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Genome-wide identification of the N6-methyladenosine regulatory genes reveals NtFIP37B increases drought resistance of tobacco (Nicotiana tabacum L.)

BMC Plant Biology volume 24, Article number: 134 (2024) Cite this article

Abstract

Background

N6-methyladenosine (m6A) is one of the common internal RNA modifications found in eukaryotes. The m6A modification can regulate various biological processes in organisms through the modulation of alternative splicing, alternative polyadenylation, folding, translation, localization, transport, and decay of multiple types of RNA, without altering the nucleotide sequence. The three components involved in m6A modification, namely writer, eraser, and reader, mediate the abundance of RNA m6A modification through complex collaborative actions. Currently, research on m6A regulatory genes in plants is still in its infancy.

Results

In this study, we identified 52 candidate m6A regulatory genes in common tobacco (Nicotiana tabacum L.). Gene structure, conserved domains, and motif analysis showed structural and functional diversity among different subgroups of tobacco m6A regulatory genes. The amplification of m6A regulatory genes were mainly driven by polyploidization and dispersed duplication, and duplicated genes evolved through purified selection. Based on the potential regulatory network and expression pattern analysis of m6A regulatory genes, a significant number of m6A regulatory genes might play important roles in growth, development, and stress response processes. Furthermore, we have confirmed the critical role of NtFIP37B, an m6A writer gene in tobacco, in enhancing drought resistance.

Conclusions

This study provides useful information for better understanding the evolution of m6A regulatory genes and the role of m6A modification in tobacco stress response, and lays the foundation for further elucidating the function of m6A regulatory genes in tobacco.

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Background

Epigenetic modifications are mechanisms that affect gene expression and function directly without altering biological gene sequences that can be passed on to offspring. Nowadays, epigenetic regulations have been found to involve in DNA/RNA methylation, histone modification, chromatin remodeling, and noncoding RNA profile changes [1, 2]. DNA methylation and histone acetylation are important strategies for the fine regulation of developmental processes and the response to environmental stresses. RNA modification, which is analogous to DNA methylation in function, also plays a prominent role throughout the life cycle of organisms. Initially discovered in mammals, chemical modifications of RNA are subsequently found to be prevalent in all living things [3]. More than 160 types of RNA modifications have been identified, most of which are present in transfer RNA (tRNA) and ribosomal RNA (rRNA). Methylation at the sixth N of adenosine, also known as N6-methyladenosine (m6A), is the earliest and most common type of mRNA modification. Further research has revealed that m6A modification also exists in non-coding RNAs, such as circular RNA (circRNA) [4] and long non-coding RNA (lncRNA) [5]. In eukaryotes, m6A modification is responsible for about 80% of all RNA methylation modifications. The identification of the m6A demethylase FTO (Fat Mass and Obesity-Associated Protein) [6] and its homologue ALKBH5 (α-ketoglutarate-dependent dioxygenase) in mammals has confirmed the dynamic nature of m6A modification [7].

The degree of m6A modification is governed by two classes of proteins, known as methyltransferase (m6A writer) and demethylase (m6A eraser), which add or remove methyl groups to the adenine located in the RNAs’ conserved motif. To recognize m6A methylation on RNA base sites, specific reading enzymes (m6A reader) are also needed. Reader proteins recognize the m6A methylation motifs and bind specifically, thereby regulating downstream translation, mRNA nucleation transport speed, and mRNA degradation [8]. In summary, the precise regulatory network formed by writers, erasers, and readers governs the production, clearance and functional realization of m6A modification in biological organisms.

The m6A modification is catalyzed by a highly conserved multi-component methyltransferase complex (MTC, also known as the m6A writer complex). In mammals, MTC comprises of two sub-complexes, designated as m6A methyltransferase-like (METTL) complex (MAC) and m6A METTL-associated complex (MACOM) [1, 9]. MAC composes of the methylase heterodimer of methyltransferase-like 3 (METTL3) and METTL14, which comprises the catalytic core of the m6A methyltransferase [10, 11]. MACOM includes Wilms’ tumor 1 associated protein (WTAP), VIRMA (KIAA1429), HAKAI, RNA Binding Motif Protein 15 (RBM15), and its paralog RBM15B, as well as the recently discovered zinc-finger CCCH domain-containing protein 13 (ZC3H13) [12,13,14,15,16]. Similar with the mammalian counterparts, the m6A methyltransferase complex has been systematically identified in Arabidopsis, demonstrating its two core methyltransferases MTA (ortholog of METTL3) and MTB (ortholog of METTL14), and several accessory proteins FKBP12 INTERACTING PROTEIN 37 KD (FIP37, ortholog of WTAP), VIRLIZER (VIR, ortholog of VIRMA/KIAA1229), HAKAI [17]. In contrast, another known methyltransferase FIONA1 (ortholog of METTL16) functions separately for the deposition of m6A markers on mRNA [18, 19]. In Arabidopsis, recent research has proposed HIZ2, a HAKAI-interacting zinc finger protein, as a plausible plant analogue to ZC3H13, but the precise biological role of HIZ2 within the m6A writer complex is still undetermined [20].

Dynamic modifications of m6A have been recognized as a crucial regulator of plant growth, development, and stress response, as they influence the expression of corresponding genes through methylation modification. M6A modification in plants performs three main functions: mRNA processing, plant growth and development, and stress response [21]. Typically, the regulation of RNA metabolism of a single transcript is associated with the position of m6A marks. Specifically, m6A modification at the 3' UTR and stop codon sites primarily governs transcript stability and transcriptome integrity, whereas m6A modification in the 5' UTR assists in translation regulation and those in the coding region affect mRNA stability and splicing [17, 21, 22]. In Arabidopsis, m6A modification in the 3' UTR and 5' UTR is positively related to gene expression, while modification in other regions leads to reduced gene expression [23]. Research suggests that m6A modification plays a significant role in the embryonic development of plants. Reduction in the post-embryonic expression level of m6A methyltransferase, including MTA, MTB, FIP37, VIRILIZER, and HAKAI, caused a sharp decline in m6A. Knocking out the genes that encode core writer genes results in embryonic death [24,25,26]. Additionally, various developmental processes, such as flowering transition [19, 27], trichome and leaf morphology [28] and fruit maturation [29] are also influenced by m6A modification. In response to abiotic stresses, such as drought [30, 31], salt [32], cold [33], and biotic stresses, including bacterial infection [34], m6A can either promote or inhibit the expression of related genes. However, the current research on m6A is limited to a few model plants, highlighting the need for further research in other plants.

Common tobacco (Nicotiana tabacum L.) is a widely cultivated non-food crop, which is also commonly utilized as a model plant for genetic research. Furthermore, as a classical allotetraploid species, it plays a critical function in evolutionary studies. Recent studies have demonstrated that the infection of tobacco mosaic virus (TMV) has altered the level of m6A within tobacco [35]. Additionally, overexpression m6A methyltransferase ClMTB of watermelon enhanced the drought tolerance of tobacco [36]. However, genes associated with m6A modification in tobacco have yet to be identified. In this context, we conducted a comprehensive analysis of the classification, evolution, gene structure, and potential interaction network of m6A regulatory genes in tobacco, as well as studied the patterns of gene expression at different stages of tissue development and in response to a range of biotic and abiotic stresses. In addition, we validated the significant roles of NtFIP37B in drought resistance of tobacco. This study provides profound insights into the biological functions of m6A regulatory genes in tobacco and reveals the potential m6A-mediated regulatory mechanism in stress response.

Materials and methods

Identification and characterization of m6A regulatory genes in tobacco

To identify all members of m6A regulatory genes in tobacco, the protein sequence of m6A regulatory genes in Arabidopsis, tomato and rice were obtained from The Arabidopsis Information Resource (TAIR) [37], Sol Genomics Network (SGN) [38] and Ensembl Genome database [39], respectively. These sequences were used as queries against the tobacco genome [40] using BLAST program with the parameter E-value < 10–5. Then, HMMER v3 [41] was applied to identify candidate of m6A regulatory genes using hidden Markov models (HMM) based on m6A conserved domains: the MT-A70 family (PF05063), WTAP family (PF17098), VIRILIZER domain (PF15912), AdoMet_MTases domain (PF05971), 20G-Fe (II) oxygenase superfamily (PF14532) and YTH domain (PF04146) [42]. Candidates with incomplete domains were further removed by Conserved Domain Search (CD-Search) [43]. The physicochemical parameters of the m6A regulatory proteins, including molecular weight (MV), and isoelectric points (PI), were examined using TBtools [44]. Protein subcellular localization was predicted by WoLF PSORT Online software (https://wolfpsort.hgc.jp/) [45].

The phylogenetic classification, gene structures and conserved motifs analysis

An unrooted phylogenetic tree was generated by MEGA 7 [46] using the neighbor-joining method with bootstrap value of 1,500. ITOL (https://itol.embl.de/) [47] was used to visualize phylogenetic trees. The protein sequences of dicotyledonous species (Arabidopsis thaliana, N. tabacum, Solanum lycopersicum, Vitis vinifera, and Gossypium hirsutum), monocotyledonous species (Zea mays, Triticum aestivum, and Oryza sativa), pteridophyte species (Selaginella moellendorffii), moss species (Marchantia polymorpha and Physcomitrella patens), and gymnospermous species (Pinus tabuliformis) for the evolutionary tree construction were derived from previous studies [48, 49]. TBtools software [44] was used to visualize the structures of m6A regulatory genes in tobacco. MEME software [50] was employed to analyze the conserved motifs in m6A regulatory proteins with maximum number of motifs of 10. InterProScan [51] was used to annotate the identified motifs.

The chromosomal distributions, gene duplication and collinearity analysis

All tobacco m6A regulatory genes were mapped to their respective chromosomes. To infer the origin of m6A regulatory genes in allotetraploid tobacco, m6A regulatory genes of its two ancestors of the modern diploids: Nicotiana sylvestris and Nicotiana tomentosiformis were identified by the same method as above. Then, the origin, loss and expansion of m6A regulatory gene in tobacco were inferred through phylogenetic tree. DupGen_finder [52] program was used to explore the duplication events of m6A regulatory genes in tobacco, with Arabidopsis as the outgroup. For these duplicated gene pairs, KaKs_Calculator3.0 [53] was used to calculate the non-synonymous (Ka) and synonymous substitution (Ks) rates. The protein sequences of duplicated m6A regulatory gene pairs were used to calculate the divergence time with the formula \(T={K}_{s}/(2 \times 1.5\times {10}^{-8})\times {10}^{-6}\) [54]. TBtools [44] and MCScanX [55] were used for the collinearity analysis of m6A regulatory genes among different species.

Promoter analysis and interaction network prediction

The STRING v11.5 database [56] was used to construct the protein–protein interaction network among m6A regulatory genes in tobacco. The 2,000 bp upstream sequences from the transcription start site, were collected and submitted to the PlantCare [57] database for cis-acting element analysis. Mature miRNAs was downloaded from the miRBase database [58]. The psRNATtarget database [59] was used to search the regulatory relationship between miRNAs and tobacco m6A regulatory genes, with an Expectation threshold of < 5 and other parameters at their default values. Cytoscape [60] was used to visualize the interaction network.

Expression profiles based on transcriptome data

Transcriptome data from eight representative tobacco tissues (root, stem, young leaf, mature leaf, senescent leaf, immature flower, mature flower and senescent flower) were utilized to investigate tissue-specific expression patterns of m6A regulatory genes. Additionally, tobacco transcriptome samples subjected to various biotic stresses such as Potato Virus Y (PVY), black shank (BS), Cucumber mosaic virus (CMV), and Ralstonia solanacearum (RS), as well as abiotic stresses including high/low temperature, drought, salt, cadmium, and topping, were obtained from the NCBI SRA database to investigate the response of m6A regulatory genes to different stresses. The accession numbers for all the transcriptome samples utilized in this study could be found in Table S2. The Salmon software (v1.10.1) [61] was employed to perform quantification on all clean reads, while the R package ‘tximport’ (https://github.com/mikelove/tximport) was utilized for calculating the transcripts per kilobase million (TPM) values. Visualization of expression profiling was performed by TBtools software.

3D structure predictions and protein docking

The three-dimensional (3D) structures of m6A regulatory proteins were predicted using the homology modeling method. All m6A regulatory proteins were queried against the Protein Data Bank (PDB) to identify the best template, and the models were built by Swiss-Model [62]. The protein docking among tobacco m6A writer proteins were performed using HDOCK software [63], and the model with the lowest docking energy score, which represents the best quality of docking, was retained for subsequent analysis. PyMOL software (https://pymol.org/2/) [64] was used to visualize these models.

Plant materials and stress treatments

The tobacco cultivar K326 was employed to investigate the tissue-specific and stress-induced expression patterns of m6A regulatory genes in tobacco. Briefly, the seedlings were grown in plastic pots with a 16-h light cycle at 28°C during the day and 23°C at night. Similar with our previous study [65], root, stem, leaf, bud tissues at seedling stage (SS), vigorous growth stage (VG), and flowering stage (FS), as well as petal, receptacle, stamen, and pistil samples of reproductive organs (RO), were collected from tobacco. The drought and cold stress were conducted during the vigorous growth stage of tobacco. For drought treatment, 28-day-old tobacco plants were subjected to 7 days of water withholding. Cold treatment was conducted in a growth chamber with the temperature set at 4°C. Untreated plantlets were used as controls. After treatment, the treated and control plantlets were collected and immediately frozen in liquid nitrogen, then stored at -80°C for further experiments. All samples were independently conducted with three biological replicates.

RNA isolation and relative expression analysis

Total RNA was extracted from the above-mentioned tobacco samples using the SuperPure Plantpoly RNA Kit (Gene Answer, Beijing, China). RNase-free DNase I (Gene Answer) was used to eliminate the DNA contamination. First-strand cDNA synthesis was performed using 1 μg of total RNA as a template using reverse transcriptase M-MLV (Takara Biomedical Technology, Beijing, China), and the resulting cDNA was diluted to a concentration of 50 ng/µL. The quantitative real-time polymerase chain reaction (qRT-PCR) of tobacco m6A regulatory genes was performed using a 20 μL reaction system and employing the SYBR Green kit (Imagene, Beijing, China). The PCR program included an initial step of 95°C for 30 s, followed by 40 cycles of 95°C for 10 s, and 60°C for 30 s. The relative gene expression was calculated using 2−∆∆Ct method, and the expression levels were standardized to the expression level of the GAPDH gene. All specific primers for qRT-PCR are listed in Table S3. Three independent biological replicates were employed for qRT-PCR analysis.

Construction of subcellular localization vectors and virus-induced gene silencing vectors

The full-length coding sequences (CDS) of the NtFIP37B spanning 300-500bp was used to design primers for constructing subcellular localization and virus-induced gene silencing (VIGS) vectors (Table S3). For the subcellular localization vector, the PCR-amplified insert was ligated into the homologous recombination vector PC1300s-NtFIP37B-GFP containing adapter primers for sequencing verification. The resulting construct was transformed into Agrobacterium tumefaciens GV3101, along with an empty vector control, and positive colonies were selected and grown in liquid cultures at 28°C until reaching an OD of 1. The bacteria were then resuspended in a mixture of MgCl2, acetosyringone (As), and 2-N-morpholinoethanesulfonic acid (MES) before being injected into Nicotiana benthamiana leaves in the dark for 3 h. The plants were then incubated in darkness for one day followed by one day in a greenhouse, after which their subcellular localization was assessed using confocal microscopy system (Nikon C2-ER, Japan). Similarly, the VIGS vector pYY13-NtFIP37B was constructed by homologous recombination and transformed into A. tumefaciens GV3101, along with TRV1, TRV2, and pTRV2-PDS controls. Positive colonies were selected and grown as above, and the bacteria were resuspended and injected into N. benthamiana leaves alongside negative controls (A. tumefaciens carrying pTRV2) and experimental groups (A. tumefaciens carrying pTRV2-NtFIP37B) as infecting agents. The bacteria carrying pTRV1 and pTRV2, pTRV1 and pTRV2-PDS, and pTRV1 and pTRV2-NtFIP37B were mixed in a 1:1 ratio and injected into the lower leaves of N. benthamiana using a sterile syringe. After one day of incubation in darkness, the plants were transferred to a greenhouse for 14 days. Once the bleaching phenotype was observed in the leaves inoculated with TRV2-PDS, the expression levels of newly grown leaves on the same site inoculated with TRV2-NtFIP37B were analyzed. Subsequently, silenced plants were subjected to drought treatment, and Fv/Fm ratios were calculated using IMAGING-PAM Chlorophyll Fluorescence System.

Results

Genome-wide identification and characterization of m6A regulatory genes in tobacco

After comprehensive screening of the tobacco genome, a total of 16 m6A writers, 16 m6A erasers and 20 m6A readers were finally identified (Table S4). All m6A regulatory genes were named according to their homologs of Arabidopsis, tomato and rice. Protein length and predicted molecular weight (MW) were significantly different between three types of m6A regulatory genes (Fig. 1a-d), especially for m6A writer members. The lengths of putative m6A writer proteins ranged from 341 (NtFIP37A/B) to 2,153 (NtVIR2) amino acid, and the MW of proteins ranged from 38.56 (NtFIP37A) to 235.81 (NtVIR2) kDa. Commonly, the length and MW of m6A writer proteins with the same domain were similar, except for NtMTB1/2 and NtMTB3/4. Although all m6A eraser proteins belonged to ALKBH family, their protein length and MW varied greatly, from the smallest NtALKBH6 (176 aa, 19.38 kDa) to the largest NtALKBH9B1 (668 aa, 75.09 kDa). In contrast, protein length and MW was similar among m6A reader proteins, with protein length (443 ~ 764 aa, mean = 636.95 aa) and MW (49.6 ~ 84.11 kDa, mean = 70.051 kDa). Similarly, theoretical isoelectric points also varied widely among m6A regulatory proteins. NtALKBH9B2 had the highest theoretical isoelectric point (9.23), while NtALKBH7A had the lowest one (4.84). In addition, subcellular localization prediction showed that most m6A regulatory proteins were located in the nucleus (40/52: 77%), and only several proteins were located in the cytoplasm (NtALKBH6, NtALKBH7A, NtALKBH8B and NtALKBH9B1/2), plasma membrane (NtMTC1 and NtVIR1/2) and chloroplast (NtMTA1/2, NtALKBH10 and NtYTHDF3D) (Fig. 1e).

Fig. 1
figure 1

Distribution and statistic analysis for (a and c) molecular weight, (b and d) isoelectric point and (e) percentage of subcellular localization of tobacco m6A regulatory proteins. The P values in c and d were analyzed by ‘t-test’ method

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The phylogenetic classifications and structural features of m6A regulatory genes in tobacco

To gain an insight into the evolutionary history of m6A regulatory genes in tobacco, the protein sequences of m6A writer, eraser and reader from five dicotyledons, three monocotyledons, one gymnosperm, one pteridophyte and two mosses were used for phylogenetic analysis. The results showed that m6A writers could be naturally grouped into five categories, namely MT, FIP37, VIR, HAKAI, and FIONA (Fig. 2a-e). The MT group was further divided into three subgroups: MTA, MTB and MTC, which belonged to their evolutionary clades. Among all the plants used for phylogenetic analysis, MTB, HAKAI and VIR subfamilies were absent from the pteridophyte and S. moellendorffii, whereas other subfamilies were present in all plants, suggesting different evolutionary roles of m6A writers among different plants. Most diploid plants contained single copy of FIONA, while polyploid plants usually had 2 to 3 paralogs of FIONA protein. The phylogenetic tree of ALKBH family of m6A eraser was clustered into three groups, with a relatively uniform distribution in all plants (Fig. 2f; Table S5). Phylogenetic analysis showed that YTH proteins of m6A reader were grouped into two main categories, namely YTHDF and YTHDC (Fig. 2g). Compared with m6A writers and eraser, the number of genes encoding YTH domain proteins was much greater, especially for YTHDF subgroups. Interestingly, m6A regulatory proteins from the same plant clade tended to cluster together. Most m6A proteins from mosses, pteridophytes and gymnosperms were located in a same branch, whereas dicotyledons and monocotyledons tended to be in other branches. In addition, as a typical allotetraploid plant, tobacco had more m6A regulatory genes than diploid plants such as Arabidopsis, grape and rice (Table S5). Similar results could be observed in hexaploid wheat and tetraploid cotton, suggesting gene family expansion for polyploidy plants [66].

Fig. 2
figure 2

Phylogenetic analysis of m6A regulatory genes from five dicotyledons, three monocotyledons, one pteridophyte, two mosses, and one gymnosperm. a Phylogenetic tree of MT-A70 genes. b Phylogenetic tree of FIP37 genes. c Phylogenetic tree of VIR genes. d Phylogenetic tree of HAKAI genes. e Phylogenetic tree of FIONA genes. f Phylogenetic tree of m6A eraser genes. g Phylogenetic tree of m6A reader genes. Stars of various hues signify distinct categories of species in accordance with the legend. The tobacco m6A regulatory genes are highlighted in bold red letters and marked with a check symbol

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To better understand the evolution of m6A regulatory genes in tobacco, TBtools and MEME Suite were used to explore their sequence characteristics, conserved domains and consensus motifs (Fig. 3). For m6A writer, the genes from the same branch had similar exon–intron structures and conserved domains, except that NtMTB3 had one more exon than NtMTB4. Interestingly, NtVIRs had a super long structure with 27 to 28 exons, which was also found in other plants such as tea [48] and poplar [67]. MT-A70 domain was found in all tobacco MT families, and NtMTB proteins also contained a MAPK-interacting and spindle-stabilizing protein-like protein domain (MISS). Both NtVIR proteins contained a conserved VIR_N domain and a PRK10263 domain, and all NtHAKAI proteins contained two conserved domains, RINGHC_HAKAI_like and PHA03378. Two homologs of Arabidopsis FIONA1 genes in tobacco contained the AdoMet_MTase domain. Compared with m6A writer members, more structural variations were found in m6A eraser genes. NtALKBH9B1 had one larger exon than NtALKBH9B2. The exon number and intron length of NtALKBH8A were significantly different from NtALKBH8B. In addition, NtALKBH2B had one bigger intron. All m6A eraser members contained the 20G-FeeII_Oxy domain, and NtALKBH8 subfamily also had another conserved domain of RRM_SF. Structural variations could also be observed in m6A reader genes. NtYTHDF3D had longer introns than NtYTHDF3C, and NtYTHDC1 lacked two exons compared with NtYTHDC2. In addition, NtCPSF30A1 had one more exon and longer intron than NtCPSF30A2. The YTH conserved domain could be found in all tobacco m6A reader proteins, while the CPSF30 subfamily also had another YTH1 conserved domain.

Fig. 3
figure 3

Phylogenetic relationships, gene structures, conserved motifs, and functional domains of m6A regulatory genes in tobacco. a Structure analysis of m6A writer genes. b Structure analysis of m6A eraser genes. c Structure analysis of m6A reader genes. The squares in the motif represent the positions of conserved domains

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Motifs analysis revealed that the genes from the same branch had similar motif composition. For m6A writer, the number of motifs varied from 2 to 10, and the NtMTB subfamily contained all 10 motifs. Interestingly, two unknown motif (7 and 9) could be found in most m6A writer members (Fig. 3a; Table S6). Among ALKBH families, no conserved motif was identified in NtALKBH6 and NtALKBH2A/B, which also had distinguished structures. Most m6A eraser genes had a similar motif composition for each branch. Two YTH domain-containing protein motifs (1 and 3) were existed in all m6A reader proteins. In general, most of the m6A regulatory proteins in same branch exhibited similar motif distribution and exon–intron structure.

The chromosomal distributions, gene duplication events and collinearity analysis of m6A regulatory genes in tobacco

Among the identified m6A regulatory genes, 21 were randomly distributed on 10 chromosomes, and the remaining ones were located on the unanchored scaffolds (Table S4). Chromosome 17 contained the most m6A regulatory genes (4), two m6A eraser and two m6A reader genes, respectively. There was only one gene on chromosomes 1, 2 and 14.

Considering that gene duplication is an important mechanism for gene family expansion, we utilized the DupGen_finder softwaree [52] to identify different duplication events of m6A regulatory genes in tobacco. The analysis revealed a total of 14 duplication events, including 10 instances of dispersed duplication (DSD), 3 cases of tandem duplication (TRD), and 1 occurrence of proximal duplication (PD), involving a set of 18 genes responsible for m6A regulation. However, we did not detect any instances of whole-genome duplication (WGD) or transposed duplication (TRD) (Table S7). Notably, although there were several gene pairs with high similarity in amino acid sequence, such as NtYTHDF1E and NtYTHDF1F (with a similarity of 96.019%), we were unable to determine their modes of duplication due to the absence of chromosomal location. Interestingly, two pairs of TRD genes (NtALKBH9B1-NtALKBH9B2 and NtCPSF30A1-NtCPSF30A2) were anchored to chromosome 17, while another pair of TRD genes were located on the same scaffold. The intricate network of DSD events might play an important role in the expansion of MT-A70, ALKBH and YTH gene families. Besides, DSD was the main event (4/6: 66.7%) for tobacco m6A reader genes. Interestingly, several genes might be involved in two or three rounds of dispersed duplication events, including NtMTA1, NtCPSF30A1 and NtYTHDF3E.

To explore the evolutionary trajectory of duplicated gene pairs in m6A regulatory genes of tobacco, we calculated the ratio of non-synonymous (Ka) and synonymous (Ks) substitution rates (Table S7). Typically, Ka/Ks ratios below 1, equal to 1, and above 1 indicated purifying selection, neutral selection, and positive selection, respectively. In this study, all analyzed duplication events yielded Ka/Ks ratios were less than 1, indicating the predominance of strong purifying selection on these genes throughout their evolutionary history. This suggested that functional differentiation following gene duplication had been limited by the action of purifying selection. Based on Ks values, we estimated divergence times of m6A duplicated gene pairs in tobacco. The Ks values of m6A duplicated gene pairs ranged from 0.047 to 2.609, with estimated divergence times ranging from 1.567 Mya to 86.975 Mya. Duplicated gene pairs with earlier divergence times (such as NtMTA1 and NtMTC1, NtYTHDF1A and NtYTHDF3E) might be associated with ancient duplication events, while those with later divergence times (such as NtCPSF30A1 and NtCPSF30A2, NtALKBH9B1 and NtALKBH9B2) might be likely due to more recent dispersed or tandem events. These findings shed light on the evolutionary history of m6A duplicated genes in tobacco.

To further explore the evolutionary patterns of m6A regulatory genes between different plants, four representative species were selected for comparative collinearity analysis with tobacco. Among the twenty m6A regulatory genes located on chromosomes in tobacco, 13 were collinear with tomato, followed by Arabidopsis (8), grape (8) and rice (1) (Fig. 4a). Obviously, the number of m6A regulatory genes with collinearity between monocotyledons and dicotyledons varied widely, suggesting that the expansion of m6A regulatory genes might occur after dicotyledonous differentiation. In addition, one eraser gene (NtALKBH9B1) and two reader genes (NtYTHDF3E and NtCPSF30A1) had more than one pair of collinear genes.

Fig. 4
figure 4

Collinearity analysis of tobacco m6A regulatory genes and inference of their diploid origins based on evolutionary relationships. a Micro-collinearity relationship between m6A regulatory genes in tobacco and those in Arabidopsis, grape, tomato, and rice. The colors represented by each line are indicated in the legend. b-d Phylogenetic analysis of tobacco m6A writer (b), reader (c), and eraser (d) and their diploid progenitors N. sylvestris and N. tomentosiformis

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As a typical allotetraploid plant, tobacco was formed from the maternal donor N. sylvestris and the male donor N. tomentosiformis about 0.2 million years ago [40]. To explore the parental origin of m6A regulatory genes in tobacco, m6A regulatory genes were also identified in two genome donors of tobacco. To investigate the parental origin of m6A regulatory genes in tobacco, a phylogenetic tree was conducted between tobacco and its ancestor donors (Fig. 4b-d; Table S4). Phylogenetic analysis showed that the m6A writer genes in tobacco were equally derived from two diploid donors, respectively. Compared with its donors, some FIP37 and VIR members were lost during the evolution of nearly 0.2 million years, and no expansion was found for these two families. For the ALKBH family, NtALKBH1A and NtALKBH6 could not assign their origins according to the phylogenetic tree, suggesting these two genes might have experienced differentiation during evolution. Our previous analysis revealed that one TRD event have occurred in NtALKBH9B during evolution, which might be the major reason for NtALKBH9B1 and NtALKBH9B2 were located in the same branch with N. sylvestris. Similarly, NtYTHDC1C-NtYTHDC1D and NtCPSF30A1-NtCPSF30A2 might also expand during evolution. Similar results could also be observed for NtYTHDF1E-NtYTHDF1F (N. tomentosiformis origin) and NtYTHDF3A-NtYTHDF3B (N. sylvestris origin). However, their duplication patterns could not be analyzed because they could not be located on chromosomes. We speculated that these two pairs of genes might also have experienced post-speculation TRD events during evolution.

Analysis of cis-acting regulatory elements (CREs) of m6A regulatory genes in tobacco

The cis-acting elements (CREs) in the promoter region of genes played an important role in determining the spatiotemporal specific expression of protein-coding genes [68]. To better understand the transcriptional regulation and potential biological functions of tobacco m6A regulatory genes, the CREs in the promoter regions (2,000 bp upstream of the transcription start site) of m6A regulatory genes were predicted using the PlantCare database. These identified CREs can be further divided into four types (Fig. 5; Table S8), including light-responsive (46%), phytohormone-responsive (27%), stress-responsive (18%) and development-related elements (9%). All m6A regulatory genes contained a large number of light-responsive elements, indicating that they may be regulated by light signaling. Abscisic acid (ABA) and methyl jasmonic acid (JA) responsive elements accounted for the majority of phytohormone-responsive elements, including 91 and 124, respectively. These large number of phytohormone-responsive elements indicated that hormone signals may activate or inhibit the expression level of m6A regulatory genes. Among the CREs associated with plant development, we observed enrichment of CAT-box, GCN4_motif, and O2-site in the promoter regions of m6A regulatory genes in tobacco. These CREs were respectively associated with meristem expression, endosperm expression, and metabolism regulation. In addition, we found that ARE elements, involved in anaerobic induction, were present in the promoter regions of the majority of m6A regulatory genes. MBS (related to drought response) and LTR (related to cold response) elements were also highly enriched (Fig. 5). These findings indicated tobacco m6A regulatory genes might respond to a variety of external stresses and internal metabolic types.

Fig. 5
figure 5

The distribution of cis-acting elements in the promoter regions of m6A regulatory genes. The bar charts situated above and the right of the heatmap depict the statistical results for horizontal and vertical comparisons, respectively. The color for different categories is described in the legend

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Regulation networks of m6A regulatory genes in tobacco

Considering that the m6A modification was performed by a multi-protein complex consisting of a catalytic core (MTA and MTB) and a series of auxiliary subunits acting together, we constructed a potential protein–protein interaction network of tobacco m6A regulatory genes by STRING database (Fig. 6a; Table S9). Among the tobacco m6A writer members, except for the NtMTC and NtFIONA subfamilies, all the other 12 members showed inter-interactions, especially the NtMTA and NtHAKAI subfamilies, suggesting that they may participate in m6A modification by forming protein complexes. However, no interaction between m6A eraser members was found. NtCPSF30B1 could also interact with two other NtCPSF30 subfamily members (NtCPSF30A2 and NtCPSF30B2), which may be related to their special roles in recognizing m6A modification (Fig. 6a). Considering that mRNA m6A modification was catalyzed by the m6A methyltransferase complex [9], we predicted 3D structural models of tobacco m6A writer proteins using a homology modeling approach, and performed protein–protein docking of different combinations (Fig. 6b; Table S10). The results indicated that the docking model of NtMTA-NtMTB exhibited a higher docking confidence score ranging from 0.8861 to 0.9999, suggesting a significant likelihood of protein complex formation. Among them, NtMTA1-NtMTB3 protein complex model with the highest docking confidence score (0.9999) exhibited a similar conformation to the human METTL3-METTL4 complex (PDB accession: 5L6D) [69] (Fig. 6b). Surprisingly, NtFIP37A and NtFIP37B also exhibited a high docking confidence score (0.9998). Studies have shown that two WTAP (ortholog of FIP37) molecules formed an asymmetric homodimer, acting as a "bridge" connecting VIRMA with the METTL3-METTL14 complex [9]. By docking NtVIR2 with the NtFIP37A-NtFIP37B protein complex, we found that the resulting ternary complex model exhibited a structure similar to the human m6A-METTL associated complex (WTAP and VIRMA complex, PDB accession: 7VF5) [70] (Fig. 6b). Consequently, we proposed that FIP37 proteins in plants might possess similar functions.

Fig. 6
figure 6

Potential m6A regulatory network in tobacco. a Protein–protein interaction network of m6A regulatory proteins in tobacco. Edge thickness represents the combined score from STRING. b Protein docking results of NtMTA1-NtMTB3 (left) and NtVIR2-NtFIP37A-NtFIP37B (right) complexes. c Interaction between m6A regulatory genes and miRNAs. Edge thickness represents the negative UPE value, indicating the likelihood of miRNA-mediated interaction and cleavage of target mRNAs. Edge color intensity reflects the number of mismatches, with darker colors indicating fewer mismatches

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Subsequently, potential miRNA binding sites of m6A regulatory genes were also investigated by psRNATarget [59]. After filtering interactions with an Expectation penalty score below 5, a total of 38 miRNAs from 16 families were identified as potential regulators targeting m6A regulatory genes including 8 writers, 3 readers, and 2 erasers (Fig. 6c; Table S9). Notably, it has been observed that distinct miRNA families often exhibited specific target genes. For instance, NtMTB4was potentially regulated by ten miRNAs, all belonging to the nta-miR172 family. Furthermore, six miRNAs from the nta-miR156 family could target the NtVIRs genes (Fig. 6c). Interestingly, compared to the m6A readers (n = 3) and m6A erasers (n = 1), tobacco m6A writers (n = 35) appeared to be subjected to greater miRNAs regulation. These m6A regulatory genes were predominantly clustered within the MTB, VIR, and FIP37 families. However, no miRNAs regulating the MTA and MTC subfamilies in tobacco were identified in our analysis. Considering the context-dependent activation of miRNA-mediated regulation, further investigations were needed to unravel the intricate interplay between m6A regulatory genes and miRNAs in plants.

Tissue expression analysis of m6A regulatory genes in tobacco

To explore the expression patterns of m6A regulatory genes in different tissues of tobacco, the expression profiles of eight representative tissues were explored (Fig. 7a, Table S11). As depicted in Fig. 7a, the expression patterns of m6A regulatory genes could be classified into five distinct clusters (C1-C5). Notably, clusters C1-C4 comprised approximately three types of m6A regulatory genes, suggesting potential co-regulation among them. However, in cluster C5, the majority of genes belonged to the m6A reader category, with only one gene from m6A eraser (NtALKBH7B). Genes in cluster C1 exhibited specific expression in stems, and relatively low in leaves. In cluster C2, gene expression gradually increased during leaf development, such as NtALKBH9A1, NtYTHDC1, and NtMTB3, implying their roles in leaf development. Genes in clusters C3 and C4 displayed high expression levels in roots and showed minimal or no expression in senescent flowers, indicating functional divergence of m6A regulatory genes during tobacco tissue development. Importantly, compared to immature flowers, the majority of genes in clusters C4 and C5 exhibited significant up-regulation in mature flowers, followed by a notable decrease in senescent flowers. This trend was particularly evident for certain m6A eraser and m6A reader members, such as NtYTHDF3C, NtYTHDF3D, NtALKBH7A, and NtALKBH7B, highlighting their dynamic regulation during tobacco flower organ development. Additionally, we observed a strong positive correlation in the expression of numerous genes across different tissues (Fig. S1a), suggesting a cooperative impact among m6A genes in tobacco. Furthermore, we randomly selected eight tobacco m6A regulatory genes with specific expression patterns in different tissues for further qRT-PCR analysis at various developmental stages, including NtFIP37B, NtMTB1, NtMTB2, NtALKBH2A, NtALKBH9A1, NtALKBH9C2, NtALKBH6, and NtYTHDF3A. Most of the qRT-PCR results were consistent with the RNA-seq data (Fig. 7b). Among the selected tobacco m6A regulatory genes, FS (Flowering stage) exhibited significantly higher expression levels in all tissues, particularly in buds, indicating the important role of m6A modification during reproductive growth stages. Additionally, individual tobacco m6A regulatory gene showed relatively high expression levels in specific floral organs, such as NtALKBH9A1 in the receptacle and NtALKBH2A and NtMTB2 in the stamen, suggesting their potentially significant roles in floral organ development.

Fig. 7
figure 7

Expression profiles of tobacco m6A regulatory genes in different tissues. a Heatmap of the expression in different tissues, scaled by rows. b qRT-PCR analysis of nine selected m6A regulatory genes in different tissues at various developmental stages. Data are presented as mean ± SD

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Expression patterns of m6A regulatory genes in tobacco under various abiotic and biotic stresses

To unveil the possible function of m6A regulatory genes in response to different stresses, the expression pattern of m6A regulatory gene under various stresses was studied (Fig. 8; Table S12). Our analysis revealed that m6A regulatory genes exhibited distinct response patterns under different stresses. The majority of m6A regulatory genes did not show significant changes relative to the control when tobacco was subjected to CMV or salt stress. Notably, the response pattern of m6A regulatory genes differed between leaf and root tissues under similar stresses such as high temperature, low temperature, and cadmium. For instance, while NtYTHDF3A and NtYTHDF3B were significantly up-regulated in leaves at low temperature, they were down-regulated in roots. Similarly, NtALKBH10, NtALKBH2A, NtHAKAI1 and NtALKBH6 displayed a significant decrease in cadmium-treated tobacco root tissue but exhibited no change or up-regulation in leaves, implying tissue specificity of m6A regulatory genes in response to different stress. Several m6A reader genes including NtYTHDF1C, NtYTHDF2A and NtYTHDF3A, especially NtYTHDF3A, were significantly up-regulated in response to high temperature, hinting their potential roles in high temperature stress. The expression of both genes, NtYTHDF3A and NtYTHDF3B, were significantly increased under drought stress, which were also highly expressed in leaves under high/low temperature. Interesting, after topping treatment, the expression of almost all tobacco m6A regulatory genes were reduced relative to the control. Comparing with black shank (BS) and Potato Virus Y (PVY), the Ralstonia solanacearum (RS) treatment resulted in the relative higher up-regulation of multiple genes, such as NtVIR1, NtVIR2, NtYTHDF2A, and NtYTHDF1E. Apart from Cucumber mosaic virus (CMV), the expression patterns of tobacco m6A regulatory genes varied greatly in response to biotic stresses including RS, BS and PVY, with only one gene, NtALKBH9A2, being significantly up-regulated in all three biotic stresses.

Fig. 8
figure 8

Expression profiles of tobacco m6A regulatory genes under various stress treatments. a Heatmap of the expression under high temperature (HT), low temperature (LT), R. solanacearum (RS), black shank (BS), Cucumber Mosaic Virus (CMV), cadmium, salt, drought, Potato Virus Y (PVY) and topping treatment. The expression change is indicated by the ratio of TPM value between the treatment and control (CK). b, c qRT-PCR analysis of eight selected m6A regulatory genes under drought (b) and cold (c) treatment. The samples were collected from 28d-old tobacco (vigorous stage). Data are presented as mean ± SD, with one, two, and three asterisks denoting statistical significance at p < 0.05, p < 0.01, and p < 0.001, respectively

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Additionally, a substantial positive correlation was identified in the expression of multiple tobacco m6A regulatory genes under various stress treatment (Fig. S1b). We focused on eight genes that showed significant responses to drought and cold stress, and further investigated their expression patterns using qRT-PCR experiments (Fig. 8b, c). Under drought stress, the expression levels of six genes (NtFIP37B, NtYTHDF3B, NtALKBH10, NtYTHDF3A, and NtMTC1) were significantly up-regulated in both roots and leaves. Notably, NtFIP37B exhibited a more than five-fold increase in leaves. Under drought stress, NtALKBH9A1 and NtALKBH2A showed opposite expression patterns in leaves and roots, indicating tissue-specific responses to drought stress (Fig. 8b). NtMTC1, which was significantly up-regulated under drought stress, showed a significant down-regulation in expression under cold stress (Fig. 8c), suggesting different response patterns of m6A modification under different stress conditions. Additionally, we observed different dynamic expression patterns between root and leaf of multiple genes under cold treatment. From 36 to 89 h of cold stress, NtFIP37B, NtALKBH9A1, NtYTHDF3B, NtALKBH10, and NtYTHDF3A exhibited a pattern of initially increased expression followed by decreased expression in leaves or roots, indicating dynamic response patterns to cold stress. Overall, the expression patterns of m6A regulatory genes in tobacco under different stress conditions suggested that they might play critical biological roles in various stress responses.

Silencing of NtFIP7B reduced drought tolerance of tobacco

We have discovered that one tobacco m6A writer genes, named NtFIP37B, exhibited significant up-regulation under drought stress (Fig. 8b). To further explore the influence of m6A modification on tobacco's drought tolerance, we employed a virus-induced gene silencing system (VIGS) to construct silenced plants for NtFIP37B. Subsequent subcellular localization studies indicated that NtFIP37B were situated within the nucleus (Fig. 9a), which was consistent with predicted results (Table S4) as well as findings in other species [1]. Compared with wild-type plants, positively silenced plants showed significantly decreased transcript abundances of NtFIP37B (Fig. 9b). Under normal growth conditions, significant differences in plant height were observed between positively-silenced NtFIP37B plants (NtFIP37B-V1, NtFIP37B-V2, NtFIP37B-V3) and wild-type plants (Fig. 9c), indicating that this gene may have a positive regulatory role in tobacco growth. After five days of drought treatment, NtFIP37B-silenced plants exhibited more severe wilting (Fig. 9c) and a significant decrease in Fv/Fm ratio (Fig. 9d) compared to the wild type, indicating that their photosynthesis was severely affected. These results suggested that silencing of NtFIP37B inhibited growth of tobacco, and enhanced drought sensitivity in tobacco plants.

Fig. 9
figure 9

Subcellular localization of NtFIP37B and drought tolerance assessment in NtFIP37B-silenced tobacco plants. a Subcellular localization of NtFIP37B. The scale bars represent 20 μM. b Relative expression of NtFIP7B detected by qRT-PCR after drought treatment. c Phenotype and (d) Fv/Fm ratios of NtFIP37B-silenced tobacco plants before and after 5 days of drought treatment. Data are presented as mean ± SD, with one, two, and three asterisks denoting statistical significance at p < 0.05, p < 0.01, and p < 0.001, respectively

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Discussion

RNA N6-methyladenosine plays an important regulatory role in plant growth and development. Three types of m6A regulatory genes dynamically control the methylation levels of target transcripts involved in development and stress responses. Based on evidence from Arabidopsis, tomato, and rice, 52 candidate m6A regulatory genes were identified in tobacco, including 16 writers, 16 erasers, and 20 readers (Table S4). Although it has been speculated that a HAKAI-interacting zinc finger protein 2 (HIZ2) in Arabidopsis shares similarities with ZC3H13, its specific biological process in m6A multi-protein complex remains unclear [20]. Furthermore, due to the absence of obvious conserved domains in the amino acid sequence of HIZ2, it is not included in the scope of this study. The number of m6A regulatory genes in tobacco (52) exceeded that of several species, including Arabidopsis (33), tomato (25), grape (40), rice (33), S. moellendorffii (22), M. polymorpha (16), P. patens (18), and Chinese pine (36) (Table S5). However, it is lower than maize (55), common wheat (85), and upland cotton (75). Despite having the largest genome size (25.4 Gb), Chinese pine exhibits a remarkably low number of m6A regulatory genes, with only 36 members, which is significantly lower compared to species such as common wheat and upland cotton. Notably, the species with a higher abundance of m6A regulatory genes have experienced polyploidization events. Common wheat (2n = 6x = 42), upland cotton (2n = 4x = 52), and tobacco (2n = 4x = 48) are all the result of hybridization between two or multiple diploid donor species [71,72,73,74], leading to their m6A regulatory gene count being two or three times that of diploid species like Arabidopsis. Likewise, maize, a segmental allopolyploid [75], also possesses a higher number of m6A regulatory genes. Additionally, a total of 14 duplication events were identified, involving 18 m6A regulatory genes in tobacco. Dispersed duplication was the most frequent event (10), followed by tandem duplication (3) and proximal duplication (1) (Table S7). Ka and Ks analysis revealed that duplicated gene pairs have undergone purifying selection, consistent with findings in studies of tea plants and tomatoes [48, 49]. Estimated divergence times based on Ks values indicated that the duplication of m6A regulatory genes in tobacco predated the formation of the common tobacco species (~ 0.2 Mya) [40]. Phylogenetic analysis showed distinct subfamilies within m6A regulatory genes, with bryophytes, pteridophytes, and gymnosperms clustering separately from monocots and dicots [76] (Fig. 2). The preferential expansion of m6A regulatory genes in monocots and dicots may be attributed to their expansion events following divergence. In summary, we proposed that the differences in the number of m6A regulatory genes among species were primarily attributed to polyploidy, whole genome duplication (WGD), and gene duplication events, and the duplicated m6A regulatory genes in tobacco underwent differentiation in its two-progenitor diploid donor and no duplication events occurred after species formation (Table S7).

Previous studies have shown that m6A modification determined mRNA fate via multiple aspects of mRNA metabolism, impacting various aspects such as alternative splicing, alternative polyadenylation, folding, translation, localization, transport, and decay, thereby regulating plant growth, development, and stress responses [1]. In tobacco, the m6A writer proteins exhibited strong interactions within a protein interaction network apart from the FIONA1 and MTC, with NtMTAs and NtFIP37s showing the most interactions, highlighting their importance as the catalytic core and auxiliary subunit, respectively. The prediction results indicated that there were no interactions among eraser proteins in tobacco, while the three reader proteins including NtCPSF30A2, NtCPSF30B1, and NtCPSF30B2 might have interactions, which required further research for validation (Fig. 6a). Using homology modeling and protein docking, the 3D structures of tobacco m6A regulatory genes were predicted, confirming the high likelihood of NtMTAs and NtMTBs forming the catalytic core for m6A methylation. Another important component of the MTC, NtVIR2-NtFIP37A-NtFIP37B, also exhibited a structure similar to that found in humans (Fig. 6b; Table S10). Moreover, similar expression pattern were observed for m6A writer genes under different stress treatment, suggesting their coordinated role in defense responses (Fig. S1). Additionally, potential miRNA binding sites were identified in tobacco m6A regulatory genes, indicating a possible role of miRNAs in regulating m6A methylation (Fig. 6; Table S9). Interestingly, compared to the m6A readers (n = 3) and m6A erasers (n = 1), m6A writers (n = 35) appeared to be subjected to greater miRNAs regulation. In other words, m6A writers in tobacco might prefer to be regulated by miRNAs (Fig. 6). Moreover, among all m6A writers, only MTB, VIR, and FIP37 families might targeted by miRNAs. Therefore, more future works were needed to explore the mutual interactions between m6A writer genes and miRNAs.

In order to explore potential functions for m6A regulatory genes in tobacco, the promoter regions were analyzed, and a significant enrichment of CREs associated with light response, hormone response, plant growth and development, and stress response were observed (Fig. 5; Table S8). Similar findings were also found in other plant species such as tea [48], tomato [49], and poplar [67]. The promoter regions of m6A regulatory genes in tobacco encompassed a substantial proportion (46%) of light-responsive CREs. In Arabidopsis, the m6A methyltransferase MTA [77] and FIONA1 [78] could indirectly influence the stability and translation efficiency of mRNA of biological clock genes through the blue light-induced photoreceptor CRY2, which played a crucial role in maintaining chlorophyll homeostasis in plants under light conditions. Transcriptome analysis revealed high expression levels of m6A regulatory genes in tobacco roots (Fig. 7a). Previous studies had shown that CPSF30L in Arabidopsis could regulate APA by binding to m6A-modified transcripts involved in nitrate signaling, such as NRT1.1 and WRKY1 [79]. Considering the crucial role of roots in nitrogen absorption, it was plausible to hypothesize that NtCPSF30s in tobacco might function through similar mechanisms. Additionally, qRT-PCR results showed that many tobacco m6A regulatory genes such as NtFIP37B, NtALKBH9C2, and NtYTHDF3A were highly expressed in multiple tissues and organs during the flowering period. These highly expressed m6A regulatory genes might play crucial roles in reproductive development, as previous studies have associated m6A modification with reproductive cell development [80] and fruit ripening [29, 81]. The promoter regions of tobacco m6A regulatory genes contained stress-responsive elements associated with diverse biotic and abiotic stresses (Fig. 5). Analysis of m6A gene expression patterns under different stress conditions revealed various responsive patterns. For instance, under high temperature stress, NtVIR2 showed significant up-regulation while NtVIR1 remained stable, indicating functional redundancy. Moreover, genes like NtALKBH10 and NtVIR1 exhibited robust responses to specific biotic stresses (RS and BS) but showed insensitivity to CMV or PVY infection (Fig. 8a). Although barley and soybean exhibited increased global m6A modification levels in response to cadmium stress [82, 83], we did not observe significant up-regulation of m6A writer genes in tobacco (Fig. 8a), possibly due to the different experimental conditions. Differential response times to drought treatment were observed among various m6A regulatory genes. For instance, genes like NtFIP37B and NtALKBH10 did not show significant changes in expression levels after 4 h of drought treatment (Fig. 8a). However, when tobacco plants were exposed to drought treatment for 7 days, these genes exhibited significant upregulation (Fig. 8b). In summary, the expression patterns of tobacco m6A regulatory genes under growth, development, and stress conditions were diverse, implying their functional diversity. Further investigations were needed to elucidate the detailed mechanisms of candidate m6A regulatory genes in tobacco.

Conclusions

This study presents the first comprehensive and systematic investigation of m6A regulatory genes that may be involved in N6-methyladenosine modification in tobacco. A total of 52 m6A regulatory genes were identified in tobacco, categorized into three types: m6A writer (16), m6A eraser (16), and m6A reader (20). Subsequently, we analyzed the features of these genes in terms of gene structure, conserved domains, and motifs. Through systematic evolutionary analysis, collinearity analysis, and identification of duplicate genes, we discovered that polyploidization and segmental duplication were the main drivers for the expansion of tobacco m6A regulatory genes. Functional analysis of tobacco m6A regulatory genes in cis-elements, interaction networks, and expression patterns demonstrated their crucial roles in tobacco growth, development, and stress responses. Notably, NtFIP37B-silenced tobacco plants exhibited significantly reduced drought tolerance. This study provides a reference framework for exploring the functional diversity of m6A regulatory genes in tobacco growth, development, and stress responses at the epigenetic level. These findings are of significant importance for enhancing tobacco plant resistance to stress and require further elucidation in future work.

Availability of data and materials

All data generated or analyzed in this study are included in the materials and methods section of this article.

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Acknowledgements

We would like to acknowledge all researchers in our laboratory for their help.

Funding

This work was supported by the Zhengzhou Tobacco Research Institute [CNTC: 110202201001(JY-01), 110202202038], Natural Science Foundation of HeNan (232300420220); Beijing Life Science Academy [BLSA: 2023000CC0110].

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Authors and Affiliations

  1. Beijing Life Science Academy, Beijing, 102200, China

    Huan Su, Peijian Cao & Jingjing Jin

  2. China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China

    Huan Su, Lijun Meng, Zechao Qu, Peijian Cao & Jingjing Jin

  3. China National Tobacco Quality Supervision & Test Center, Zhengzhou, 450003, China

    Wei Zhang & Nan Liu

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  1. Huan Su
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Contributions

JJJ and PJC conceived and designed the experiments. HS performed bioinformatics data analysis. LJM and ZCQ did qRT-PCR experiments, the subcellular localization and VIGS experiments. HS, WZ, NL, PJC and JJJ wrote the manuscript and all authors read and approved the final version.

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Correspondence to Peijian Cao or Jingjing Jin.

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Su, H., Meng, L., Qu, Z. et al. Genome-wide identification of the N6-methyladenosine regulatory genes reveals NtFIP37B increases drought resistance of tobacco (Nicotiana tabacum L.). BMC Plant Biol 24, 134 (2024). https://0-doi-org.brum.beds.ac.uk/10.1186/s12870-024-04813-2

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BMC Plant Biology

ISSN: 1471-2229

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