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Article

AT-Hook Transcription Factors Show Functions in Liriodendron chinense under Drought Stress and Somatic Embryogenesis

by
Yao Tang
1,
Weihuang Wu
1,
Xueyan Zheng
2,
Lu Lu
1,
Xinying Chen
1,
Zhaodong Hao
1,
Siqin Liu
1 and
Ying Chen
3,*
1
Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
2
National Germplasm Bank of Chinese fir at Fujian Yangkou Forest Farm, Shunchang 353211, China
3
Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
*
Author to whom correspondence should be addressed.
Plants 2023, 12(6), 1353; https://doi.org/10.3390/plants12061353
Submission received: 12 February 2023 / Revised: 8 March 2023 / Accepted: 8 March 2023 / Published: 17 March 2023
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Abstract

:
AT-hook motif nuclear localized (AHL) is a transcription factor that can directly induce plant somatic embryogenesis without adding exogenous hormones. One of its functional domains, the AT-hook motif, has a chromatin-modifying function and participates in various cellular processes, including DNA replication and repair and gene transcription leading to cell growth. Liriodendron chinense (Hemsl.) Sargent is an important ornamental and timber tree in China. However, its low drought-resistant ability further leads to a low natural growth rate of its population. Based on bioinformatics analysis, this study identified a total of 21 LcAHLs in L. chinense. To explore the expression pattern of the AHL gene family under drought and somatic embryogenesis, we performed a systematic analysis including basic characteristics, gene structure, chromosome localization, replication event, cis-acting elements and phylogenetic analyses. According to the phylogenetic tree, the 21 LcAHL genes are divided into three separate clades (Clade I, II, and III). Cis-acting element analysis indicated the involvement of the LcAHL genes in drought, cold, light, and auxin regulation. In the generated drought stress transcriptome, a total of eight LcAHL genes showed increased expression levels, with their expression peaking at 3 h and leveling off after 1 d. Nearly all LcAHL genes were highly expressed in the process of somatic embryogenesis. In this study, we performed a genome-wide analysis of the LcAHL gene family and found that LcAHLs take part in resistance to drought stress and the development of somatic embryos. These findings will provide an important theoretical basis for understanding of the LcAHL gene function.

1. Introduction

The AHL gene family (AT-hook motif nuclear localized gene family) has been studied in a wide variety of plant species, such as Oryza sativa L., Arabidopsis thaliana, Gossypium raimondii, Zea mays, Vitis vinifera, Glycine max L. Merr, Populus trichocarpa and others [1,2,3,4,5,6]. For example, 29 AHL gene family members were identified in Arabidopsis, and 48, 51, and 99 AHLs were identified within the G. Raimondi, G. arboretum, and G. hirsutum genomes, respectively [2,3]. Furthermore, 14 AHLs were found in grape [4], and 37 AHLs were identified in maize [1]. Recently, some reports have shown that AHL plays an important role in stress response, especially in abiotic stress [6]. In P. trichocarpa and Oryza sativa L., the expression of AHL was significantly upregulated under drought stress [7]. The abiotic stress-responsive SOB3/AHL29 transcription factor limits petiole elongation by antagonizing growth and promoting PIF [8]. In addition, AHLs are related to plant growth and development, as AtAHL16 plays a role in the transcriptional activation of anther development [9], and AtAHL18 is involved in regulating root system architecture and growth [10]. Furthermore, some researchers speculated that AtAHLs might involve either direct transcriptional regulation of target genes or more global regulation by altering chromosome structure in the process of somatic embryogenesis and polyploid generation [11,12].
Liriodendron, belonging to the magnolia family, was previously widely distributed in temperate regions of the northern hemisphere, but numerous species have gone extinct as a consequence of the expanding quaternary glaciers. At present, just two species of L. chinense and L. tulipifera remain [13]. Hybrids between Liriodendron chinense and Liriodendron tulipiferea possess a highly productive somatic embryogenesis system [14]. L. chinense is an ancient relic plant and one of the nationally rare and endangered protected plants in China. As a precious commercial tree species [15], it has a high growth speed, high-quality wood texture, mandarin jacket shape leaves and calendula-like flowers. Drought stress is the most prevalent environmental factor limiting plant growth and reproduction [16]. However, the adaptability to arid environments of L. chinense is weak, resulting in a low natural reproduction rate. Previous studies have shown that L. chinense grows in subtropical monsoon climate areas and that precipitation in the warmest quarter exerts the greatest impact on its growth [17]. Under drought stress, its low natural reproduction efficiency and seed germination rate limit regeneration of the natural populations [18]. The embryogenic callus of L. Hybrid possessed a mature genetic transformation system [19]. Therefore, finding an alternative gene that improves drought resistance and somatic embryogenesis efficiency can help to cultivate and promote new transgenic varieties with excellent resistance.
Somatic embryogenesis is a type of plant cell totipotency where embryos develop from nonreproductive cells without fertilization [20]. Two main methods for inducing somatic embryogenesis have been reported, which are direct somatic embryogenesis and indirect somatic embryogenesis [21,22]. A suspension culture system of embryogenic calli of the Liriodendron hybrid was established with high proliferation after explants successfully regenerated from immature zygotic embryos [14]. Somatic embryogenesis is widely used in plants such as Arabica coffee [23], ornamental bananas (Musa, spp) [24], and tree peony (Paeonia sect. Moutan) [25]. In Arabidopsis, overexpression of AHL15 can induce direct somatic embryogenesis without adding exogenous hormones [12]. All these studies have not systematically explored the expression of AHLs at different stages of somatic embryogenesis; furthermore, most of the studies on AHLs resistance to abiotic stress are focused on model species such as Arabidopsis thaliana, and few studies were conducted in woody species. As an important transcription factor and direct downstream target gene of BBM, there is no detailed report on the genome-wide identification of the LcAHL gene family in L. chinense at present. With the publication of the L. chinense genome [17,26], we can explore and study its important functional genes [27] to provide candidate genes for the cultivation of transgenic elite species with high somatic embryogenesis efficiency and drought resistance. We identified 21 LcAHL genes and analyzed using bioinformatics, including a description of their physical and chemical properties, basic characteristics, gene structure, chromosome localization, replication events, cis-acting elements, protein tertiary structure and phylogenetics. Afterward, our transcriptome analysis showed that the expression of LcAHL increased significantly during drought stress and ABA-induced somatic embryogenesis. The evolutionary analysis is helpful in fully understanding the origin and evolution of the AHL genes in L. chinense and to lay the foundation for its gene function research. Many gene structures and promoter analyses also provide a basis for exploring its gene regulatory network. Targeted research and transformation of genes related to drought stress and somatic embryogenesis in the L. chinense genome help to improve the ability to adapt to a drought environment and lay the foundation for further development of quality timber industry. The study also provides candidate genes for the cultivation of transgenic elite species with high somatic embryogenesis efficiency and drought resistance.

2. Results

2.1. Identification and Physicochemical Property Analysis of LcAHL Gene Family Members

We identified a total of 21 putative full-length genes encoding LcAHL proteins in the L. chinense genome (Table S1). Our analysis of the tertiary structure suggests that the LcAHL proteins are composed of α-helices, β-folds and multiple γ-corners. The proteins are coiled and folded to form a precise and complex tertiary structure (Figure 1a). They possess coincident conserved PPC/DUF296 domains and AT-hook motifs (Figure 1b).
We then analyzed the physical and chemical properties of LcAHLs (Table 1), such as their pI (isoelectric point), MW (molecular weight), instability index and subcellular localization. Their predicted pI values ranged from 4.71 to 10.62; thus, 14 LcAHLs can be classified as basic proteins with theoretical isoelectric points exceeding 7, and the remaining LcAHLs are acidic proteins. Their molecular weight ranged from 22.38 kDa (Lc06945) to 72.82 kDa (Lchi06288), and their grand average of hydropathicity was from −0.551 (Lchi06750) to 0.055 (Lchi01373). The instability index of all LcAHL proteins scored a value over 40; since proteins with an instability index below 40 are generally considered stable [28], we conclude that all the LcAHL proteins are unstable proteins. Subcellular localization predictions indicated that most LcAHL (16/21) proteins localize to the nucleus, which is consistent with previous studies. The remaining LcAHLs are predicted to localize to either chloroplast and/or mitochondria: Lchi04180 localizes to mitochondria, Lchi30606 and Lchi12845 to chloroplasts, Lchi22185 to both mitochondria and chloroplasts and finally Lchi13190 to both the nucleus and chloroplasts.

2.2. Phylogenetic Analysis of LcAHL Proteins

The result of multiple sequence alignment and evolutionary tree clustering showed that all 21 LcAHLs, with only Lchi22185 excluded, possess both a PPC/DUF296 domain and AT-hook motif (Figure 2). The AT-hook motif is composed of three amino acids, which is R-G-R. The PCC domain is volatile and can be divided into two types: L-R-S-H and F-T-P-H [29]. Based on the protein sequence of their conserved domains, the 21 LcAHLs could be divided into two clades: Clade A and Clade B. To infer the evolutionary relationship between LcAHLs and AtAHLs, we carried out Bayesian evolutionary analysis using BEAST (v2.2.6) software [30]. A phylogenetic tree was constructed with the full-length AtAHLs (29) and LcAHLs (21), which could be divided into three clades: Clade I, Clade II, and Clade III (Figure S1). Clade A was consistent with Clade I, and Clade B was further subdivided into Clade II and Clade III (Figure 3a).
Previous studies suggested that L. chinense is one of the earliest diverging core angiosperms [31]. To further analyze the phylogenetic interrelatedness of the LcAHL gene family, the protein sequences of the AHL gene family members from 21 species (Table S2), including 2 Bryophyta and Pteridophyta, 4 Monocots and 15 Dicots, were constructed into an evolutionary tree (Figure 3b). In conclusion, the phylogenetic tree showed the relative consistency and diversity of the evolutionary status of AHL in different species. It provided evidence for the homology analysis of AHL among different species.
The species tree indicates that the evolutionary position of the LcAHL proteins lies between Ricinus communis and Carica papaya (Figure 3b), meaning that LcAHLs are most closely related to homologous proteins from dicotyledonous species. However, Liriodendron itself is classified as a basic angiosperm based on its full genomic sequence. This discrepancy could be caused by differing speeds of functional differentiation within the AHL family. From the species tree analysis, we found that the number of AHL family members in dicotyledonous was higher than the number in monocots and basic angiosperms. We infer that the expansion rate of the LcAHL gene family is not the same as that of the Liriodendron genome. The number of left-after genome-wide replication events and environmental selection is close to the number of dicots. Most dicots have experienced genome-wide duplication events; thus, the number of AHLs is higher than that of monocots and basal angiosperms.

2.3. Distribution of the LcAHL Gene Family across the Liriodendron Genome

Based on the available Liriodendron genome annotation data, we mapped the chromosome locations of 21 LcAHLs (Figure 4 and Table S3). We found that a total of nineteen LcAHLs are unevenly distributed across nine chromosomes, and two LcAHLs are located on a scaffold. Four LcAHL genes are located on chromosome 11, and only one LcAHL is present on chromosomes 4, 7, and 18. Chromosomes 1 and 8 contain three LcAHLs, while chromosomes 3, 6, 10 and Scaffold1025 each contain two LcAHLs. Gene tandem duplication and fragment duplication events are frequent in the process of gene evolution (Table S4). Through the analysis of replication events, we found that 14 LcAHL genes show signs of fragment replication, while only a single pair of genes is the result of a tandem replication, being Lchi06945 and Lchi22185. Therefore, the results of this study indicated that follows that fragment duplication was the fundamental expansion mechanism of the LcAHL gene family, while a small number of genes experienced tandem replication.

2.4. LcAHL Gene Structure and Promoter Analysis

We used the MEME website to predict six conserved domain models of LcAHL protein family members, including 11–50 amino acids and 5–20 sites (Figure 5a and Table S5). Combined with multiple sequence alignment analyses, we found motifs 1 and 2 to be highly conserved. In agreement with previous studies, these two motifs are the core conserved sequences of LcAHLs. Almost all proteins contain motif 1 or motif 2, indicating the high degree of sequence conservation within the LcAHL protein family.
Gene structure analysis (Figure 5b) showed the LcAHL gene length and the quantitative relationship between the coding sequence (CDS) and untranslated region (UTR). CDS length ranges from 600 to 1000 bp, genomic sequence length from 904 to 27,410 bp, and LcAHL protein length ranges from 151 aa to 474 aa (Table 2). The introns make up a large proportion of the gene space, and the number of exons varies from 3 to 6. Genes in Clade II and Clade III possess at least two introns more than those in Clade I. Most members of Clade I subgroup did not have UTR, except for Lchi06288. Clade II members contain more introns and have a relatively dense and short CDS. Excluding a small number of genes that do not have UTRs, such as Lchi01372 and Lchi04864, other gene members in Clade II possess one to three UTRs. These results indicate the diversity of the LcAHL protein sequences.
The cis-acting elements within promoters are generally related to transcriptional regulation of gene activity dynamic networks, including abiotic stress responses, hormone responses, and developmental processes [32]. The cis-acting elements present within the LcAHL promoter include elements that function in stress resistance, such as MBS, which is related to drought resistance, LTR, which has a role in low-temperature stress, and AE-box, MRE, I-box, GT1 motif, GATA motif, and G-box elements, which are related to light response and hormone response elements (Table 3). There are many cis-acting elements of LcAHL related to abiotic stress, such as LTR, TC-rich repeats and MBS [33]. Therefore, we hypothesized that the AHL protein may be involved in stress resistance. At the same time, the promoter region of LcAHLs also possesses many cis-acting elements related to cell cycle regulation (MSA-like) and endosperm expression [34,35]. Therefore, we speculate that AHL proteins may be involved in early embryonic development.

2.5. LcAHLs Expression Analysis during Drought Stress and Somatic Embryogenesis

We performed transcriptome analysis of the AHL gene in different tissues of Liriodendron chinense. The results showed that LcAHLs are mainly expressed in the stigma, bud, stamen, leaf, bark, and sepal (Figure 6a and Table S6). For example, Lchi13190 and Lchi05954 are mainly expressed in reproductive organs, such as the stamen, sigma, and sepal, while their overall expression levels are low in vegetative organs. Lchi06945 is mainly expressed in the stamen, while Lchi32451 is mainly expressed in the xylem. If a gene is expressed highly in a specific tissue, this usually indicates that the gene’s function is related to that organ’s function [36]. Through tissue-specific expression information, we found that LcAHLs’ expression in reproductive organs is significantly higher than that in vegetative organs. Therefore, we speculate that LcAHL gene function may be related to plant reproductive growth, such as embryogenesis.
Subsequently, transcriptome analysis of AHL gene under drought stress was also performed. It shows that the expression of LcAHLs increased during drought stress (Figure 6b and Table S7). After one hour of drought stress, different AHL genes showed three different expression patterns (Figure S2). Pattern I: gene expression began to increase one hour after drought stress, including Lchi13190 and Lchi13244. Pattern II: Gene expression began to rise after three hours of drought stress and stabilized after one day. Pattern III: the remaining did not respond significantly to drought stress. In conclusion, the gene expression levels of LcAHLs increased from 3 to 12 h and thereafter gradually decreased to their previous levels.
In addition, we used qRT-PCR to quantify the expression trends of three LcAHLs (Lchi05954, Lchi06280, and Lchi13190) in different seedling tissues after drought stress treatment simulated by 15% PEG6000 (Table S8). The results showed that the LcAHL genes responded immediately to drought stress, especially after 3 h of drought stress. The expression of LcAHLs began to decrease after 12 h, consistent with the results of our transcriptome analysis. At the same time, we found that upon 15% PEG6000 treatment, LcAHL expression responded earlier in roots and stems than in leaves. For example, Lchi05954 expression was upregulated after 3 h in roots and stems, while the expression in leaves only began to rise after 72 h (Figure 7).
During the process of somatic embryogenesis, the gene expression of LcAHLs increased significantly during the transformation from proembryo to spherical embryo (Figure 8). Pro-embryogenic masses were cultured for 20 days on 3/4 MS medium to generate embryogenic callus (PEMs) and then cultured in liquid suspension for another 10 days, after which single cells were cultured for 2 days. Embryo samples were induced by ABA for increasing time intervals to collect successively staged embryos under the microscope: 1 day for early embryos (ES3), 7 days for globular embryos (ES5), 31 days for mature cotyledon embryos (ES9) and 37 days for plantlets (PL). Transcriptome analysis of somatic embryos shows that LcAHL genes are expressed during somatic embryogenesis; we could discriminate two unique LcAHL expression patterns during this process. Expression pattern I: after ABA treatment, the expression of AHLs increased and then reached the lowest expression at the spherical embryo stage (ES5), finally increasing at the later stages of somatic embryogenesis. Pattern II is lower during the early stage (ES1-4) and then increases during the mid-term (ES5-7) and later stages (ES7-9).
We selected nine LcAHL genes to verify the transcriptome data in five critical periods by qRT-PCR (Figure 9a and Figure S3). Somatic embryos were collected at PEM, S3, S5, S9 and PL stages (Figure 9b and Table S9). We divided the expression patterns into three types. Type I: the expression of LcAHLs has no significant difference with PEMs during somatic embryogenesis. However, when induced by ABA (S3), the expression trend decreased. Type II: after ABA induction (S3), the expression of AHL increased (S5), then decreased and finally peaked at the stage of plants (PL). Type III: the expression of AHLs increased continuously during somatic embryogenesis.

2.6. LcAHL Subcellular Localization

To explore the potential function of LcAHL genes in transcriptional regulation, we verified their predicted subcellular localization using L. chinense callus protoplast transient transformation (Figure 10). We used a ZEISS LSM 800 fluorescence microscope (Carl Zeiss, Germany) to observe the expression pattern of LcAHLs under different light waves. Cellular morphology and certain cellular structures, such as starch granules, vacuoles, etc., can be seen using visible light, while we used GFP fluorescence to visualize GFP-tagged LcAHL proteins. Then, 35S::GFP was used as a control construct, lighting up the entire cell in GFP fluorescence. The subcellular localization assay showed that the encoded proteins of Lchi05954 and Lchi13190 only exhibited fluorescent signal in the nucleus but not in the cytoplasm and cell membrane. Therefore, we speculate that it may play a regulatory role as a nuclear transcription factor during transcription.

3. Discussion

3.1. Diversity of LcAHL Family Members, Their Gene Structure and Physicochemical Properties

We initially identified 28 LcAHL proteins in L. chinense that possess a PCC domain. However, after verifying their protein domains using the Pfam website, we found that only 21 proteins possess a bona fide AT-hook motif and PCC domain. Although Lchi22185 has no conserved domain sequence, it nonetheless can be clustered within the AtAHL evolutionary tree. Genome duplications, non-neutral selection, and co-evolving residues may lead to changes in the conserved domain of proteins [37]. Thus, we speculate that Lchi22185 may have lost its conserved domain during evolution. Previous studies have shown that there are 28 AHLs in Arabidopsis, 63 family members in soybean [5], 37 AHLs in popular [6], 14 in grape [4], 37 family members in maize [1] and 47 AHL genes in carrot [38]. In our study, we divided them into two clades, according to their characteristics and distribution of conserved domains. Based on phylogenetic tree analysis with A. thaliana (S 1), we further divided Clade B into two subgroups. We found that the Clade A protein sequences have remained relatively conserved, whereas the Clade B proteins were more strongly diversified during evolution. From a protein level, the PPC domain in Clade A changes greatly, which is consistent with analyses performed in soybean [5]. It may be related to the diversity of LcAHL gene function [39].
In soybean, AHL genes can reach more than 6 kb in length, with a CDS length of approximately 1 kb [5]. The longest gene sequence in L. chinense is over 20 kb, with the average CDS length being similar to soybean [5]. In plants, the number of genes containing introns is significantly higher than in previously reported studies [40]. We found that all 21 LcAHLs contain introns, indicating that this feature may have been conserved evolutionarily and could be important functionally. These genes may use introns to create novel splice variants to tune gene function to a specific developmental stage and tissue type [41]. In maize, only one gene in Clade I has a UTR, indicating that the AHL gene structure has diversified among different species [1]. A combination of the motif and gene structure analysis showed that Clade II and Clade III evolved from Clade I [5], similar to what has been found for the maize AHL gene family [1].
Most LcAHL proteins are neutral to weak basic proteins, similar to cotton AHLs [3], while soybean AHLs are more acidic. Previous studies have shown that high hydrophobicity is not only conducive to the internal folding of proteins but is also important for the nuclear localization of the PPC domain [42]. The amino acid hydrophobicity of LcAHLs can reach 70 kDa, higher than that of soybean, cotton, and grape, indicating that the LcAHL proteins are relatively stable.
According to species tree analysis, the evolutionary status of LcAHLs is closely related to Carica papaya and Ricinus communis, which belong to dicotyledons in evolutionary status. Transcription factor genes of the same family but from diverse eukaryotic organisms show structural and functional similarity, suggesting that they evolved from a common ancestor [43]. In prokaryotes and early eukaryotes, the association with AT-hook motifs is not necessary for the function of PPC protein domains [44]. With the occurrence of gene duplication events, the number of AHL gene family members increases and gene functions differentiated. Similar reports have been reported in rice. The authors speculate that gene replication may be a key mechanism for the functional diversification of the rice YSL (yellow stripe-Like) gene family, leading to changes in spatial and/or temporal gene expression [45]. In the basal Bryophyta Pteridophyta genome, a small number of AHLs is present, while in later diverging species, the number of AHL genes gradually increased. The gene number variation of the AHL gene family may be regulated by several factors. However, natural selection may play a more important role in ginseng [46].
Based on subcellular localization algorithms, LcAHLs were predicted to be localized to the nucleus. Previous studies have shown that the hydrophobic region of the PPC domain is crucial for its nuclear localization. Mutations of the AT-hook motif may lead to the chromatin-binding function being lost [47]. We used homeostatic transformation to transfer Lchi05954/13190 into protoplasts and verified these two AHLs to be localized to the nucleus. We further speculate that they may function as transcription factors.

3.2. LcAHLs Have Expanded Primarily through Fragment Duplication

Eukaryotic genomes are replicated from large numbers of replication origins distributed across multiple chromosomes [48]. To explore the evolution of LcAHLs, we investigated the collinearity between genomes. In our research, we found the LcAHL genes to be distributed across nine chromosomes and one scaffold, unrelated to chromosome size and location. We also found that fragment replication has been the dominant form of replication in the LcAHL gene family, with a small amount of tandem replication taking place, which contrasted with the most common dispersed replication observed in maize [1]. In cotton, the amplification of the AHL gene family has taken place via fragment replication or genome-wide replication, with no tandem replication having taken place [3]. This indicates that the amplification mode of the AHL gene family varies across different species. Large-scale replication events (21/15) have occurred in the LcAHL gene family, mainly in Clade A. A large number of examples exist where changes in gene activation state follow replication events: genes may be either transcriptionally activated or repressed [49].

3.3. LcAHLs Expression Pattern Analysis

In soybeans, AHLs are mainly expressed in roots, meristems and epicotyls. In cabbage, AHLs are mainly expressed in roots and buds. In maize, they are mainly expressed in roots, embryos, endosperm, and seeds [1]. We analyzed the expression of LcAHLs in different Liriodendron tissues and found that, excluding a small number of LcAHL genes expressed in the phloem, such as Lchi06945, Lchi13190, and Lchi05954, they are mainly expressed in floral organs, which may be related to their biological function. Among them, Lchi13190 and Lchi05954 are highly expressed in various floral tissues, while Lchi06945 is mainly expressed in stamens with low expression in other tissues. AHL15 and other AHL Clade A genes function directly downstream of flowering genes, such as SOC1 (SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1), FUL(FRUITFULL), and upstream of the flowering-promoting hormone gibberellic acid [50]. Drought is an important stress, having a huge impact on the growth and productivity of plants [51]. In order to resist drought stress, it is urgent to explore drought resistance genes and cultivate high drought-resistant varieties. However, comprehensive phenotyping at the seedling stage is an efficient way to select a drought-tolerant germplasm [52]. Our results suggest that LcAHLs increase gene expression after 3 h of drought stress in somatic embryo seedlings. Therefore, we speculate that they may be involved in drought stress resistance.
The cis-acting elements are usually closely related to the function of the downstream gene, such as the 150 bp cis-acting sequence located upstream of the TATA box of AtNRT2.1, which confers regulation of NO3−, sugars and N metabolites [53]. Our analysis of cis-acting elements present in the promoters of LcAHL genes detected many elements related to drought stress. For example, Lchi01373 and Lchi04864 possess MYB binding sites that are inducible by drought. Drought is one of the major causes of dramatic yield loss in plants [43]. Plants respond and adapt to water stress by increasing the expression of water-stress-inducible genes that respond to mitigate the effects of water stress [54]. The qRT-PCR results of LcAHLs showed that roots respond faster than stems and leaves under drought stress. Lchi05954 expression gradually increased after 3 h in the root and stem, experiencing a peak after 12 h, after which it gradually declined, while it only increased after a period of 72 h in leaves.
The AHL gene family encodes embryophyte-specific nuclear proteins with DNA binding activity [10]. AtAHL15 and other AtAHL genes are necessary for normal embryonic pattern formation and development after the globular stage [12]. From our transcriptome analysis, we found that the expression of LcAHL increased during the transformation from proembryo to globular embryo and that the expression of Lchi04180 and Lchi12845 increased significantly at the ES5 stage. Previous studies have shown that AHL functions during the decondensation of chromatin during cellular mitosis. Overexpression of AtAHL15 can increase the probability of tetraploid formation during somatic embryo induction [12]. Therefore, exploring LcAHL genes could improve the efficiency of L. chinense somatic embryogenesis in a meaningful way.

4. Materials and Methods

4.1. Genome-Wide Identification of LcAHL Proteins

The genome sequence file, annotation file and CDS sequence of L. chinense were acquired from NCBI (https://www.ncbi.nlm.nih.gov/, accessed on 5 September 2022), while the 29 AtAHL amino acid sequences were downloaded from TAIR (https://www.arabidopsis.org/, accessed on 5 September 2022). The HMM file (Hidden Markov model file) of the PCC domain was retrieved from the Pfam database (http://pfam.xfam.org/, accessed on 5 September 2022) and used to search for protein sequences containing a PCC domain with the HMMER program (v3.3.6) in the total proteome of L. chinense. Next, the protein sequences of the LcAHL family were extracted from the L. chinense protein sequence database using the identified protein number. BLAST+(2.7.1) was used for homology comparison to 29 AtAHLs, and the CDD website (https://www.ncbi.nlm.nih.gov/cdd, accessed on 5 September 2022) and Pfam were used to confirm and delete proteins without a PCC domain. Subsequently, the correct nonredundant family members were obtained.
The LcAHL motif was predicted using the MEME website [55] (https://meme-suite.org/meme/doc/meme.html, accessed on 5 September 2022) at an E-value of 10−5 (maximum number of motifs is 6; maximum width is 50; minimum sites is 2; maximum sites is 600), after which an evolutionary tree was constructed using TBtools software (v1.09). The intron/exon gene structure was determined using the gene feature file (gff3) and displayed with the GSDS website (http://gsds.gao-lab.org/, accessed on 5 September 2022). The basic protein physical and chemical properties, such as protein length, molecular weight (MW) and isoelectric point (pI), were determined with the ProtParam tool of the ExPASY website (https://www.expasy.org/, accessed on 5 September 2022). Subcellular localization analysis was performed using the Plant-mPLoc website (http://www.csbio.sjtu.edu.cn/bioinf/plant-multi/, accessed on 5 September 2022). Promoter element analysis was completed using the PlantCARE website (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/, accessed on 5 September 2022).
Protein tertiary structure was predicted using the SWISS-MODEL website (https://swissmodel.expasy.org/interactive, accessed on 5 September 2022). The corresponding PDB file was downloaded, visualizing the tertiary structure of the protein using the Swiss PDB viewer (v4.0.1).

4.2. Multiple Sequence Alignment and Evolutionary Analysis

ClustalX2 (v2.1) software was used to construct a multiple sequence alignment of LcAHL protein sequences (the gap being set as the default value), which was subsequently visualized on the ESPript website (https://espript.ibcp.fr/ESPript/cgi-bin/ESPript.cgi, accessed on 5 September 2022). The evolutionary tree of L. chinense and A. thaliana was drawn using RAxMAL (v8.2.11) and then displayed on the iTOL website (https://itol.embl.de/, accessed on 5 September 2022).
AHL protein sequences of 21 species, including Bryophyta, Pteridophyte, Monocots, and Dicotyledoneae, were retrieved from the Phytozome website (https://phytozome-next.jgi.doe.gov/, accessed on 5 September 2022) and aligned with ClustalX. Multiple sequence alignment was saved in FASTA format and converted into an XML file with the BEAUti program, selecting Dayhoff for the site model. Finally, we used the TreeAnnotator program to annotate the evolutionary tree, where the burin percentage was set to 90 and the limit to 1. A Bayesian tree was completed and visualized by Figtree software (v1.4.3).

4.3. LcAHL Chromosomal Location and Replication Event Analysis

Genome annotation files were used to calculate gene length, chromosome length, and gene chromosomal position. MCScanX software was applied to calculate replication events while setting the parameters as follows: similarity > 70%, e-value cutoff < 1E−6. The R software package Circlize [56] was used to visualize the chromosomal location.

4.4. Cis-Acting Element Analysis

The 1.5 kb upstream region of LcAHL family members was extracted and analyzed using the PlantCARE website (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/, accessed on 5 September 2022), and the cis-acting elements were visualized by TBtools software.

4.5. LcAHL Expression Pattern Analysis under Drought Stress and Somatic Embryogenesis

The drought stress transcriptome data of L. hybrid is annotated with accession number PRJNA679101 and can be downloaded through NCBI (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA679101/, accessed on 5 September 2022). The date of somatic embryogenesis is unpublished. Heatmaps visualizing expressions were displayed with TBtools software (v1.09). The log2 (TPM + 1) value was used for standardization and hierarchical cluster analysis.
Plant materials used were the L. hybrid somatic embryo line 166,302, cultivated in the greenhouse for 2 weeks (16 h of light/8 h of darkness and 75% relative humidity). Then, 15% PEG6000 [57] was used to simulate a naturally arid environment, performing three biological replicates. Roots, stems and leaves were harvested after 3 h, 12 h and 3 d drought treatment, immediately frozen with liquid nitrogen and stored at −80 °C. Somatic embryogenesis was induced from immature zygotic embryos. Pro-embryogenic masses were cultured for 20 days on ¾ MS medium to generate embryogenic callus (PEMs) and then cultured in liquid suspension for another 10 days, after which single cells were cultured for 2 days. Embryo samples were induced by ABA for increasing time intervals to collect successively staged embryos under the microscope: 1 day for early embryo’s (ES3), 7 days for globular embryos (ES5), 31 days for mature cotyledon embryo (ES9) and 37 days for plantlets (PL).
Total RNA was extracted using a fast pure total RNA Isolation Kit (enzyme, Nanjing, China) 527 (RC401) and then reverse transcribed into cDNA with a script ® III 1st strand cDNA synthesis 529 Kit (Vazyme, Nanjing, China). CDS sequences were obtained from NCBI (https://www.ncbi.nlm.nih.gov/assembly/GCA_003013855.2. , accessed on 5 September 2022). Primers were designed using Oligo7 (v7.6) with a length from 80 to 200 bp and then blasted against the L. chinense genome using TBtools to ensure their specificity (Table S10). Lc18S was used as an internal reference gene. The composition of the amplification mix was 20 μL: 10 μL 2x AceQ ® qPCR SYBR ® Green Master Mix (Without ROX), 0.4 μL specific primers (Forward/reverse primers), 2 μL cDNA template, and 7.2 μL ddH2O in a final volume of 20 μL. The reaction procedure was as follows: pre-denaturation at 95 °C for 30 s; denaturation at 95 °C for 10 s; annealing at 60 °C for 30 s; extension at 72 °C for 30 s; with 40 cycles in total, repeated three times. Then, the fluorescence value (CP value) obtained from the reaction result was calculated with the 2−∆∆CT method [58].

4.6. LcAHLs Subcellular Localization

We used the pJIT166-GFP vector to construct a LcAHL-GFP fusion protein [59]. To obtain the fusion protein expression vectors, Lchi05954 and Lchi13190 were recombined with pJIT166-GFP, using the SalI and XbaI restriction enzymes. L. chinense callus was hydrolyzed with cellulose, hemicellulose and pectinase for 8 h to prepare protoplasts. The two recombinant plasmids and the empty plasmid pJIT166-GFP as control were then transformed into the prepared protoplasts using a PEG8000 mediated method [60], after which they were cultured in the dark for 24 h. We used a ZEISS LSM 800 fluorescence microscope (Carl Zeiss, Germany) to observe LcAHL subcellular localization.

5. Conclusions

In this study, we identified and analyzed 21 LcAHL proteins in L. chinense, finding that they have similar protein structures and functional domains. Based on comparison of their amino acid sequences and AT-hook and PPC domain, the LcAHL genes were divided into two phylogenetic clades. We investigated the cis-acting elements of the promoter regions and found that the promoters of AHL possess drought stress-related cis-regulatory elements. After that, we systematically studied the LcAHLs expression profiles in different tissues and the response to stress conditions, as well as the expression at different stages of somatic embryogenesis. Our study found that the LcAHL genes show functions on drought stress resistance and take part in somatic embryogenesis. RNA-seq analysis showed that the expression of LcAHLs increases during somatic embryo formation, especially in torpedo-shaped embryos and mature cotyledon embryos. Transcriptome data of tissue and drought stress showed that LcAHLs are mainly expressed in floral organs and that their expression level increased under drought stress. These results laid a molecular foundation for improving the efficiency of somatic embryos and cultivating drought resistant plants. It provides alternative genes for L. chinense to better adapt to the arid natural environment and improve its somatic embryogenesis efficiency.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/plants12061353/s1, Figure S1: Bayesian tree indicating the phylogenetic relationships between 21 AHL proteins from Liriodendron chinense (Lc) and 29 from Arabidopsis.; Figure S2: Quantitative real-time PCR (qRT-PCR) dissolution curve and standard curve of three LcAHL genes under drought stress; Figure S3: Quantitative real-time PCR (qRT-PCR) dissolution curve and standard curve of nine LcAHL genes at different stages of somatic embryogenesis; Table S1: Protein sequences of 21 LcAHLs; Table S2: AHL protein sequences of 21 species; Table S3: Gene position of LcAHLs; Table S4: Synteny gene pairs of LcAHLs; Table S5: LcAHL gene annotation information of LcAHLs; Table S6: Eight tissues’ FPKM values for LcAHLs; Table S7: TPM value of LcAHLs under drought stress; Table S8: Quantitative real-time PCR (qRT-PCR) value of LcAHLs under drought stress; Table S9: qRT-PCR value of LcAHLs at different stages during somatic embryogenesis; Table S10: Primer sequences of eight LcAHLs for q-RT PCR.

Author Contributions

Methodology, W.W. and S.L.; Investigation, X.Z. and Z.H.; Resources, Z.H.; Writing—original draft, Y.T.; Writing—review and editing, Y.C.; Visualization, X.C.; Supervision, L.L.; Project administration, Z.H.; Funding acquisition, Z.H. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the National Key R&D Program of China (2021YFD2200103), the Nature Science Foundation of China (32071784) and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).

Data Availability Statement

Transcriptome data of somatic embryogenesis and tissues have not yet been published. The drought stress transcriptome data of L. hybrid is annotated with accession number PRJNA679101 and can be downloaded through NCBI (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA679101/, accessed on 5 September 2022). The complete genome, transcript/protein sequences, and genome feature file of Lchi were downloaded from https://www.ncbi.nlm.nih.gov/assembly/GCA_003013855.2, accessed on 5 September 2022.

Acknowledgments

The authors thank Hao Fang, Bojun Liao, Zhenyu Chen and all other laboratory colleagues for the constructive discussion and technical support.

Conflicts of Interest

The authors declare no conflict of interest.

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Figure 1. The tertiary structure of Lchi06280 protein. (a) The complete protein tertiary structure of Lchi06280. Different colors represent different structures. (b) The conserved domain of Lchi06280.
Figure 1. The tertiary structure of Lchi06280 protein. (a) The complete protein tertiary structure of Lchi06280. Different colors represent different structures. (b) The conserved domain of Lchi06280.
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Figure 2. Multiple sequence alignment analysis results of LcAHLs. (a) The obtained phylogenetic tree is shown on the left, and the conserved domain in two functional units of the AHL proteins, the AT-hook motif and PPC domains, is shown on the right. (b) Sequence information of conserved domain proteins in different branches. The x-axis and y-axis suggest the conserved sequences of the domain and the conservation rate of each amino acid, respectively. (c) The topology of two LcAHLs types (type I and type II) was consistent with the PCC domain and AT-hook motifs.
Figure 2. Multiple sequence alignment analysis results of LcAHLs. (a) The obtained phylogenetic tree is shown on the left, and the conserved domain in two functional units of the AHL proteins, the AT-hook motif and PPC domains, is shown on the right. (b) Sequence information of conserved domain proteins in different branches. The x-axis and y-axis suggest the conserved sequences of the domain and the conservation rate of each amino acid, respectively. (c) The topology of two LcAHLs types (type I and type II) was consistent with the PCC domain and AT-hook motifs.
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Figure 3. Phylogenetic analysis and species tree of the AHL proteins in 21 species. (a) Different colors indicate different evolutionary clades. The Bayesian tree shows the phylogenetic relationships between AHL proteins. The tree is divided into three branches, including Clade I, Clade II, and Clade III. (b) The green highlight is classified as Bryophyta and Pteridophyte, the orange highlight is classified as the monocots, and the blue highlight is classified as Dicotyledonae. Red stars represent the branching sites of L. chinense, and the red font represents the evolutionary position of L. chinense.
Figure 3. Phylogenetic analysis and species tree of the AHL proteins in 21 species. (a) Different colors indicate different evolutionary clades. The Bayesian tree shows the phylogenetic relationships between AHL proteins. The tree is divided into three branches, including Clade I, Clade II, and Clade III. (b) The green highlight is classified as Bryophyta and Pteridophyte, the orange highlight is classified as the monocots, and the blue highlight is classified as Dicotyledonae. Red stars represent the branching sites of L. chinense, and the red font represents the evolutionary position of L. chinense.
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Figure 4. Chromosome mapping and gene replication event analysis of 21 LcAHLs. Chromosomes are represented by different colors, and the outer circle represents the scale. The inner circle is the location information of the gene. The arcs of different colors represent gene pairs of different gene replication events.
Figure 4. Chromosome mapping and gene replication event analysis of 21 LcAHLs. Chromosomes are represented by different colors, and the outer circle represents the scale. The inner circle is the location information of the gene. The arcs of different colors represent gene pairs of different gene replication events.
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Figure 5. Conserved motif and gene structure information of LcAHLs. (a) Conserved motif information of 21 LcAHLs. We predicted 6 conserved motifs of LcAHL proteins and have marked them with different colors. (b) The x-axis represents the predicted length of different LcAHL genes (5′ to 3′). Different colors represent different structures. Yellow rectangles are CDS, blue rectangles are UTRs, and the black straight line represents introns. The scale represents gene length (bp).
Figure 5. Conserved motif and gene structure information of LcAHLs. (a) Conserved motif information of 21 LcAHLs. We predicted 6 conserved motifs of LcAHL proteins and have marked them with different colors. (b) The x-axis represents the predicted length of different LcAHL genes (5′ to 3′). Different colors represent different structures. Yellow rectangles are CDS, blue rectangles are UTRs, and the black straight line represents introns. The scale represents gene length (bp).
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Figure 6. Expression pattern of LcAHL genes in eight tissues and under drought stress. (a) Heatmap of LcAHL genes in eight tissues. The color scale represents the values of log2 fold change, red represents a high level, and blue indicates a low level of transcript abundance. The heatmap includes phloem, stigma, xylem, bud, stamen, leaf, bark, and sepal. We performed row clustering and column clustering so that similar expression patterns were clustered together. (b) Heatmap of 8 LcAHL genes under drought stress. We performed row clustering so that genes with the same expression trend were clustered together.
Figure 6. Expression pattern of LcAHL genes in eight tissues and under drought stress. (a) Heatmap of LcAHL genes in eight tissues. The color scale represents the values of log2 fold change, red represents a high level, and blue indicates a low level of transcript abundance. The heatmap includes phloem, stigma, xylem, bud, stamen, leaf, bark, and sepal. We performed row clustering and column clustering so that similar expression patterns were clustered together. (b) Heatmap of 8 LcAHL genes under drought stress. We performed row clustering so that genes with the same expression trend were clustered together.
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Figure 7. qRT-PCR verification of LcAHLs expression in different tissues under drought stress. Different colors of the pillars represent different tissues. A histogram in the same row represents different tissues of the same gene. Error bars represent the deviations from three biological replicates. Mark the letter a on the maximum average and marker b with significant difference, otherwise marker a (α = 0.05), and so on.
Figure 7. qRT-PCR verification of LcAHLs expression in different tissues under drought stress. Different colors of the pillars represent different tissues. A histogram in the same row represents different tissues of the same gene. Error bars represent the deviations from three biological replicates. Mark the letter a on the maximum average and marker b with significant difference, otherwise marker a (α = 0.05), and so on.
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Figure 8. Expression profiles of 21 LcAHL genes in somatic embryogenesis. The color scale represents the values of log2 fold change, red represents a high level, and blue indicates a low level of transcript abundance. Similar expression patterns are clustered together.
Figure 8. Expression profiles of 21 LcAHL genes in somatic embryogenesis. The color scale represents the values of log2 fold change, red represents a high level, and blue indicates a low level of transcript abundance. Similar expression patterns are clustered together.
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Figure 9. qRT-PCR verification of LcAHL gene expression at different stages during somatic embryogenesis. (a) qRT-PCR result of AHLs during somatic embryogenesis. The y-axis shows the relative expression level, and the x-axis indicates different stages of somatic embryogenesis. At the same time, three biological and three technical replicates per period are shown. Error bars represent the deviations from three biological replicates. Mark the letter a on the maximum average and marker b with significant difference, otherwise marker a (α = 0.05), and so on. (b) Different sampling periods of somatic embryogenesis in Liriodendron chinense. The scale represents 1 mm. PEMs: proembryogenic mass cultured for 20 days for embryogenic callus, ES3: induced by ABA for 1 day, ES5: 7-day globular embryo, ES9: 31-day mature cotyledon embryo.
Figure 9. qRT-PCR verification of LcAHL gene expression at different stages during somatic embryogenesis. (a) qRT-PCR result of AHLs during somatic embryogenesis. The y-axis shows the relative expression level, and the x-axis indicates different stages of somatic embryogenesis. At the same time, three biological and three technical replicates per period are shown. Error bars represent the deviations from three biological replicates. Mark the letter a on the maximum average and marker b with significant difference, otherwise marker a (α = 0.05), and so on. (b) Different sampling periods of somatic embryogenesis in Liriodendron chinense. The scale represents 1 mm. PEMs: proembryogenic mass cultured for 20 days for embryogenic callus, ES3: induced by ABA for 1 day, ES5: 7-day globular embryo, ES9: 31-day mature cotyledon embryo.
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Figure 10. Subcellular location of LcAHL proteins. The scale represents 10 μm.
Figure 10. Subcellular location of LcAHL proteins. The scale represents 10 μm.
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Table
Table 1. Physicochemical properties of LcAHLs.
Table 1. Physicochemical properties of LcAHLs.
Gene IDpIMW(kDa)Subcellular LocalizationGRAVYInstability Index (II)Clade
Lchi013729.5437.35Nucleus−0.45045.15III
Lchi059549.7537.14Nucleus−0.44852.16III
Lchi0628010.2533.71Nucleus−0.37257.95III
Lchi0676110.6236.90Nucleus−0.19157.51III
Lchi048648.5327.28Nucleus−0.36741.69II
Lchi305999.4871.46Nucleus−0.28144.51II
Lchi294349.2439.47Nucleus−0.23455.52II
Lchi1319010.1434.91Nucleus−0.38749.51II
Lchi221856.9525.80Chloroplast0.01061.85II
Mitochondrion
Lchi013738.5523.58Nucleus0.05550.15I
Lchi059636.3832.57Nucleus−0.14853.22I
Lchi062886.4372.82Chloroplast−0.10749.43I
Lchi067504.7136.33Nucleus−0.55171.02I
Lchi281998.8829.33Chloroplast−0.19061.53I
Nucleus
Lchi048746.2536.05Nucleus−0.54755.18I
Lchi324515.8534.12Nucleus−0.42744.06I
Lchi3060610.0023.17Chloroplast−0.44642.67I
Lchi0418010.2533.71Mitochondrion−0.16650.88I
Lchi128458.2343.19Chloroplast−0.28845.90I
Lchi069459.5722.38Nucleus−0.49340.80I
Lchi132445.9827.41Nucleus−0.48748.11I
Note: pI: isoelectric point; MW: molecular weight; GRAVY: grand average of hydropathicity.
Table
Table 2. The length and position information of LcAHL.
Table 2. The length and position information of LcAHL.
IDGene LengthPos. (Chr)CDs LengthExon NumberProtein Length (aa)
Lchi013726154Chr1110835270
Lchi01373830Chr116962163
Lchi0418015,499Chr49362219
Lchi048649361Chr117924201
Lchi0487426,530Chr1110263229
Lchi0595427,582Chr810865275
Lchi0596328,703Chr89303207
Lchi0628016,339Chr110115248
Lchi0628815,233Chr120285474
Lchi067505428Chr610353232
Lchi067617049Chr611015278
Lchi06945762Chr36302158
Lchi1284520,351Chr1812426305
Lchi1319014,467Chr1010265256
Lchi13244904Chr108132203
Lchi221853109Chr37356187
Lchi281992170Chr78492212
Lchi2943415,391Chr111255269
Lchi3059919,424Scaffold10259455329
Lchi3060627,410Scaffold10256513151
Lchi324519846Chr89872225
Table
Table 3. Cis-acting element quantification and function prediction.
Table 3. Cis-acting element quantification and function prediction.
Cis-Acting ElementNumberFunction
GARE-motif14gibberellin-responsive element
TCA-element9salicylic acid responsiveness
CGTCA-motif19MeJA-responsiveness
MBSI15flavonoid biosynthetic genes regulation
O2-site8zein metabolism regulation
ABRE56abscisic acid responsiveness
AuxR-core8auxin responsiveness
auxin responsiveness
TGA-element4
GCN4_motif6endosperm expression
MSA-like2cell cycle regulation
LTR25low-temperature responsiveness
TC-rich repeats5defense and stress responsiveness
MBS15drought-inducibility
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MDPI and ACS Style

Tang, Y.; Wu, W.; Zheng, X.; Lu, L.; Chen, X.; Hao, Z.; Liu, S.; Chen, Y. AT-Hook Transcription Factors Show Functions in Liriodendron chinense under Drought Stress and Somatic Embryogenesis. Plants 2023, 12, 1353. https://doi.org/10.3390/plants12061353

AMA Style

Tang Y, Wu W, Zheng X, Lu L, Chen X, Hao Z, Liu S, Chen Y. AT-Hook Transcription Factors Show Functions in Liriodendron chinense under Drought Stress and Somatic Embryogenesis. Plants. 2023; 12(6):1353. https://doi.org/10.3390/plants12061353

Chicago/Turabian Style

Tang, Yao, Weihuang Wu, Xueyan Zheng, Lu Lu, Xinying Chen, Zhaodong Hao, Siqin Liu, and Ying Chen. 2023. "AT-Hook Transcription Factors Show Functions in Liriodendron chinense under Drought Stress and Somatic Embryogenesis" Plants 12, no. 6: 1353. https://doi.org/10.3390/plants12061353

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