  13. Wang, J.F.; Tian, S.W.; Yu, Y.T.; Ren, Y.; Guo, S.G.; Zhang, J.; Li, M.Y.; Zhang, H.Y.; Gong, G.Y.; Wang, M.; et al. Natural variation in the NAC transcription factor NONRIPENING contributes to melon fruit ripening. J. Integr. Plant Biol. 2022, 64, 1448–1461. [Google Scholar] [CrossRef] [PubMed]
  14. Wang, Q.; Guo, C.; Li, Z.Y.; Sun, J.H.; Deng, Z.C.; Wen, L.C.; Li, X.X.; Guo, Y.F. Potato NAC transcription factor StNAC053 enhances salt and drought tolerance in transgenic Arabidopsis. Int. J. Mol. Sci. 2021, 22, 2568. [Google Scholar] [CrossRef]
  15. Trishla, V.S.; Kirti, B. Structure-function relationship of Gossypium hirsutum NAC transcription factor, GhNAC4 with regard to ABA and abiotic stress responses. Plant Sci. 2021, 302, 110718. [Google Scholar] [CrossRef] [PubMed]
  16. Nuruzzaman, M.; Sharoni, A.M.; Kikuchi, S. Roles of NAC transcription factors in the regulation of biotic and abiotic stress responses in plants. Front. Microbiol. 2013, 4, 248. [Google Scholar] [CrossRef]
  17. Liu, M.Y.; Ma, Z.T.; Sun, W.J.; Huang, L.; Wu, Q.; Tang, Z.Z.; Bu, T.L.; Li, C.L.; Chen, H. Genome-wide analysis of the NAC transcription factor family in Tartary buckwheat (Fagopyrum tataricum). BMC Genom. 2019, 20, 113. [Google Scholar] [CrossRef]
  18. Li, W.H.; Zeng, Y.L.; Yin, F.L.; Wei, R.; Mao, X.F. Genome-wide identification and comprehensive analysis of the NAC transcription factor family in sunflower during salt and drought stress. Sci. Rep. 2021, 11, 19865. [Google Scholar] [CrossRef]
  19. Jensen, M.K.; Hagedorn, P.H.; de Torres-Zabala, M.; Grant, M.R.; Rung, J.H.; Collinge, D.B.; Lyngkjaer, M.F. Transcriptional regulation by an NAC (NAM-ATAF1,2-CUC2) transcription factor attenuates ABA signalling for efficient basal defence towards Blumeria graminis f. sp. hordei in Arabidopsis. Plant J. 2008, 56, 867–880. [Google Scholar] [CrossRef]
  20. Jung, S.E.; Kim, T.H.; Shim, J.S.; Bang, S.W.; Bin Yoon, H.; Oh, S.H.; Kim, Y.S.; Oh, S.J.; Seo, J.S.; Kim, J.K. Rice NAC17 transcription factor enhances drought tolerance by modulating lignin accumulation. Plant Sci. 2022, 323, 111404. [Google Scholar] [CrossRef]
  21. Guan, C.J.; Wang, Y.; Zhang, Y.N. Molecular characterization and transcription profiling of NAC genes in Lilium pumilum under abiotic stresses. Int. J. Agric. Biol. 2020, 23, 484–492. [Google Scholar]
  22. Cheng, Z.H.; Zhang, X.M.; Zhao, K.; Zhou, B.R.; Jiang, T.B. Ectopic expression of a poplar gene NAC13 confers enhanced tolerance to salinity stress in transgenic Nicotiana tabacum. J. Plant Res. 2020, 133, 727–737. [Google Scholar] [CrossRef] [PubMed]
  23. Chen, S.; Lin, X.; Zhang, D.; Li, Q.; Zhao, X.; Chen, S. Genome-wide analysis of NAC gene family in Betula pendula. Forests 2019, 10, 741. [Google Scholar] [CrossRef]
  24. Li, W.; Li, X.X.; Chao, J.T.; Zhang, Z.L.; Wang, W.F.; Guo, Y.F. NAC family transcription factors in tobacco and their potential role in regulating leaf senescence. Front. Plant Sci. 2018, 9, 1900. [Google Scholar] [CrossRef] [PubMed]
  25. Lee, S.; Seo, P.J.; Lee, H.J.; Park, C.M. A NAC transcription factor NTL4 promotes reactive oxygen species production during drought-induced leaf senescence in Arabidopsis. Plant J. 2012, 70, 831–844. [Google Scholar] [CrossRef]
  26. de Zelicourt, A.; Diet, A.; Marion, J.; Laffont, C.; Ariel, F.; Moison, M.L.; Zahaf, O.; Crespi, M.; Gruber, V.; Frugier, F. Dual involvement of a Medicago truncatula NAC transcription factor in root abiotic stress response and symbiotic nodule senescence. Plant J. 2012, 70, 220–230. [Google Scholar] [CrossRef]
  27. He, H.; Li, Q.Y.; Fang, L.; Yang, W.; Xu, F.C.; Yan, Y.; Mao, R.J. Comprehensive analysis of NAC transcription factors in Scutellaria baicalensis and their response to exogenous ABA and GA3. Int. J. Biol. Macromol. 2023, 244, 125290. [Google Scholar] [CrossRef]
  28. Liu, C.; Zhao, M.Z.; Ma, H.D.; Zhang, Y.; Liu, Q.; Liu, S.Z.; Wang, Y.F.; Wang, K.Y.; Zhang, M.P.; Wang, Y. The NAC transcription factor PgNAC41-2 gene involved in the regulation of ginsenoside biosynthesis in Panax ginseng. Int. J. Mol. Sci. 2023, 24, 11946. [Google Scholar] [CrossRef]
  29. Wang, Z.; Zhang, Z.P.; Wang, P.P.; Qin, C.; He, L.Q.; Kong, L.Y.; Ren, W.C.; Liu, X.B.; Ma, W. Genome-wide identification of the NAC transcription factors family and regulation of metabolites under salt stress in Isatis indigotica. Int. J. Biol. Macromol. 2023, 240, 124436. [Google Scholar] [CrossRef]
  30. Ding, X.P.; Mei, W.L.; Lin, Q.; Wang, H.; Wang, J.; Peng, S.Q.; Li, H.L.; Zhu, J.H.; Li, W.; Wang, P.; et al. Genome sequence of the agarwood tree Aquilaria sinensis (Lour.) Spreng: The first chromosome-level draft genome in the Thymelaeceae family. Gigascience 2020, 9, giaa013. [Google Scholar] [CrossRef]
  31. Li, W.; Chen, H.Q.; Wang, H.; Mei, W.L.; Dai, H.F. Natural products in agarwood and Aquilaria plants: Chemistry, biological activities and biosynthesis. Nat. Prod. Rep. 2021, 38, 528–565. [Google Scholar] [CrossRef] [PubMed]
  32. Dafni, A.; Böck, B. Medicinal plants of the Bible—Revisited. J. Ethnobiol. Ethnomed. 2019, 15, 57. [Google Scholar] [CrossRef]
  33. Yang, H.R.; Wang, P.; Liu, F.Z.; Yuan, J.Z.; Cai, C.H.; Wu, F.; Jiang, B.; Mei, W.L.; Dai, H.F. Dimeric 2-(2-phenethyl)chromones from agarwood of Aquilaria filaria. Fitoterapia 2023, 165, 105422. [Google Scholar] [CrossRef] [PubMed]
  34. Ma, J.; Huo, H.; Zhang, H.; Wang, L.; Meng, Y.; Jin, F.; Wang, X.; Zhao, Y.; Zhao, Y.; Tu, P. 2-(2-phenylethyl) chromone-enriched extract of the resinous heartwood of Chinese agarwood (Aquilaria sinensis) protects against taurocholic acid-induced gastric epithelial cells apoptosis through Perk/eIF2α/CHOP pathway. Phytomedicine 2022, 98, 153935. [Google Scholar] [CrossRef]
  35. Chen, L.Y.; Chen, H.Q.; Cai, C.H.; Yuan, J.Z.; Gai, C.J.; Liu, S.B.; Mei, W.L.; Dai, H.F. Seven new 2-(2-phenethyl)chromone derivatives from agarwood of Aquilaria walla. Fitoterapia 2023, 165, 105421. [Google Scholar] [CrossRef] [PubMed]
  36. Wang, H.N.; Dong, W.H.; Huang, S.Z.; Li, W.; Kong, F.D.; Wang, H.; Wang, J.; Mei, W.L.; Dai, H.F. Three new sesquiterpenoids from agarwood of Aquilaria crassna. Fitoterapia 2016, 114, 7–11. [Google Scholar] [CrossRef]
  37. Yu, Z.X.; Wang, C.H.; Zheng, W.; Chen, D.L.; Liu, Y.Y.; Yang, Y.; Wei, J.H. Anti-inflammatory 5,6,7,8-tetrahydro-2-(2-phenylethyl)chromones from agarwood of Aquilaria sinensis. Bioorg. Chem. 2020, 99, 103789. [Google Scholar] [CrossRef]
  38. Mallika, V.; Sivakumar, K.C.; Soniya, E.V. Evolutionary implications and physicochemical analyses of selected proteins of type III polyketide synthase family. Evol. Bioinform. 2011, 7, 41–53. [Google Scholar] [CrossRef]
  39. Yang, Y.; Zhu, J.H.; Wang, H.; Guo, D.; Wang, Y.; Mei, W.L.; Peng, S.Q.; Dai, H.F. Systematic investigation of the R2R3-MYB gene family in Aquilaria sinensis reveals a transcriptional repressor AsMYB054 involved in 2-(2-phenylethyl) chromone biosynthesis. Int. J. Biol. Macromol. 2023, 244, 125302. [Google Scholar] [CrossRef]
  40. Jauhal, A.A.; Newcomb, R.D. Assessing genome assembly quality prior to downstream analysis: N50 versus BUSCO. Mol. Ecol. Resour. 2021, 21, 1416–1421. [Google Scholar] [CrossRef]
  41. Zhang, H.; Ding, X.P.; Wang, H.; Chen, H.Q.; Dong, W.H.; Zhu, J.H.; Wang, J.; Peng, S.Q.; Dai, H.F.; Mei, W.L. Systematic evolution of bZIP transcription factors in Malvales and functional exploration of AsbZIP1 and AsbZIP41 in Aquilaria sinensis. Front. Plant Sci. 2023, 14, 1243323. [Google Scholar] [CrossRef] [PubMed]
  42. Crow, K.D.; Wagner, G.P.; Investigators, S.T.-N.Y. What is the role of genome duplication in the evolution of complexity and diversity? Mol. Biol. Evol. 2006, 23, 887–892. [Google Scholar] [CrossRef]
  43. Tiffin, P.; Hahn, M.W. Coding sequence divergence between two closely related plant species: Arabidopsis thaliana and Brassica rapa ssp. pekinensis. J. Mol. Evol. 2002, 54, 746–753. [Google Scholar] [CrossRef] [PubMed]
  44. Gao, H.; Suo, X.M.; Zhao, L.; Ma, X.L.; Cheng, R.H.; Wang, G.P.; Zhang, H.S. Molecular evolution, diversification, and expression assessment of MADS gene family in Setaria italica, Setaria viridis, and Panicum virgatum. Plant Cell Rep. 2023, 42, 1003–1024. [Google Scholar] [CrossRef] [PubMed]
  45. Wang, X.H.; Gao, B.W.; Nakashima, Y.; Mori, T.; Zhang, Z.X.; Kodama, T.; Lee, Y.E.; Zhang, Z.K.; Wong, C.P.; Liu, Q.Q.; et al. Identification of a diarylpentanoid-producing polyketide synthase revealing an unusual biosynthetic pathway of 2-(2-phenylethyl)chromones in agarwood. Nat. Commun. 2022, 13, 348. [Google Scholar] [CrossRef] [PubMed]
  46. Su, H.; Zhang, S.; Yuan, X.; Chen, C.; Wang, X.-F.; Hao, Y.-J. Genome-wide analysis and identification of stress-responsive genes of the NAM–ATAF1, 2–CUC2 transcription factor family in apple. Plant Physiol. Bioch. 2013, 71, 11–21. [Google Scholar] [CrossRef]
  47. Gong, X.; Zhao, L.; Song, X.; Lin, Z.; Gu, B.; Yan, J.; Zhang, S.; Tao, S.; Huang, X. Genome-wide analyses and expression patterns under abiotic stress of NAC transcription factors in white pear (Pyrus bretschneideri). BMC Plant Biol. 2019, 19, 161. [Google Scholar] [CrossRef]
  48. Ma, J.H.; Yuan, M.; Sun, B.; Zhang, D.J.; Zhang, J.; Li, C.X.; Shao, Y.; Liu, W.; Jiang, L.N. Evolutionary divergence and biased expression of NAC transcription factors in hexaploid bread wheat (Triticum aestivum) L. Plants 2021, 10, 382. [Google Scholar] [CrossRef]
  49. Fu, C.; Liu, M. Genome-wide identification and molecular evolution of NAC gene family in Dendrobium nobile. Front. Plant Sci. 2023, 14, 1232804. [Google Scholar] [CrossRef]
  50. Li, Y.; Zhang, T.; Xing, W.; Wang, J.; Yu, W.; Zhou, Y. Comprehensive genomic characterization of the NAC transcription factors and their response to drought stress in Dendrobium catenatum. Agronomy 2022, 12, 2753. [Google Scholar] [CrossRef]
  51. Olsen, A.N.; Ernst, H.A.; Leggio, L.L.; Skriver, K. NAC transcription factors: Structurally distinct, functionally diverse. Trend. Plant Sci. 2005, 10, 79–87. [Google Scholar] [CrossRef] [PubMed]
  52. So, H.A.; Lee, J.H. NAC transcription factors from soybean (Glycine max L.) differentially regulated by abiotic stress. J. Plant Biol. 2019, 62, 147–160. [Google Scholar] [CrossRef]
  53. Le, D.T.; Nishiyama, R.; Watanabe, Y.; Mochida, K.; Yamaguchi-Shinozaki, K.; Shinozaki, K.; Tran, L.S.P. Genome-wide survey and expression analysis of the plant-specific NAC transcription factor family in soybean during development and dehydration stress. DNA Res. 2011, 18, 263–276. [Google Scholar] [CrossRef] [PubMed]
  54. Ling, L.; Song, L.L.; Wang, Y.J.; Guo, C.H. Genome-wide analysis and expression patterns of the NAC transcription factor family in Medicago truncatula. Physiol. Mol. Biol. Plants 2017, 23, 343–356. [Google Scholar] [CrossRef]
  55. Jensen, M.K.; Skriver, K. NAC transcription factor gene regulatory and protein-protein interaction networks in plant stress responses and senescence. IUBMB Life 2014, 66, 156–166. [Google Scholar] [CrossRef] [PubMed]
  56. Vision, T.J.; Brown, D.G.; Tanksley, S.D. The origins of genomic duplications in Arabidopsis. Science 2000, 290, 2114–2117. [Google Scholar] [CrossRef]
  57. Blanc, G.; Hokamp, K.; Wolfe, K.H. A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res. 2003, 13, 137–144. [Google Scholar] [CrossRef] [PubMed]
  58. Mohanta, T.K.; Yadav, D.; Khan, A.; Hashem, A.; Tabassum, B.; Khan, A.L.; Abd_Allah, E.F.; Al-Harrasi, A. Genomics, molecular and evolutionary perspective of NAC transcription factors. PLoS ONE 2020, 15, e0231425. [Google Scholar] [CrossRef]
  59. Birchler, J.A.; Yang, H. The multiple fates of gene duplications: Deletion, hypofunctionalization, subfunctionalization, neofunctionalization, dosage balance constraints, and neutral variation. Plant Cell 2022, 34, 2466–2474. [Google Scholar] [CrossRef]
  60. Hu, W.; Wei, Y.X.; Xia, Z.Q.; Yan, Y.; Hou, X.W.; Zou, M.L.; Lu, C.; Wang, W.Q.; Peng, M. Genome-wide identification and expression analysis of the NAC transcription factor family in Cassava. PLoS ONE 2015, 10, e0136993. [Google Scholar] [CrossRef]
  61. Baranwal, V.K.; Khurana, P. Genome-wide analysis, expression dynamics and varietal comparison of NAC gene family at various developmental stages in Morus notabilis. Mol. Genet. Genom. 2016, 291, 1305–1317. [Google Scholar] [CrossRef] [PubMed]
  62. Liu, L.; White, M.J.; MacRae, T.H. Transcription factors and their genes in higher plants functional domains, evolution and regulation. Eur. j. Biochem. 1999, 262, 247–257. [Google Scholar] [CrossRef] [PubMed]
  63. Sakamoto, S.; Mitsuda, N. Reconstitution of a secondary cell wall in a secondary cell wall-deficient Arabidopsis mutant. Plant. Cell Physiol. 2014, 56, 299–310. [Google Scholar] [CrossRef] [PubMed]
  64. Adachi, S.; Minamisawa, K.; Okushima, Y.; Inagaki, S.; Yoshiyama, K.; Kondou, Y.; Kaminuma, E.; Kawashima, M.; Toyoda, T.; Matsui, M.; et al. Programmed induction of endoreduplication by DNA double-strand breaks in Arabidopsis. Proc. Natl. Acad. Sci. USA 2011, 108, 10004–10009. [Google Scholar] [CrossRef] [PubMed]
  65. Yoshiyama, K.O.; Kimura, S.; Maki, H.; Britt, A.B.; Umeda, M. The role of SOG1, a plant-specific transcriptional regulator, in the DNA damage response. Plant Signal Behav. 2014, 9, e28889. [Google Scholar] [CrossRef] [PubMed]
  66. Wu, Y.R.; Deng, Z.Y.; Lai, J.B.; Zhang, Y.Y.; Yang, C.P.; Yin, B.J.; Zhao, Q.Z.; Zhang, L.; Li, Y.; Yang, C.W.; et al. Dual function of Arabidopsis ATAF1 in abiotic and biotic stress responses. Cell Res. 2009, 19, 1279–1290. [Google Scholar] [CrossRef]
  67. Klok, E.J.; Wilson, I.W.; Wilson, D.; Chapman, S.C.; Ewing, R.M.; Somerville, S.C.; Peacock, W.J.; Dolferus, R.; Dennis, E.S. Expression profile analysis of the low-oxygen response in Arabidopsis root cultures. Plant Cell 2002, 14, 2481–2494. [Google Scholar] [CrossRef]
  68. Huh, S.U.; Lee, S.B.; Kim, H.H.; Paek, K.H. ATAF2, a NAC transcription factor, binds to the promoter and regulates NIT2 gene expression involved in auxin biosynthesis. Mol. Cells 2012, 34, 305–313. [Google Scholar] [CrossRef]
  69. Dalman, K.; Wind, J.J.; Nemesio-Gorriz, M.; Hammerbacher, A.; Lunden, K.; Ezcurra, I.; Elfstrand, M. Overexpression of PaNAC03, a stress induced NAC gene family transcription factor in Norway spruce leads to reduced flavonol biosynthesis and aberrant embryo development. BMC Plant Biol. 2017, 17, 6. [Google Scholar] [CrossRef]
  70. Zhang, H.H.; Xu, J.F.; Chen, H.M.; Jin, W.B.; Liang, Z.S. Characterization of NAC family genes in Salvia miltiorrhiza and NAC2 potentially involved in the biosynthesis of tanshinones. Phytochemistry 2021, 191, 112932. [Google Scholar] [CrossRef]
  71. Zhou, H.; Kui, L.W.; Wang, H.L.; Gu, C.; Dare, A.P.; Espley, R.V.; He, H.P.; Allan, A.C.; Han, Y.P. Molecular genetics of blood-fleshed peach reveals activation of anthocyanin biosynthesis by NAC transcription factors. Plant J. 2015, 82, 105–121. [Google Scholar] [CrossRef] [PubMed]
  72. Zou, S.C.; Zhuo, M.G.; Abbas, F.; Hu, G.B.; Wang, H.C.; Huang, X.M. Transcription factor LcNAC002 coregulates chlorophyll degradation and anthocyanin biosynthesis in litchi. Plant Physiol. 2023, 192, 1913–1927. [Google Scholar] [CrossRef] [PubMed]
  73. Shan, W.; Kuang, J.-F.; Lu, W.-J.; Chen, J.-Y. Banana fruit NAC transcription factor MaNAC1 is a direct target of MaICE1 and involved in cold stress through interacting with MaCBF1. Plant Cell Environ. 2014, 37, 2116–2127. [Google Scholar] [CrossRef] [PubMed]
  74. Xiang, P.; Chen, H.Q.; Cai, C.H.; Wang, H.; Zhou, L.M.; Mei, W.L.; Dai, H.F. Six new dimeric 2-(2-phenylethyl)chromones from artificial agarwood of Aquilaria sinensis. Fitoterapia 2020, 142, 104542. [Google Scholar] [CrossRef] [PubMed]
  75. Bisht, R.; Bhattacharyya, A.; Shrivastava, A.; Saxena, P. An overview of the medicinally important plant type III PKS derived polyketides. Front. Plant Sci. 2021, 12, 746908. [Google Scholar] [CrossRef]
  76. Wang, J.; Wang, X.H.; Liu, X.; Li, J.; Shi, X.P.; Song, Y.L.; Zeng, K.W.; Zhang, L.; Tu, P.F.; Shi, S.P. Synthesis of unnatural 2-substituted quinolones and 1, 3-diketones by a member of type III polyketide synthases from Huperzia serrata. Org. Lett. 2016, 18, 3550–3553. [Google Scholar] [CrossRef]
  77. Jin, J.; Tian, F.; Yang, D.C.; Meng, Y.Q.; Kong, L.; Luo, J.; Gao, G. PlantTFDB 4.0: Toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res. 2016, 45, D1040–D1045. [Google Scholar] [CrossRef]
  78. Altschul, S.F.; Madden, T.L.; Schaffer, A.A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D.J. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 1997, 25, 3389–3402. [Google Scholar] [CrossRef]
  79. Paysan-Lafosse, T.; Blum, M.; Chuguransky, S.; Grego, T.; Pinto, B.L.; Salazar, G.A.; Bileschi, M.L.; Bork, P.; Bridge, A.; Colwell, L.; et al. InterPro in 2022. Nucleic Acids Res. 2022, 51, D418–D427. [Google Scholar] [CrossRef]
  80. Lu, S.N.; Wang, J.Y.; Chitsaz, F.; Derbyshire, M.K.; Geer, R.C.; Gonzales, N.R.; Gwadz, M.; Hurwitz, D.I.; Marchler, G.H.; Song, J.S.; et al. CDD/SPARCLE: The conserved domain database in 2020. Nucleic Acids Res. 2020, 48, D265–D268. [Google Scholar] [CrossRef]
  81. Bailey, T.L.; Johnson, J.; Grant, C.E.; Noble, W.S. The MEME Suite. Nucleic Acids Res. 2015, 43, W39–W49. [Google Scholar] [CrossRef] [PubMed]
  82. Cantalapiedra, C.P.; Hernandez-Plaza, A.; Letunic, I.; Bork, P.; Huerta-Cepas, J. eggNOG-mapper v2: Functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 2021, 38, 5825–5829. [Google Scholar] [CrossRef] [PubMed]
  83. Artimo, P.; Jonnalagedda, M.; Arnold, K.; Baratin, D.; Csardi, G.; de Castro, E.; Duvaud, S.; Flegel, V.; Fortier, A.; Gasteiger, E.; et al. ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res. 2012, 40, W597–W603. [Google Scholar] [CrossRef]
  84. Emms, D.M.; Kelly, S. OrthoFinder: Phylogenetic orthology inference for comparative genomics. Genome Biol. 2019, 20, 238. [Google Scholar] [CrossRef] [PubMed]
  85. Rozewicki, J.; Li, S.L.; Amada, K.M.; Standley, D.M.; Katoh, K. MAFFT-DASH: Integrated protein sequence and structural alignment. Nucleic Acids Res. 2019, 47, W5–W10. [Google Scholar] [CrossRef]
  86. Price, M.N.; Dehal, P.S.; Arkin, A.P. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 2010, 5, e9490. [Google Scholar] [CrossRef]
  87. Chen, K.; Durand, D.; Farach-Colton, M. NOTUNG: A program for dating gene duplications and optimizing gene family trees. J. Comput. Biol. 2000, 7, 429–447. [Google Scholar] [CrossRef]
  88. Wang, Y.P.; Li, J.P.; Paterson, A.H. MCScanX-transposed: Detecting transposed gene duplications based on multiple colinearity scans. Bioinformatics 2013, 29, 1458–1460. [Google Scholar] [CrossRef]
  89. Wang, Y.P.; Tang, H.B.; DeBarry, J.D.; Tan, X.; Li, J.P.; Wang, X.Y.; Lee, T.H.; Jin, H.Z.; Marler, B.; Guo, H.; et al. MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012, 40, e49. [Google Scholar] [CrossRef]
  90. Sun, P.; Jiao, B.; Yang, Y.; Shan, L.; Li, T.; Li, X.; Xi, Z.; Wang, X.; Liu, J. WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes. Mol. Plant 2022, 15, 1841–1851. [Google Scholar] [CrossRef]
  91. Koch, M.A.; Haubold, B.; Mitchell-Olds, T. Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol. Biol. Evol. 2000, 17, 1483–1498. [Google Scholar] [CrossRef]
  92. Edgar, R.C. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32, 1792–1797. [Google Scholar] [CrossRef]
  93. Kumar, S.; Stecher, G.; Tamura, K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 2016, 33, 1870–1874. [Google Scholar] [CrossRef]
  94. Minh, B.Q.; Schmidt, H.A.; Chernomor, O.; Schrempf, D.; Woodhams, M.D.; Von Haeseler, A.; Lanfear, R. IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 2020, 37, 1530–1534. [Google Scholar] [CrossRef] [PubMed]
  95. Trifinopoulos, J.; Nguyen, L.T.; von Haeseler, A.; Minh, B.Q. W-IQ-TREE: A fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res. 2016, 44, W232–W235. [Google Scholar] [CrossRef] [PubMed]
  96. Letunic, I.; Bork, P. Interactive Tree Of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021, 49, W293–W296. [Google Scholar] [CrossRef] [PubMed]
  97. Krzywinski, M.; Schein, J.; Birol, I.; Connors, J.; Gascoyne, R.; Horsman, D.; Jones, S.J.; Marra, M.A. Circos: An information aesthetic for comparative genomics. Genome Res. 2009, 19, 1639–1645. [Google Scholar] [CrossRef] [PubMed]
  98. Goll, J.; Rusch, D.B.; Tanenbaum, D.M.; Thiagarajan, M.; Li, K.; Methé, B.A.; Yooseph, S. METAREP: JCVI metagenomics reports—An open source tool for high-performance comparative metagenomics. Bioinformatics 2010, 26, 2631–2632. [Google Scholar] [CrossRef] [PubMed]
  99. Hu, B.; Jin, J.P.; Guo, A.Y.; Zhang, H.; Luo, J.C.; Gao, G. GSDS 2.0: An upgraded gene feature visualization server. Bioinformatics 2015, 31, 1296–1297. [Google Scholar] [CrossRef]
  100. Chen, H.L.; Song, X.M.; Shang, Q.; Feng, S.Y.; Ge, W.N. CFVisual: An interactive desktop platform for drawing gene structure and protein architecture. BMC Bioinform. 2022, 23, 178. [Google Scholar] [CrossRef]
  101. Imai, T.; Ubi, B.E.; Saito, T.; Moriguchi, T. Evaluation of reference genes for accurate normalization of gene expression for real time-quantitative PCR in Pyrus pyrifolia using different tissue samples and seasonal conditions. PLoS ONE 2014, 9, e86492. [Google Scholar] [CrossRef] [PubMed]
  102. Ding, X.; Mei, W.; Huang, S.; Wang, H.; Zhu, J.; Hu, W.; Ding, Z.; Tie, W.; Peng, S.; Dai, H. Genome survey sequencing for the characterization of genetic background of Dracaena cambodiana and its defense response during dragon’s blood formation. PLoS ONE 2018, 13, e0209258. [Google Scholar] [CrossRef] [PubMed]
  103. Yan, P.; Tuo, D.; Shen, W.T.; Deng, H.D.; Zhou, P.; Gao, X.Z. A Nimble Cloning-compatible vector system for high-throughput gene functional analysis in plants. Plant Commun. 2023, 4, 100471. [Google Scholar] [CrossRef] [PubMed]
Ijms 24 17384 g001
Figure 1. Expansion and contraction of the NAC gene families in A. sinensis and 11 other species. The + and − represent gene expansion and loss events, respectively; red circles indicate the total number of NAC family members per species; blue and yellow circles indicate the total number of genes gained and lost during evolution, respectively; different color bands indicate cues to different species. The red font in the evolutionary tree indicates the number of ancestor genes.
Figure 1. Expansion and contraction of the NAC gene families in A. sinensis and 11 other species. The + and − represent gene expansion and loss events, respectively; red circles indicate the total number of NAC family members per species; blue and yellow circles indicate the total number of genes gained and lost during evolution, respectively; different color bands indicate cues to different species. The red font in the evolutionary tree indicates the number of ancestor genes.
Ijms 24 17384 g001
Ijms 24 17384 g002
Figure 2. Homology analysis of NAC genes between A. sinensis and 10 plant species. Color lines indicate NAC genes with interspecies synteny with each specie. Gray lines in the background indicate all the collinear genes in the genomes of A. sinensis and other plants.
Figure 2. Homology analysis of NAC genes between A. sinensis and 10 plant species. Color lines indicate NAC genes with interspecies synteny with each specie. Gray lines in the background indicate all the collinear genes in the genomes of A. sinensis and other plants.
Ijms 24 17384 g002
Ijms 24 17384 g003
Figure 3. Ka, Ks, Ka/Ks and evolutionary time analyses of the NAC homologous gene pairs in A. sinensis and other species. Different colors represent species. The dot matrix represents the raw data distribution; the peaks are data density curves, which indicated the trend of data concentration. The box-and-line plot represents the data distribution characteristics. (A) Ka. (B) Ks. (C) Ka/Ks.
Figure 3. Ka, Ks, Ka/Ks and evolutionary time analyses of the NAC homologous gene pairs in A. sinensis and other species. Different colors represent species. The dot matrix represents the raw data distribution; the peaks are data density curves, which indicated the trend of data concentration. The box-and-line plot represents the data distribution characteristics. (A) Ka. (B) Ks. (C) Ka/Ks.
Ijms 24 17384 g003
Ijms 24 17384 g004
Figure 4. Chromosomal localization and intraspecific homology of the AsNACs in A. sinensis genome. Gray lines indicate the synteny regions in the A. sinensis genome. Red line and * represent the synteny gene pairs of AsNACs. Blue, red, green, yellow and purple colors represent the type of duplicates, singleton, duplication dispersed, proximal, tandem and WGD or segmental, respectively.
Figure 4. Chromosomal localization and intraspecific homology of the AsNACs in A. sinensis genome. Gray lines indicate the synteny regions in the A. sinensis genome. Red line and * represent the synteny gene pairs of AsNACs. Blue, red, green, yellow and purple colors represent the type of duplicates, singleton, duplication dispersed, proximal, tandem and WGD or segmental, respectively.
Ijms 24 17384 g004
Ijms 24 17384 g005
Figure 5. Phylogenetic tree of the relationship of NAC proteins between A. sinensis and Arabidopsis. Bands and branches of different colors represent different subfamilies. Solid circles of different colors represent different duplication types.
Figure 5. Phylogenetic tree of the relationship of NAC proteins between A. sinensis and Arabidopsis. Bands and branches of different colors represent different subfamilies. Solid circles of different colors represent different duplication types.
Ijms 24 17384 g005
Ijms 24 17384 g006
Figure 6. Phylogenetic tree, conserved motifs and gene structure of the AsNACs. (A) Phylogenetic relationships were evaluated by IQ-TREE with the best model of VT + F + I + I + R8), where the full-length sequences of the NAC protein of A. sinensis were used. (B) Ten conserved motifs in AsNAC proteins are represented by the corresponding numbers of colored boxes. (C) Exon structures of the AsNAC genes are shown, where yellow boxes indicate exons, and black lines indicate introns.
Figure 6. Phylogenetic tree, conserved motifs and gene structure of the AsNACs. (A) Phylogenetic relationships were evaluated by IQ-TREE with the best model of VT + F + I + I + R8), where the full-length sequences of the NAC protein of A. sinensis were used. (B) Ten conserved motifs in AsNAC proteins are represented by the corresponding numbers of colored boxes. (C) Exon structures of the AsNAC genes are shown, where yellow boxes indicate exons, and black lines indicate introns.
Ijms 24 17384 g006
Ijms 24 17384 g007
Figure 7. Heat map of RNA-seq-based expression of AsNAC genes in response to the treatment with agarwood inducer. The red to purple color represents the log2 scale of the highest to the lowest expression levels. d: days.
Figure 7. Heat map of RNA-seq-based expression of AsNAC genes in response to the treatment with agarwood inducer. The red to purple color represents the log2 scale of the highest to the lowest expression levels. d: days.
Ijms 24 17384 g007
Ijms 24 17384 g008
Figure 8. Expression and correlation of AsNAC and AsPKS genes. (A) The relative expression levels of AsNAC genes at each time point after treatment were compared with those under normal conditions. (B) Relative expression of the AsPKS genes. (C) Correlation of gene expression of AsNACs and AsPKSs. Expression at 0 h (no-treatment control) was normalized to 1. Data represent the means ± SD, calculated from three biological replicates. Asterisks (*) indicate significant differences from 0 h after ANOVA; **: p < 0.01, ***: p < 0.001, ****: p < 0.0001.
Figure 8. Expression and correlation of AsNAC and AsPKS genes. (A) The relative expression levels of AsNAC genes at each time point after treatment were compared with those under normal conditions. (B) Relative expression of the AsPKS genes. (C) Correlation of gene expression of AsNACs and AsPKSs. Expression at 0 h (no-treatment control) was normalized to 1. Data represent the means ± SD, calculated from three biological replicates. Asterisks (*) indicate significant differences from 0 h after ANOVA; **: p < 0.01, ***: p < 0.001, ****: p < 0.0001.
Ijms 24 17384 g008
Ijms 24 17384 g009
Figure 9. Assays to determine the binding and interaction activities of AsNAC098 and AsNAC019 proteins. (A) Subcellular localization map of AsNAC098, and AsNAC019 in the onion epidermal cells. (B) Yeast one-hybrid experiments of the AsPKS07 gene promoter with AsNAC098 and AsNAC019. (C) Schematic diagrams of the effector and reporter plasmids used in Dual-LUC assays. REN, Renilla luciferase internal reference gene. LUC, firefly luciferase reporter gene. (D) Transcriptional activation of AsNAC019 and AsNAC098. A reporter alone, without the effectors, is used as a control. Statistical significance was determined with Student’s t-tests: ****: p < 0.0001.
Figure 9. Assays to determine the binding and interaction activities of AsNAC098 and AsNAC019 proteins. (A) Subcellular localization map of AsNAC098, and AsNAC019 in the onion epidermal cells. (B) Yeast one-hybrid experiments of the AsPKS07 gene promoter with AsNAC098 and AsNAC019. (C) Schematic diagrams of the effector and reporter plasmids used in Dual-LUC assays. REN, Renilla luciferase internal reference gene. LUC, firefly luciferase reporter gene. (D) Transcriptional activation of AsNAC019 and AsNAC098. A reporter alone, without the effectors, is used as a control. Statistical significance was determined with Student’s t-tests: ****: p < 0.0001.
Ijms 24 17384 g009
Table 1. Number and duplication types of NAC genes in 12 species.
Table 1. Number and duplication types of NAC genes in 12 species.
SpeciesDuplication TypeTotal
SingletonDispersedProximalTandemWGD
A. trichopoda *44////44
V. vinifera1 (1%)36 (43%)6 (7%)6 (7%)35(42%)84
A. thaliana3 (3%)38 (34%)5 (4%)27 (24%)40 (35%)113
A. sinensis2 (2%)53 (48%)5 (5%)16 (14%)35 (32%)111
H. hainanensis/18 (14%)11 (9%)/98 (77%)127
D. turbinatus/22 (17%)8 (6%)3 (2%)93 (74%)126
C. olitorius/47 (58%)6 (7%)5 (6%)23 (28%)81
C. capsularis1 (1%)49 (57%)6 (7%)5 (6%)25 (29%)86
T. cacao2 (2%)40 (38%)23 (22%)12 (11%)28 (27%)105
D. zibethinus1 (1%)18 (8%)4 (2%)70 (31%)136 (59%)229
G. raimondii1 (1%)40 (26%)7 (5%)10 (7%)95 (62%)153
H. cannabinus/38 (16%)23 (9%)21 (9%)161 (66%)243
Total553991041757691502
* The genome of A. trichopoda was a scaffold-level genome.
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

MDPI and ACS Style

Yang, Z.; Mei, W.; Wang, H.; Zeng, J.; Dai, H.; Ding, X. Comprehensive Analysis of NAC Transcription Factors Reveals Their Evolution in Malvales and Functional Characterization of AsNAC019 and AsNAC098 in Aquilaria sinensis. Int. J. Mol. Sci. 2023, 24, 17384. https://doi.org/10.3390/ijms242417384

AMA Style

Yang Z, Mei W, Wang H, Zeng J, Dai H, Ding X. Comprehensive Analysis of NAC Transcription Factors Reveals Their Evolution in Malvales and Functional Characterization of AsNAC019 and AsNAC098 in Aquilaria sinensis. International Journal of Molecular Sciences. 2023; 24(24):17384. https://doi.org/10.3390/ijms242417384

Chicago/Turabian Style

Yang, Zhuo, Wenli Mei, Hao Wang, Jun Zeng, Haofu Dai, and Xupo Ding. 2023. "Comprehensive Analysis of NAC Transcription Factors Reveals Their Evolution in Malvales and Functional Characterization of AsNAC019 and AsNAC098 in Aquilaria sinensis" International Journal of Molecular Sciences 24, no. 24: 17384. https://doi.org/10.3390/ijms242417384

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop