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Article

Genome-Wide Analysis of AP2/ERF Gene Superfamily in Ramie (Boehmeria nivea L.) Revealed Their Synergistic Roles in Regulating Abiotic Stress Resistance and Ramet Development

by
Xiaojun Qiu
1,†,
Haohan Zhao
1,†,
Aminu Shehu Abubakar
1,2,
Deyi Shao
1,
Jikang Chen
1,3,4,
Ping Chen
1,
Chunming Yu
1,
Xiaofei Wang
1,
Kunmei Chen
1,* and
Aiguo Zhu
1,3,4,*
1
Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
2
Department of Agronomy, Bayero University Kano, Kano PMB 3011, Nigeria
3
Key Laboratory of Genetic Breeding and Microbial Processing for Bast Fiber Product of Hunan Province, Changsha 410221, China
4
National Breeding Center for Bast Fiber Crops, Changsha 410221, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Int. J. Mol. Sci. 2022, 23(23), 15117; https://doi.org/10.3390/ijms232315117
Submission received: 17 October 2022 / Revised: 25 November 2022 / Accepted: 29 November 2022 / Published: 1 December 2022
(This article belongs to the Special Issue Phytohormone Signaling and Crosstalk in Regulation of Plant Growth and Environmental Stress Responses)
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Abstract

:
AP2/ERF transcription factors (TFs) are one of the largest superfamilies in plants, and play vital roles in growth and response to biotic/abiotic stresses. Although the AP2/ERF family has been extensively characterized in many species, very little is known about this family in ramie (Boehmeria nivea L.). In this study, 138 AP2/ERF TFs were identified from the ramie genome and were grouped into five subfamilies, including the AP2 (19), RAV (5), Soloist (1), ERF (77), and DREB (36). Unique motifs were found in the DREB/ERF subfamily members, implying significance to the AP2/ERF TF functions in these evolutionary branches. Segmental duplication events were found to play predominant roles in the BnAP2/ERF TF family expansion. Light-, stress-, and phytohormone-responsive elements were identified in the promoter region of BnAP2/ERF genes, with abscisic acid response elements (ABRE), methyl jasmonate response elements, and the dehydration response element (DRE) being dominant. The integrated transcriptome and quantitative real-time PCR (qPCR) revealed 12 key BnAP2/ERF genes positively responding to waterlogging. Five of the genes are also involved in ramet development, with two (BnERF-30 and BnERF-32) further showing multifunctional roles. The protein interaction prediction analysis further verified their crosstalk mechanism in coordinating waterlogging resistance and ramet development. Our study provides new insights into the presence of AP2/ERF TFs in ramie, and provides candidate AP2/ERF TFs for further studies on breeding varieties with coupling between water stress tolerance and high yield.

1. Introduction

Ramie (Boehmeria nivea L.) is a multipurpose crop, widely used as fiber, medicinal preparation, forage, phytoremediation, and as biofuel [1]. It has been cultivated in Asia for over 4000 years [2]. Ramie production is, however, ravaged by water stress [3], and the plant dies within 48 h of water submergence. An estimated 26.7% yield reduction was also reported after 7 days of drought stress [3]. Nowadays, the cultivation of ramie has transferred from good land to marginal lands, such as slope hillsides, poor lowlands, and heavy-metal-contaminated fields, leaving enough acreage for food crops in major producing countries. These land areas are constantly experiencing either water shortages, submergence, and nutrient deficiency, thus risking ramie production, which urgently calls for new resistant varieties that will withstand these threats. However, the genetic and molecular–physiological basis of stress tolerance of ramie is still largely unknown.
AP2/ERF is one of the most significant gene families in plants, encoding plant-specific transcription factors (TFs) that regulate signaling networks for various plant biological processes [4]. AP2/ERF TFs are mainly found in higher plants, and play a critical role in regulating environmental stress responses, including abiotic (temperature, salinity, and water stress) and biotic stresses [5,6,7,8]. Numerous reports showed that genetically modified plants of overexpressing AP2/ERF TFs exhibited increased tolerance to abiotic/biotic stresses [9,10]. AP2/ERF TFs are important regulators involved in plant growth and development, such as root initiation and development [11], stem growth [12], leaf size [13], control of flower growth and development [14,15], and fruit/seed development and maturation [16,17]. Recent studies have shown that AP2/ERF TFs are also involved in plant patterns of tillering or branch regulation [18,19]. These results suggest that AP2/ERF family genes should be unique gene resources for improving crop production coupling with stress tolerance, yet, little is known about this family in ramie.
In this study, we attempted to build an extensive map of the AP2/ERF gene family based on the third-generation sequencing data of ramie. We performed a genome-wide identification of AP2/ERF family genes, gene structure, chromosome distribution, gene duplication, cis-acting elements and transcription factor binding sites, the conserved motifs, and the phylogenetic relationships of their encoded proteins. In addition, expression patterns of the identified genes in different tissues and in response to water deficit, nitrogen deficit, and waterlogging stresses were analyzed. Key genes are identified and discussed in response to waterlogging stress and ramet development regulation.

2. Results

2.1. Identification, Characteristics, Phylogeny Relationship, and Classification of AP2/ERF Transcription Factors in Ramie

A total of 138 putative AP2/ERF superfamily TFs were identified from the ramie genome, and their sequence information and physical properties are shown in Supplementary Table S1. The number of amino acids varied from 109 to 819. The molecular weight and isoelectric point (pI) were 12,579.27–89,274 Da and 4.51–11.32, respectively. Most of the genes (112), as predicted, were localized in the nuclear region, with only 26 located extracellularly.
Phylogenetic analysis was performed with the 138 proteins of ramie and the 147 AP2/ERF superfamily TFs of A. thaliana using MEGAX software. The results show that the BnAP2/ERFs were clustered into four major clusters: Soloist, RAV (related to ABI3/VP), AP2 (APETALA2), and ERF (ethylene-responsive factors) subfamilies (Figure 1). The ERF cluster was further divided into ERF and DREB (dehydration-responsive element binding) subfamilies. The naming convention of AP2/ERFs of Brachypodium distachyon was followed for nomenclature [20]. The results of the analysis performed using the NCBI Batch CD-Search Tool confirmed the presence of the AP2 domain in each of the 138 identified proteins (Figure 2). According to gene structure and characteristics of the conserved domain sequences, thirteen proteins with two AP2 domains and six proteins (BnAP2-02, BnAP2-03, BnAP2-04, BnAP2-05, BnAP2-18, and BnAP2-19) with a single AP2 domain were classified as the AP2 subfamily. Five proteins with AP2 and B3 domains were classified as the RAV subfamily. BnSolo-01, which was highly homologous to At4g13040, was classified as the Soloist subfamily. Most identified proteins (113) were from the ERF family, with 36 and 77 DREB and ERF members, respectively. All of the DREB proteins had conserved amino acids at the 14th (V) and 19th (E) position, and several of these proteins showed E replaced by L, V, A, or Q (Supplementary Figure S1A). At the same time, the ERF proteins showed conserved amino acids at the 14th (A) and 19th (D) positions, with few having V and H in the places of A and D, respectively (Supplementary Figure S1B).
According to the classification of A. thaliana [21], the BnDREB subfamily was categorized into I–IV groups, and the BnERF subfamily into V–X groups (Table 1). None of the ramie members fell into the Xb-L group, as similarly reported in jute and rice [22].

2.2. Gene Structure and Conserved Motifs Analysis of BnAP2/ERFs

Gene structure analysis is crucial for understanding the structural diversity of genes, revealing such information as the position of the coding sequence (CDS) and the untranslated regions (UTR) (Figure 2). The number of introns in the 138 identified genes ranged from 0 to 12, of which 83 genes had no introns. Genes in the same phylogenetic group had a similar gene structure. For example, all members of the VII group (BnERF-21, BnERF- BnERF-22, BnERF-23, BnERF-24, and BnERF-25) had 5’ UTR, 3’UTR, and one intron, with the intron occurring in AP2 conserved domain, which suggests their critical function roles in ramie. Noticeably, all members of the AP2, RAV, and Soloist subfamilies in ramie had introns except BnRAV-04.
The putative conserved motifs (CMs), possibly reflecting the functional domains involved in specific protein binding sites, such as nucleases and transcription factors, are shown in Figure 3 and Supplemental Table S2. Members in the same groups generally had similar CMs, demonstrating structural similarities among the proteins. Some groups contained CMs specific to them, such as CMVII-4 and CMVIII-3, which were generally outside the conserved domain. The divergence of these CMs may be the cause of their functional differentiation.

2.3. Chromosome Distribution and Gene Duplication of BnAP2/ERFs

The identified BnA2/ERF superfamily TFs were unevenly located on the 14 chromosomes of ramie, except for BnAP2-07, BnDREB-36, and BnERF-09 genes, which were not assembled (Figure 4). Eighteen BnAP2s were located on the chr6, while there were four genes located, each on the chr10 and chr11, respectively. Gene duplication events were also analyzed to understand the AP2/ERF gene family expansion and differentiation in ramie, and the results are shown in Figure 4. Eleven pairs of tandem duplicated genes were distributed on six chromosomes. Chr6 had four tandem duplicated pairs, chr1 had two, whereas the remaining (chr5, 6, 8, 12, and chr13) each had one. All tandem duplicated gene pairs fell into the III and IX subgroups. There were higher numbers of segmentally duplicated gene pairs (43) compared to the tandem, suggesting segmentally duplicated events as the main driving force in BnAP2/ERFs evolution.
Ka/Ks represents the ratio between non-synonymous substitutions (Ka) and synonymous substitutions (Ks), which can determine whether the gene encoding the protein is under selection pressure. Ka/Ks >> 1 stands for positive selection, Ka/Ks ≈ 1 represents neutral selection, and Ka/Ks << 1 means purifying selection [21,23]. With the exception of BnERF-03/01 and BnERF-05/01 duplicated pairs, which have a higher sequence divergence degree and farther evolutionary distance, the Ka/Ks ratio of all duplicated gene pairs was less than one (Supplementary Table S3).
The orthologous relationships between ramie and other plants, dicotyledons (Arabidopsis thaliana and Cannabis sativa female) and monocotyledons (Oryza sativa and Zea mays), were also investigated to further understand the evolutionary relationship of AP2/ERF genes (Figure 5). A total of 94 BnAP2/ERF genes had syntenic relationships with those of A. thaliana (65), C. sativa (74), O. sativa (33), and Z. mays (38), respectively, among which 20 BnAP2/ERF genes were collinear with all four species (Supplementary Table S4). We can intuitively establish from Figure 5 that the orthologous gene pairs of ramie and dicotyledons were significantly higher than those of monocotyledons, and some collinear genes only existed between ramie and other dicotyledons.

2.4. The Putative Promoter Regions Analysis of BnAP2/ERF Subfamily

Cis-elements play critical roles in plant growth, stress response, and tissue-specific expression. A total of 55 cis-acting elements were retrieved from the promoter region of BnAP2/ERF genes, of which 28 were light-responsive elements, 11 were phytohormone-responsive elements, 9 were plant growth and developmental elements, and 7 were stress-responsive elements (Figure 6). Light-responsive elements were found in the promoters of all the BnAP2/ERFs, with the highest being G-box (466). Box 4 (423) was found in all the BnAP2/ERFs promoters, but that of BnDREB-03, BnDREB-30, BnERF-06, BnERF-16, BnERF-73 and BnAP2-01. Among the phytohormone-responsive elements, BnAP2/ERFs contained abundant abscisic acid response elements (ABRE) (405) and methyl jasmonate response elements (CGTCA-motif and TGACG-motif) (398). Moreover, BnAP2/ERFs were found to contain many ARE elements for the stress-responsive elements (315), indicating that most BnAP2/ERF TFs may be induced by low oxygen stress, such as waterlogging. The significant presence of these elements suggests that most BnAP2/ERF TF members are involved in plant development and biotic/abiotic stress responses.

2.5. Gene Ontology Annotation and KEGG Enrichment Analysis of BnAP2/ERF Target Genes

Based on two approaches, 1700 genes with at least one DRE/CRT in their putative promoters and 1009 genes with at least one GCC-box in their promoters were manually searched from the ramie genome. After removing the redundant genes, 2197 potential BnAP2/ERF target genes were confirmed. It contained disease-resistance-related PRs genes, transcription factors such as WRKY, NAC, and MYB, as well as F-box proteins, D14L, GLT1, and GRF1/3, which may be related to tiller traits of plants.
The target genes were assigned to 54 functional groups and divided into 3 main ontologies: biological processes, molecular functions, and cellular components (Figure 7A). Some target genes were enriched in GO terms for immune system processes, response to stimulus, detoxification effects, antioxidant activity, and growth and development.
The most enriched KEGG pathways included riboflavin metabolism, cellular autophagy, gluconeogenesis, glutathione metabolism, and MAPK signaling pathways (Figure 7B). Many target genes were enriched in various metabolic pathways, transcription and repair, signal transduction, and environmental adaptation of KEGG pathways (Figure 7C). These results suggest that BnAP2/ERF genes are involved in biotic/abiotic stress responses as well as plant growth and development pathways.

2.6. Expression Analysis of BnAP2/ERF Genes Based on Transcriptome Data

2.6.1. Tissue Specific Expression of BnAP2/ERF Genes

In this study, based on the expression profiles obtained from RNA-Seq analysis data, we constructed a heat map of the gene expression patterns in different tissues of ramie (Figure 8A). Thirty-nine genes were not expressed in any analyzed tissues, indicating that these genes may be pseudogenes or require certain specific developmental stages and environments for induction. The expression levels of different BnAP2/ERFs varied among tissues, with 70 genes expressed in all tissues (FPKM > 0). Seven genes (BnDREB-06, BnDREB-08, BnERF-21, BnERF-30, BnERF-32, BnERF-51, and BnERF-77) had high expression levels in all tissues, and most genes were expressed at higher levels in root and bast fiber than that in the stem and leaf.

2.6.2. Expression Patterns of BnAP2/ERF Genes in Response to Various Abiotic Stresses

To determine the involvement of BnAP2/ERF genes in response to abiotic stresses, relative expression profiles in ramie leaves under water deficit, nitrogen deficit, and waterlogging stresses were constructed based on transcriptomic data (Figure 8B). Fifty-seven genes were differentially expressed (25 up-regulated and 32 down-regulated) under water deficit, most of which were members of I, II, V, and X groups. Among the down-regulated genes, the expressions of BnDREB-11, BnERF-39, and BnERF-49 showed significant differences compared with those in the control (|log2FC| > 4). Seventy-two differentially expressed genes (DEGs) were detected under nitrogen deficiency stress, with 44 being up-regulated and 28 down-regulated. Members of the DREB subgroup showed a stronger response under nitrogen starvation than the other subgroups. Sixty-nine DEGs were detected under waterlogging stress, of which 49 members were up-regulated and 20 members were down-regulated. Some members of the DREB subgroup and most of the ERFs showed significant up-regulation, and most BnAP2/ERF genes showed positive feedback to waterlogging stress. Of particular interest is that the up-regulated genes were mainly from the ERF subfamily, and the down-regulated genes from the DREB subfamily.
Furthermore, BnERF-17 and BnERF-18 were up-regulated only under water stress (water deficit and waterlogging), while BnERF-22, BnERF-23, and BnERF-25 in group VII were up-regulated only under waterlogging. BnERF-30 and BnERF-31 of the VIII group were up-regulated under waterlogging, and BnERF-26 and BnERF-32 showed up-regulation under both nitrogen deficit and waterlogging. Some genes up-regulated under waterlogging (BnDREB-11, BnERF-02, BnERF-30, BnERF-32, BnERF-39, BnERF-40, BnERF-49, BnERF-50, BnAP2-02) showed relative expression patterns in water deficit, further indicating that these genes have essential regulatory roles under water stress. On top of that, BnERF-03, BnERF-07, BnERF-08, BnERF-10, BnERF-11, BnERF-18, BnERF-22, BnRAV-03, BnAP2-03, BnAP2-17, and BnAP2-19 were only expressed under abiotic stress, and no expression was detected under normal development, suggesting that these genes may play roles in response to abiotic stress.

2.6.3. Expression Patterns of BnAP2/ERF Genes in Various Ramie Varieties with Significantly Different Ramet Numbers

Members in group VIII of the AP2/ERF superfamily, such as AtESR1 (AT1G12980), AtESR2 (AT1G24590), AtPUCHI (AT5G18560), AtERF4 (AT3G15210), and AtERF11 (AT1G28370) from Arabidopsis, have been reported to be involved in axillary meristem and branch development and stem elongation and growth [24]. Therefore, we hypothesize that the BnAP2/ERF members in group VIII may have a similar function in the regulation of ramet in ramie. The transcriptome data from two ramie varieties with different ramet numbers (Figure 9A) were used to evaluate the expression pattern of these BnERFs. The results (Figure 9B) show that BnERF-26, BnERF-28, BnERF-30, BnERF-31, BnERF-32, BnERF-33, BnERF-34, and BnERF-35 were expressed in all tissues of the two varieties. BnERF-27 was only minimally expressed in the root, while BnERF-29, BnERF-36, BnERF-37, and BnERF-38 were not detected in any tissues. All detected genes were up-regulated in variety “Zhongzhu No.1” with a low ramet number, suggesting that they may be involved in the negative regulation of the ramet number. Based on these results, we speculate that these genes may have potential roles in the ramet traits of ramie.

2.6.4. Verification of Gene Expression by qPCR

Considering that waterlogging can have a fatal impact on ramie in a very short time, and the enormous cost to be paid for establishing a new ramie field according to the perennial habit of the crop, expression profiles of BnAP2/ERF genes under waterlogging stress were analyzed by pot experiment in the present study. Based on the reported Arabidopsis homologs of members in group VIII in ramie, and the highly differentially expressed members in the transcriptome data of waterlogging stress, 12 BnAP2/ERF genes were identified as candidate genes involved in the waterlogging response.
Furthermore, qPCR analysis was performed to confirm the expression of the 12 candidate genes. The results (Figure 10) indicate that the expression of BnERF-14, BnERF-21, BnERF-22, BnERF-24, BnERF-40, and BnERF-50 increased with the prolongation of stress duration under light. BnERF-25 and BnERF-32 showed an increasing and then decreasing trend in expression under stress induction, while BnDREB-11, BnERF-39, and BnERF-49 decreased, only increased at 12 h. These results suggest that BnAP2/ERF members exhibited multiple roles under stress induction. Interestingly, instead of returning to normal expression in the recovery state after stress, some of the genes showed a significant increase. These genes may be related to plant growth and development after stress. The expression pattern of the genes under light avoidance conditions was significantly different from that under light. Some genes were not induced under darkness (BnERF-21, BnERF-14, BnERF-39, and BnERF-40), and some genes showed the exact opposite trend (BnDREB-11, BnERF-22, BnERF-24, BnERF-25, BnERF-32, BnERF-40, BnERF-49, and BnERF-50). BnERF-26 showed strongly inhibited expression under stress as well as in the recovery state after stress.
The light-or-dark treatments significantly changed the patterns of gene expression profile under waterlogging. While some genes were not significantly induced by the waterlogging stress under darkness (BnERF-21 and BnERF-39), some showed the exact opposite trend under both conditions (BnDREB-11, BnERF-22, BnERF-24, BnERF-25, BnERF-32, BnERF-40, BnERF-49, and BnERF-50). The expression of BnERF-26 showed the same trend as that under the light condition. These results imply that BnAP2/ERF genes regulate ramie through a complex network under different conditions.

3. Discussion

3.1. Global Profile of AP2/ERF Gene Family of Ramie

The TFs are considered as ideal candidates for crop improvement because their overexpression enhances tolerances to multiple abiotic and biotic stresses in transgenic plants [25]. Extensive studies have demonstrated that AP2/ERF TFs are crosstalk factors in stress signal pathways involved in salicylic acid, jasmonic acid, ethylene, and abscisic acid signal transduction pathways [26], and hence play vital roles in regulating plant growth and development as well as in response to diverse stresses [27,28]. Although AP2/ERF TFs have been thoroughly identified and characterized in many plant species, very little is known about the AP2/ERF gene family in ramie. In the present study, we performed a comprehensive screening of AP2/ERF genes in the ramie genome, and performed analyses including genome-wide identification, gene structure, gene localization, cis-acting element analysis, motif analysis, cis-linkage, and downstream target gene function and expression patterns, which laid an important foundation for better understanding the molecular mechanisms of development and physiological adaptation in this crop.
The AP2/ERF superfamily genes are defined by the presence of at least one highly conserved AP2 DNA binding structural domain consisting of three β-folds and one α-helix of approximately 60 to 70 amino acids in length. Based on the number and sequence characteristics of the structural domains, the AP2/ERF superfamilies of ramie were divided into AP2 (APETALA2), RAV (related to ABI3/VP), DREB (dehydration-responsive element binding), ERF (ethylene-responsive factors) and Soloist subfamilies, which contain 18, 5, 36, 72, and 1 members, respectively. Our results also support the large difference in the number of DREB and ERF occurrences, while Soloist and RAV are small subfamilies with few members in land plants [29,30,31,32]. It is widely known that ancestral species have intron-rich genes, and most plant species have experienced extensive loss or insertion of introns due to selection pressure [33]. Our results show that almost all AP2 and Soloist subfamily genes of ramie, like in other plant species [20,32,34], had introns, whereas most DREB and ERF subfamily genes (71.3%) were intronless. Nevertheless, the RAV subfamily genes in ramie, unlike other plants, all have introns except BnRAV-04. The insertion of introns may be a special mechanism that developed during the evolution of the RAV subfamily in ramie to better adapt to survival pressures [35]. Most members of the AP2 subfamily contained two AP2 domains, while some had a single domain lacking a conserved WLG motif. The RAV subfamily contained two distinct DNA binding domains, AP2 and B3. The DREB and ERF subfamilies each contained two highly conserved amino acids located in the β-fold at the 14th position, valine/alanine (V14/A14), and at the 19th position, glutamate/aspartate (E19/D19), in the AP2 domain. These conserved amino acids may play an essential role in site-specific binding to DNA sequences, such as the dehydration response element (DRE)/C-repeat element (CRT) or the GCC-box in the promoter region of the target gene [36,37]. KEGG and GO analysis revealed that these target genes contained disease-resistance-related PRs genes, stress-related genes RAB18, LEA3, TIP2, and POX2, transcription factors such as WRKY, NAC, and MYB, as well as F-box genes, D14L, GLT1, and GRF1/3, which may be related to tiller traits of plants. BnAP2/ERFs may regulate ramie response to environmental pressures and ramet development by binding to the corresponding sites in the promoter regions of these genes.
An exciting feature of the AP2/ERF superfamily is that these members have transcriptional activation or repression activity. Amphipathic repressor (EAR) motifs found at the C-terminus of proteins are responsible for their transcriptional repression activity, which involves biotic and abiotic stress responses, plant internode elongation, and leaf senescence [38,39,40,41]. On the other hand, members lacking this motif had transcriptional activation activity. CMVII-4, a MCCGGAI(I/L) motif, was characteristic of the VII group members. Five ERF-VII members in Arabidopsis had N-terminal structures, and two of them (HRE1, HRE2) were anaerobic response proteins. In addition, numerous studies have shown that members in the VII group of the ERF subfamily play a central role in regulating waterlogging tolerance [42,43,44,45]. Therefore, we hypothesize that AP2/ERF TFs with these characteristics have the same functions in ramie, which provides useful information for the research of BnAP2/ERF genes.
In ramie, the number of members is similar to that in Arabidopsis and rice, suggesting that the number of AP2/ERF family members is relatively stable, independent of genome size, and that the difference in number may be due to expansion events during the evolution of different plant species. Nonetheless, gene evolution and duplication induced the differentiation of the numbers of AP2/ERF genes among plants. Thus, we calculated the Ka, Ks, and Ka/Ks ratios of BnAP2/ERF repeating gene pairs, including tandem repeats and fragment repeats, to estimate divergence time and selection pressure. All Ka/Ks values were below 1, suggesting that these genes might have experienced strong purifying selective pressure during evolution [46]. In addition, the gene density was 2.3734 AP2/ERF genes per Mb in ramie, while the values for rice and Arabidopsis were 0.4047 and 1.1760, respectively. These data indicate that the AP2/ERF family genes were retained during the evolution of ramie in the presence of extensive gene loss, which proves the significance of the AP2/ERF family in the growth and development of ramie [47,48].

3.2. The Roles of the BnAP2/ERF Gene Family in Responding to Abiotic Stresses

Plants must adapt to a variety of biotic/abiotic pressures because they are immobile throughout their life cycle. AP2/ERF genes play important roles in stress responses, including drought, waterlogging, heat, and salt stress. From the RNA-seq data, the DEGs of BnAP2/ERFs were identified. Under different pressures, each subfamily showed different behaviors. For example, under nitrogen deficit, the up-regulated genes were mainly in the DREB subfamily and the down-regulated genes were mainly in the ERF subfamily; this was the opposite for water deficit. However, the response genes under waterlogging were predominantly in the ERF subfamily. Furthermore, we found that BnDREB-25, BnDREB-26, BnDREB-32, BnDREB-33, and BnDREB-34 in the DREB subfamily, BnERF-04, BnERF-05, BnERF-09, BnERF-12, BnERF-13, BnERF-29, BnERF-36, BnERF-37, BnERF-38, BnERF-47, BnERF-53, BnERF-54, BnERF-56, BnERF-57, BnERF-71, and BnERF-72 in the ERF subfamily, BnAP2-06, BnAP2-09, BnAP2-11, BnAP2-14, BnAP2-16, and BnAP2-18 in the AP2 subfamily, and BnRAV-02 were not expressed under either normal developmental or abiotic stress conditions, suggesting that these genes may be pseudogenes. However, the possibility that these genes respond to other stressful environments cannot be excluded.
The involvement of AP2/ERF family genes in the waterlogging response has been reported for several crops, with the most attention being given to members of group VII. We found from qPCR results that group VII members such as BnERF-21, BnERF-22, BnERF-24, and BnERF-25 were all up-regulated under waterlogging stress, with the latter three strongly induced even after reoxygenation, indicating their importance in stress tolerance and in growth and development. In addition, plants still have to balance the presence and absence of varying degrees of light under field conditions [49]. The results of cis-element analysis also show that the promoter region of the BnAP2/ERFs was enriched in light-responsive elements, in addition to elements such as ABRE and ARE, in response to biotic/abiotic stresses. This indicates that BnAP2/ERFs also play important roles in regulating plant development in response to photoperiod. Expression pattern analysis showed that some AP2/ERF genes had to be expressed earlier under shade conditions to cope with these stresses to ensure their growth and nutrient accumulation. It has been demonstrated that plants improve their tolerance to stress under different light environments by responding appropriately to abiotic stresses [50].

3.3. Candidate Genes for Improving Waterlogging Tolerance Coupling with Ramet Development

Plants actively slow down their growth when they are under stress, a complementary strategy they use to cope with adverse conditions [51]. While plants can adapt to adversity, this comes at the expense of yield under normal growth conditions. Therefore, under-standing the mutual synergy between the stress response and growth may be the key to resetting the stress–growth balance. Indeed, designing more stress-resistant but high-yielding crops is the target of breeders.
Ramie is a vital fiber crop that exhibits defeat, stalk shrinkage, and stunted chloroplast development in response to stress to ensure its growth [3,52]. Meanwhile, ramet has an important characteristic that is significantly related to the yield of ramie [53]. Our results show that the genes in group VIII of BnAP2/ERF played positive roles in coping with water stress and regulating the development of ramet. The homologs of BnERF-27, BnERF-38, BnERF-36, BnERF-37, BnERF-32, and BnERF-30 were AtESR1, AtESR2, AtPUCHI, AtERF4, and AtERF11 in Arabidopsis, respectively. However, the analysis of transcriptome data revealed that BnERF-27, BnERF36, BnERF-37, and BnERF38 did not show differential expression in the two ramie varieties with different ramet numbers. Therefore, we predicted that BnERF-30 and BnERF-32 were likely to be involved in the multifunctional role of waterlogging tolerance and ramet development in ramie.
Protein interaction analysis is more intuitive and rapid for understanding gene function, and is also important for regulatory network relationships between functional proteins. We used STRING software to map an integrated protein interaction network based on AtERF11 and AtERF4. The results (Figure 11) show that they first formed a complex through their EAR-motif and TPL protein, which in turn bind to genes related to WUS [54] and the growth hormone pathway [55,56,57,58] to regulate tillering and branching in plants. These results reinforce the potential role of BnERF-30 and BnERF-32 in the ramet traits of ramie. In addition, the ERF-TPL complex can also interact with jasmonic-acid-pathway-related proteins to alleviate stress damage, such as JAZ1, NINJA, and TIFY8 [59,60,61].
Moreover, BnERF-32 (AtERF4) can directly bind to the repressor proteins SPL2 and SPL6 involved in axillary meristematic tissue to regulate plant structure. Studies have shown that the number of branches or tillers of some plants increases or decreases after waterlogging stress, which may be related to the growth regulation of the plants themselves after exposure to adversity. For example, waterlogging-tolerant species Alternanthera philoxeroides and Hemarthria altissima with well-developed root systems are more likely to grow new branches after waterlogging [62], while wheat grown in drylands exhibits a significant reduction in tillers [63]. Thus, BnAP2/ERF family genes may also act as a more complex crosstalk mechanism in coordinating stress and growth development.

4. Materials and Methods

4.1. Identification of BnAP2/ERF Gene Superfamily

The AP2/ERF gene sequences were identified from the ramie genome derived from the whole genome data sequenced by our laboratory. The hidden Markov model (HMM) file of the AP2 domain (PF00847) was obtained from the Pfam database (http://pfam.xfam.org/ (accessed on 18 April 2022)), and the target genes were searched using HMMER3.0 software with a threshold E-value < 0.05 [64]. To confirm that the gene sequences obtained were those of the target, the presence of the AP2 conserved domain was checked against the NCBI Batch CD-Search Tool with E-value < 0.01. The physical and chemical parameters of BnAP2/ERF proteins, including the number of amino acids, molecular weight, theoretical pI, instability index, aliphatic index, and grand average of hydropathicity (GRAVY) were predicted using the Expasy ProtParam (https://web.expasy.org/protparam/ (accessed on 28 April 2022)). The sub-cellular location was predicted using the Softberry ProtComp v.9.0 (http://www.softberry.com/ (accessed on 29 April 2022)).

4.2. Phylogeny, Conserved Motifs, and Gene Structure Analysis

Arabidopsis thaliana AP2/ERF protein sequences (147) were downloaded from TAIR (https://www.arabidopsis.org/ (accessed on 18 April 2022)) and used to establish the phylogeny. Multiple alignments of BnAP2/ERF and AtAP2/ERF genes were performed by MUSCLE with default parameters, and the result was pruned using the Trimmer function in TBtools [65]. A phylogenetic tree was constructed in the MEGA11 program using the neighbor-joining method with 1000 bootstrap and other default parameters [66,67]. The Interactive Tree of Life (iTOL) was used for visualization of the phylogenetic tree (https://itol.embl.de/ (accessed on 13 May 2022)) [68].
The MEME Suite 5.4.1 online tool (https://meme-suite.org/meme/tools/meme (accessed on 15 May 2022)) was used for predicting the BnDREB/ERF conserved motifs (CMs), with the maximum number of motifs set to 10 and other parameters set to default. The gene structure of BnAP2/ERF and the final overall figure was generated with Gene Structure View in TBtools [65].

4.3. Chromosome Distribution, Gene Duplication, and Evolutionary Analysis of AP2/ERF Homologous Genes

The ramie genome annotation files were used to obtain the BnAP2/ERF chromosome distribution. Gene replication within the ramie genome and between ramie and other species was analyzed using MCscanX software [69]. Advanced Circos and Multiple Synteny Plot functions of TBtools [65] were used for visualization. Using KaKs_Calculator 2.0 [70], we computed the synonymous (Ks) and non-synonymous (Ka) substitution of the BnAP2/ERF gene pairs.

4.4. Cis-Element Analysis

All sequences 2.0 kb upstream of the BnAP2/ERF genes were selected as promoter regions and submitted to PlantCARE (https://bioinformatics.psb.ugent.be/webtools/plantcare/html/ (accessed on 22 May 2022)) for prediction. The results are summarized in Supplementary Table S5.

4.5. KEGG Enrichment Analysis and Gene Ontology Functional Annotation of BnAP2/ERFs Target Genes

Target genes with DREB protein binding site elements DRE (TACCGACAT) and CRT (G/ACCGAC) were screened. In addition, genes with AP2/ERF TF binding site elements (GCC-box) with sequence “AGCCGCC” were manually searched and used in the subsequent enrichment analysis. Pathway enrichment analysis for the potential BnAP2/ERF target genes was conducted using the KEGG database [71]. Gene ontology (GO) annotations of the target genes were performed using the Blast2GO tool with default parameters [72]. The program’s output was divided into biological processes, molecular functions, and cellular components. The advanced 20 enriched KEGG pathways and GO enrichment analyses were plotted using the R package ggplot2.

4.6. Transcriptome Data Sources and Expression Analysis of the BnAP2/ERF Genes

Transcriptome analysis of tissue-specific expression was conducted using four different tissue samples of “Zhongzhu No.1” sequenced by our laboratory. Transcriptome data of water deficit and nitrogen deficit were obtained from [73]. The additional “Zhongzhu No.2” ramie transcriptome changes in leaves of 3-week-old seedlings exposed to waterlogging for 12 h and to normal conditions were profiled using RNA-Seq data in our recent research. In this study, transcript fragments per kilobase representing BnAP2/ERF expression levels per mapped read per million (FPKM) values were calculated from these transcriptome data. Heat maps were generated using TBtools with log2(FPKM + 1) normalization [65].

4.7. BnAP2/ERF Protein–Protein Interaction Network Prediction

The homology of AP2/ERF genes between Arabidopsis and ramie was determined using OrthoVeen2 [74]. The interaction predictions of BnAP2/ERF proteins with other proteins based on Arabidopsis homologs were obtained with high confidence of >0.400 using the STRING v11.5 online program, and used to build a correlation network [75]; the networks were visualized in Cytoscape v3.8.2.

4.8. Plant Materials and Sampling

The ramie seedlings of variety “Zhongzhu No.2”, which has the largest cultivation area in the world, were prepared by hydroponic methods. Seedlings with even sizes were transplanted in earthen pots in the greenhouse under controlled conditions of 60 ± 5% humidity at 30 ± 2 ℃, and cultured for more 3 weeks with only water. Then, the seedlings with similar height, leaf number, and leaf area were selected and divided into four groups with six biological replicates for each treatment. The CK group was grown by applying 100 mL nutrient solution every day and additional water to keep the soil moisture at 80% of soil field capacity for 10 days. The waterlogging group was grown under the same conditions as the CK group, but for 9 days, and the pots were immersed by maintaining 2 cm water level above the underlying soil surface [76] for 12 h, which was then drained. Samples of CK and waterlogging were collected at 0, 3, and 12 h after waterlogging treatment and 12 h after drainage. Two groups of identical waterlogging treatments were set up in light and dark environments, respectively [62]. The composition of the nutrient solutions of the treatments shown in Supplementary Table S6 refer to Tan [77].

4.9. RNA Sample Extraction and qPCR Analysis

Samples from the waterlogging treatment were used for qPCR analysis. Total RNA was extracted using a SteadyPure Plant RNA Extraction Kit (Accurate Biotechnology (Changsha, China) Co., Ltd.). The RNA was reverse transcribed, using an Evo M-MLV One Step RT-PCR Kit (Accurate Biotechnology (Changsha, China) Co., Ltd.), into cDNA, and qPCR analysis was performed using gene-specific primers (Supplementary Table S7). The 18s gene was used as an internal control (Accession number: EU747115). The qPCR was performed using an SYBR® Green Premix Pro Taq HS qPCR Kit II (Accurate Biotechnology (Changsha, China) Co., Ltd.) on a CFX96 Touch Deep Well Real-Time Quantitative PCR System (Bio-Rad) following standard procedures. Relative transcript levels were calculated using the 2-ΔΔCt formula, and the results were depicted in histograms drawn using GraphPad Prism v8.0 software.

5. Conclusions

A comprehensive analysis of the AP2/ERF family genes in ramie was carried out in this study. A total of 138 BnAP2/ERF genes were identified using bioinformatics, and further classified into five subfamilies based on conserved sequence characteristics, gene structure, and motif constituent. Synteny analysis revealed that fragment replication events were the key drivers of BnAP2/ERF evolution. Analysis of gene promoter cis-acting elements and target gene predictions indicated that BnAP2/ERF members actively respond to plant growth and stress stimuli such as water stress, mineral substance stress, and temperature stress. Based on the expression patterns analysis of BnAP2/ERFs, we identified some key genes involved in water stress and ramet development. In addition, transcriptome data and results from the protein interaction network analysis suggest that BnERF-30 and BnERF-32 had multifunctional regulatory effects on waterlogging stress and ramet development in ramie. In short, these results guide us a step further towards understanding the basic information of the AP2/ERF genes in ramie, which might serve as a first step toward the comprehensive functional characterization of the AP2/ERF gene family via genetic approaches in the future.

Supplementary Materials

The supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/ijms232315117/s1. Figure S1: Multiple sequence alignment analysis of conserved domains of ERF subfamily; Table S1: Basic information of the BnAP2/ERF gene family identified in this study; Table S2: Classification of BnERF family genes and the summary of conserved motifs (CMs) within BnERF subfamily; Table S3: Ka/Ks calculation of the duplicated BnAP2/ERF gene pairs; Table S4: Orthologous relationships between ramie and other four species; Table S5: The information of cis-elements in this study; Table S6: The com position of the nutrient solutions of the treatments (mg/L); Table S7: Primers information for selected BnAP2/ERF genes.

Author Contributions

Methodology, K.C.; Software, X.Q. and H.Z.; Validation, K.C. and P.C.; Formal analysis, X.Q. and H.Z.; Investigation, X.Q., H.Z. and C.Y.; Resources, X.Q., H.Z., D.S., C.Y., J.C. and X.W.; Data Curation, X.Q., H.Z., J.C. and K.C.; Writing—Original Draft, X.Q. and H.Z.; Writing—Review and Editing, A.S.A., J.C., K.C. and A.Z.; Visualization, X.Q. and H.Z.; Supervision, C.Y. and A.Z.; Project administration, C.Y. and A.Z.; Funding acquisition, J.C. and A.Z. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by the China Agriculture Research System for Bast and Leaf Fiber Crops (CARS-16), the Agriculture Science and Technology Innovation Program for Perennial Bast Fiber Crops (ASTIP-IBFC04), the Youth Talent Program of Hunan Province (2022RC1013), and the Innovative Provinces Building Program of Hunan Province (2019Nk2061).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.

Conflicts of Interest

The authors declare no competing interest.

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Figure 1. An unrooted phylogenetic tree constructed by the neighbor-joining method using AP2/ERF transcription factor domains in ramie and Arabidopsis.
Figure 1. An unrooted phylogenetic tree constructed by the neighbor-joining method using AP2/ERF transcription factor domains in ramie and Arabidopsis.
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Figure 2. The phylogenetic tree, conserved domain, and gene structure of the AP2/ERF superfamily in ramie: (A) The neighbor-joining tree with 1000 bootstrap replicates of all BnAP2/ERF proteins. (B) The conserved domain identified by the NCBI Batch CD-Search Tool. The blue blocks are the AP2 domain, red blocks are the B3 domain. (C) The gene structure of BnAP2/ERF genes. The green blocks are CDS, yellow blocks are UTR, and grey lines are introns. The number stands for the phase information of intron–exon junctions.
Figure 2. The phylogenetic tree, conserved domain, and gene structure of the AP2/ERF superfamily in ramie: (A) The neighbor-joining tree with 1000 bootstrap replicates of all BnAP2/ERF proteins. (B) The conserved domain identified by the NCBI Batch CD-Search Tool. The blue blocks are the AP2 domain, red blocks are the B3 domain. (C) The gene structure of BnAP2/ERF genes. The green blocks are CDS, yellow blocks are UTR, and grey lines are introns. The number stands for the phase information of intron–exon junctions.
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Figure 3. The composition of conserved motifs in ERF subfamily proteins of ramie: (A) I–IV group for the BnDREB subfamily; (B) V–X group for the BnERF subfamily.
Figure 3. The composition of conserved motifs in ERF subfamily proteins of ramie: (A) I–IV group for the BnDREB subfamily; (B) V–X group for the BnERF subfamily.
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Figure 4. Distribution and gene duplication of BnAP2/ERF genes on 14 ramie chromosomes. Blue lines represent tandem duplicates of BnAP2/ERF gene pairs, red lines represent segmental duplicates of BnAP2/ERF gene pairs, and grey lines represent all synteny gene pairs in the ramie genome.
Figure 4. Distribution and gene duplication of BnAP2/ERF genes on 14 ramie chromosomes. Blue lines represent tandem duplicates of BnAP2/ERF gene pairs, red lines represent segmental duplicates of BnAP2/ERF gene pairs, and grey lines represent all synteny gene pairs in the ramie genome.
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Figure 5. Gene duplication and synteny relationship of BnAP2/ERF genes between ramie and A. thaliana, C. sativa, O. sativa, and Z. mays. The deep gray lines stand for the syntenic AP2/ERF gene pairs, and the light gray stands for collinear blocks.
Figure 5. Gene duplication and synteny relationship of BnAP2/ERF genes between ramie and A. thaliana, C. sativa, O. sativa, and Z. mays. The deep gray lines stand for the syntenic AP2/ERF gene pairs, and the light gray stands for collinear blocks.
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Figure 6. Analysis of cis-acting elements in the promoter region of BnAP2/ERFs. The left panel shows the distribution of cis-acting elements in the promoter region. The heat maps of cis-acting elements for the light-responsive, phytohormone-responsive, stress-responsive, and the color concentration of the squares indicates the number of cis-acting elements.
Figure 6. Analysis of cis-acting elements in the promoter region of BnAP2/ERFs. The left panel shows the distribution of cis-acting elements in the promoter region. The heat maps of cis-acting elements for the light-responsive, phytohormone-responsive, stress-responsive, and the color concentration of the squares indicates the number of cis-acting elements.
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Figure 7. Gene ontology annotation and KEGG enrichment analysis of BnAP2/ERF target genes: (A) gene ontology (GO) annotation of BnAP2/ERF target genes; (B) top 20 of KEGG enrichment; (C) KEGG pathway annotation.
Figure 7. Gene ontology annotation and KEGG enrichment analysis of BnAP2/ERF target genes: (A) gene ontology (GO) annotation of BnAP2/ERF target genes; (B) top 20 of KEGG enrichment; (C) KEGG pathway annotation.
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Figure 8. Expression profiles of 138 BnAP2/ERF genes based on RNA-seq data: (A) The heat map of the expression profiles of BnAP2/ERF in four different tissues, which was generated using TBtools software based on log2(FPKM + 1) conversion counts of RNA-seq data. Red and white boxes indicate high and low expression levels of BnAP2/ERFs, respectively. (B) The heat map of the relative expression (converted by log2FC values) of BnAP2/ERF under water deficit (Wd), nitrogen deficit (Nd), and waterlogging (WL), with up-regulated genes marked in red and down-regulated genes marked in blue.
Figure 8. Expression profiles of 138 BnAP2/ERF genes based on RNA-seq data: (A) The heat map of the expression profiles of BnAP2/ERF in four different tissues, which was generated using TBtools software based on log2(FPKM + 1) conversion counts of RNA-seq data. Red and white boxes indicate high and low expression levels of BnAP2/ERFs, respectively. (B) The heat map of the relative expression (converted by log2FC values) of BnAP2/ERF under water deficit (Wd), nitrogen deficit (Nd), and waterlogging (WL), with up-regulated genes marked in red and down-regulated genes marked in blue.
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Figure 9. (A) Differences in the number of ramets of two ramie varieties. H denotes the ramie variety “He jiang qing ma” with a high number of ramet. Z denotes the ramie variety “Zhongzhu No.1” with a low number of ramet. (B) Relative expression profiles of group VIII members of BnAP2/ERF TFs in different tissues of the two ramie varieties.
Figure 9. (A) Differences in the number of ramets of two ramie varieties. H denotes the ramie variety “He jiang qing ma” with a high number of ramet. Z denotes the ramie variety “Zhongzhu No.1” with a low number of ramet. (B) Relative expression profiles of group VIII members of BnAP2/ERF TFs in different tissues of the two ramie varieties.
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Figure 10. The qPCR results of selected BnAP2/ERF genes in ramie leaf samples at 0, 3, and 12 h after waterlogging, and at 12 h (R12h) recovery to normal growth condition. The blue and red bars represent the relative expression level of BnAP2/ERF genes of ramie under light and dark conditions, respectively. The error bars represent the standard deviation of three biological duplicates.
Figure 10. The qPCR results of selected BnAP2/ERF genes in ramie leaf samples at 0, 3, and 12 h after waterlogging, and at 12 h (R12h) recovery to normal growth condition. The blue and red bars represent the relative expression level of BnAP2/ERF genes of ramie under light and dark conditions, respectively. The error bars represent the standard deviation of three biological duplicates.
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Figure 11. A BnAP2/ERF protein interaction network based on Arabidopsis homologs.
Figure 11. A BnAP2/ERF protein interaction network based on Arabidopsis homologs.
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Table
Table 1. The profile and comparison of AP2/ERF superfamily TF genes between ramie and Arabidopsis.
Table 1. The profile and comparison of AP2/ERF superfamily TF genes between ramie and Arabidopsis.
ArabidopsisRamie
ClassificationGroupNo.GroupNo.
AP2 familyTotal18Total19
Double AP2/ERF domain14Double AP2/ERF domain13
Single AP2/ERF domain4Single AP2/ERF domain6
ERF familyTotal122Total113
DREB subfamilyGroups I to IV57Groups I to IV36
ERF subfamilyGroups V to X58Groups V to X75
ERF subfamilyGroups VI-L and Xb-L7Groups VI to L2
SoloistAt4g130401BnSolo-011
RAV family 6 5
Total147Total138
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Qiu, X.; Zhao, H.; Abubakar, A.S.; Shao, D.; Chen, J.; Chen, P.; Yu, C.; Wang, X.; Chen, K.; Zhu, A. Genome-Wide Analysis of AP2/ERF Gene Superfamily in Ramie (Boehmeria nivea L.) Revealed Their Synergistic Roles in Regulating Abiotic Stress Resistance and Ramet Development. Int. J. Mol. Sci. 2022, 23, 15117. https://doi.org/10.3390/ijms232315117

AMA Style

Qiu X, Zhao H, Abubakar AS, Shao D, Chen J, Chen P, Yu C, Wang X, Chen K, Zhu A. Genome-Wide Analysis of AP2/ERF Gene Superfamily in Ramie (Boehmeria nivea L.) Revealed Their Synergistic Roles in Regulating Abiotic Stress Resistance and Ramet Development. International Journal of Molecular Sciences. 2022; 23(23):15117. https://doi.org/10.3390/ijms232315117

Chicago/Turabian Style

Qiu, Xiaojun, Haohan Zhao, Aminu Shehu Abubakar, Deyi Shao, Jikang Chen, Ping Chen, Chunming Yu, Xiaofei Wang, Kunmei Chen, and Aiguo Zhu. 2022. "Genome-Wide Analysis of AP2/ERF Gene Superfamily in Ramie (Boehmeria nivea L.) Revealed Their Synergistic Roles in Regulating Abiotic Stress Resistance and Ramet Development" International Journal of Molecular Sciences 23, no. 23: 15117. https://doi.org/10.3390/ijms232315117

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