Genome-wide characterization and identification of candidate ERF genes involved in various abiotic stress responses in sesame (Sesamum indicum L.).

BACKGROUND: The adverse effects of climate change on crop production are constraining breeders to develop high-quality environmentally stable varieties. Hence, efforts are being made to identify key genes that could be targeted for enhancing crop tolerance to environmental stresses. ERF transcription factors play an important role in various abiotic stresses in plants. However, the roles of the ERF family in abiotic stresses tolerance are still largely unknown in sesame, the "queen" of oilseed crops.
RESULTS: In total, 114 sesame ERF genes (SiERFs) were identified and characterized. 96.49% of the SiERFs were distributed unevenly on the 16 linkage groups of the sesame genome. The phylogenetic analysis with the Arabidopsis ERFs (AtERFs) subdivided SiERF subfamily proteins into 11 subgroups (Groups I to X; and VI-L). Genes in the same subgroup exhibited similar structure and conserved motifs. Evolutionary analysis showed that the expansion of ERF genes in sesame was mainly induced by whole-genome duplication events. Moreover, cis-acting elements analysis showed that SiERFs are mostly involved in environmental responses. Gene expression profiles analysis revealed that 59 and 26 SiERFs are highly stimulated under drought and waterlogging stress, respectively. In addition, qRT-PCR analyses indicated that most of SiERFs are also significantly up-regulated under osmotic, submerge, ABA, and ACC stresses. Among them, SiERF23 and SiERF54 were the most induced by both the abiotic stresses, suggesting their potential for targeted improvement of sesame response to multiple abiotic stresses.
CONCLUSION: This study provides a comprehensive understanding of the structure, classification, evolution, and abiotic stresses response of ERF genes in sesame. Moreover, it offers valuable gene resources for functional characterization towards enhancing sesame tolerance to multiple abiotic stresses.

Background

Sesame (Sesamum indicum L.) is a worldwide important oilseed crop cultivated mainly in tropical and subtropical regions and providing humans with high-quality nutrients and nutraceuticals [1-3]. It represents a priceless material for food, cosmetics, and medicine [4]. For instance, its lignans have been reported to possess various physiological properties, such as antioxidant, antiaging, serum lipid-lowering, blood pressure-lowering, anti-cancer, etc. [5-7]. Therefore, the global market of sesame products is being expanded. Unfortunately, sesame productivity, yield, and seed quality are influenced by several abiotic stresses, including drought, waterlogging, salt, and heat [8, 9]. Among them, drought and waterlogging are the leading environmental adverse impairing physiological and biochemical processes in sesame [10-12]. Studies revealed that plants initiate a series of transcription factors (TFs) phosphorylation/dephosphorylation under stress to enable them to bind cis-elements of stress-related genes to enhance or suppress their transcription, thus inducing stress tolerance [13, 14]. TFs are critical in regulating plant’s defense responses to stresses and are emerging as promising resources for engineering improved crop varieties with tolerance for multiple abiotic stresses [15]. In sesame, studies carried out by Dossa et al., and Wang et al. disclosed that ERF, MYB, bHLH, and WRKY TF families are the main genes involved in sesame responses to abiotic stresses [16, 17]. MYB and WRKY TFs have been widely identified in sesame, and their expression under various abiotic stresses was evaluated [18, 19]. However, the ERF gene family is not well characterized in sesame, and only DREB genes expression under drought stress was investigated [20].

ERF, together with AP2 (APETALA2), DREB (dehydration responsive element binding), RAV (related to ABI3/VP), and Soloist (specific proteins) genes are members of the AP2/ERF TFs superfamily [21, 22]. The ERF gene family includes ERF and DREB genes and encodes a protein with a single AP2/ERF domain [23]. The structure of the domain is unique, with three-stranded β-sheets and an α-helix consisting of approximately sixty conserved amino acids [24]. ERF and DREB genes could be distinguished by their DNA binding domains [21]. The ERF subfamily binds to the AGCCGCC of GCC-box, while the DREB subfamily usually interacts with the CCGAC core sequence. ERF TFs are widespread in plants, and numerous ERF genes have been successfully identified in crops, including Arabidopsis [22], rice [25], soybean [26], tomato [27], peanuts [28], Zea mays [29], Brassica napus [30], and wheat [31]. Their roles in plants’ response to abiotic stresses have been extensively studied [32]. For example, AtERF1 is reported to play a positive role in salt, drought, and heat stress tolerance by regulating stress-specific genes in Arabidopsis [33]. Overexpression of AtERF019 delayed Arabidopsis plant growth and senescence and improved drought tolerance [34]. Overexpression of AtERF71 enhanced the Arabidopsis plant tolerance to salt stress and its ability to resist osmotic stress [35]. AtERF98 enhanced tolerance to salt through the transcriptional activation of ascorbic acid synthesis [36]. In rice, it was demonstrated that OsERF71 increases the plant tolerance to drought by binding to the promoter of OsCC1 [37]. Conversely, overexpression of OsERF922 impaired the plant tolerance to salt stress [38]. In soybean, GmERF3 was reported to be essential for plant survival under salinity and drought [39]. In cotton, GhERF38 is essential for the plant response to salt and drought stresses [40].

In the present, the ERF gene family was re-identified in sesame under stringent conditions. Through a comprehensive bioinformatic analysis, their structure, chromosomal distribution and duplication events, phylogeny, and conserved motifs were revealed. Moreover, their expression patterns in response to drought, waterlogging, osmotic, submerge, ABA, and ACC treatments were analyzed. Our findings provide new insights into the ERF gene family and reveal key SiERF genes for targeted improvement of the sesame tolerance to abiotic stresses.

Results

Genome-wide identification of ERF family genes in sesame

In total, 114 putative ERF genes were identified and named from SiERF1 to SiERF114 based on their appearance on the sesame linkage groups. Detailed information of SiERFs such as gene name, gene ID, mRNA accession, protein accession, linkage group, gene start position, gene end position, protein length, and the number of exons are shown in Table S1.

The proteins of the 114 SiERF ranged from 121 (SiERF091) to 419 (SiERF114) amino acids (aa) in length. The molecular weights (MWs) and the isoelectric points (pIs) of the sesame ERF proteins varied from 13.42804 (SiERF114) to 46.17756 kDa (SiERF091) and 4.5 (SiERF072) to 10.24 (SiERF114), respectively. Table S2 presents detailed information about the physiochemical proprieties of each identified ERF protein.

Chromosomal localization and gene duplication analysis of SiERF genes

96.49% of the SiERF genes (110 genes) were distributed unequally on the 16 linkage groups (LGs) (Fig. 1). The remaining four SiERF genes (SiERF111, 112, 113, and 114) are located on the unanchored scaffolds (Table S1). The LG1 harbored the largest number of 19 SiERF genes, accounting for 16.67% of the total number. In contrast, the LG14, LG15, and LG16 contained only one SiERF gene, respectively. Some SiERF genes formed one, two or three clusters on LG1、LG2、LG3、LG4、LG6、LG8、LG10、LG11 and LG12.

Fig. 1

Distribution of SiERF genes within the sesame linkage groups (LGs). Vertical bars represent the LGs within the sesame genome. The LG number is indicated at the top of each LG. The scale on the left is in megabases

In order to reveal the evolution mechanism of the ERF gene family in sesame, we analyzed the duplication events. The result indicated that the SiERF gene family underwent whole-genome duplication (WGD) and tandem duplication events (Fig. S1). Fifty-eight (58) SiERF genes accounting for 52.73% were derived from WGD events, indicating that whole-genome duplication plays a major role in ERF gene family expansion in sesame. The tandem gene duplication involved 18 SiERF genes.

Phylogenetic analysis among the Arabidopsis and sesame ERFs

To get insight into the phylogenetic relationships of the ERF gene families, a phylogenetic tree was constructed using the neighbor-joining (NJ) method and based on AP2/ERF domain of 122 Arabidopsis ERFs and the 114 SiERFs. As presented in Fig. 2, the SiERFs were distinctly divided into eleven (11) groups (groups I, II, III, IV, V, VI, VII, VIII, IX, X, and VI-L), which closely agrees with the phylogenetic analysis of ERFs in cassava and Andrographis paniculate [41, 42]. One additional group (group Xb-L) was composed uniquely of three Arabidopsis ERFs. Groups I ~ X and VI-L constituted of 9, 10, 21, 6, 5, 7, 4, 15, 23, 6, and 8 SiERFs, respectively. The largest group (class III) included 45 ERF proteins (21 SiERFs and 24 AtERFs), suggesting that genes of this subfamily might undergo duplication events and retain more genes.

Fig. 2

Phylogenetic analysis of the ERF proteins in sesame and Arabidopsis. Multiple sequence alignments of ERF amino-acid sequences were conducted using ClustalX, and the phylogenetic tree was constructed using MEGA5 by the neighbor-joining (NJ) method and 1000 bootstrap replicates. The blue triangles and red dots represent ERF proteins in Arabidopsis and sesame, respectively

Gene structure, conserved domain, and cis-acting elements analyses of SiERF genes

Phylogenetic evolution and gene structure usually have a strong correlation. To study the structural characteristics of the SiERF genes, the conserved motifs and the number of exons and introns were identified and analyzed. Totally, we identified 16 conserved motifs (motif 1–16) through MEME motif detection software (Fig. 3A). The motifs were constituted of 6 to 49 aa (Fig. S2). Each SiERF contained two to eight motifs. The motifs 1, 2, 3, and 4 aligned in the order 4–2–1-3 were shared by 95 SiERFs, indicating that ERF family genes are relatively conserved in sesame. Motifs 5 and 13 were shared by 28 SiERFs, and motif 6 was shared by 29 SiERFs. SiERF proteins in the same group displayed similar conserved motif types (Fig. 3A). For instance, 20, 17, and 13 SiERFs in the same groups shared motif 8, motif 7, and motif 11, respectively, indicating that subgroups of SiERF are different. To determine the number and location of exons and introns, the structure of SiERF genes was further analyzed via the TBtools software. The result showed a weak variation of the number of exons and introns in the sesame ERF gene family (Fig. 3B). 90 of the 114 (78.9%) sesame ERF genes contained only one exon and no intron. Twenty (17.5%) SiERF genes contained two exons and one intron.

Fig. 3

Phylogenetic relationships, gene structure, and motif compositions of SiERFs. A Left: the phylogenetic tree of SiERFs. Right: conserved motif composition of the SiERFs. Different colored boxes represent different motifs. B Intron-Exon structure of SiERFs. The green boxes represent UTR, grey lines represent introns, and yellow boxes represent exons

To identify the putative cis-acting regulatory elements in the promoter regions of the SiERFs, the sequences 1500-bp upstream from the protein start codons (ATG) of each gene were analyzed by the PLACE database [43]. All SiERFs contained cis-acting elements within the analyzed interval. Totally, 40 cis-elements mainly related to hormone response, stress response, and light-response were identified (Table S3; Table S4). Light responsive elements, including I-box, TCT-motif, TCA-element, TCCC-motif, GT1-motif, GA-motif, G-Box, AE-box, Box 4, MRE, etc., were the most abundant (Fig. S3). Hypoxia response elements (ARE), ABA response elements (ABRE), methyl jasmonate response elements (CGTCA-motif and TGACG-motif), and ethylene response elements (ERE) were detected in 82, 89, 67, 67, and 72 genes, respectively (Table S3).

Expression profiles of SiERF genes under drought and waterlogging stresses

To explore the roles of SiERF genes in sesame response to drought and waterlogging stresses, we investigated their expression in roots at different time points based on RNA-seq data from previous studies [9, 44]. Unfortunately, eleven (SiERF006, 007, 013, 016, 048, 073, 074, 075, 082, 083, and 099) and thirteen genes (SiERF006, 007, 019, 028, 034, 041, 048, 067, 076, 086, 089, 093, and 099) lacked RNA-Seq data under progressive drought and waterlogging stress, respectively. As shown in Fig. 4A, the SiERF genes exhibited significant transcriptional changes in responses to drought stress. 59 (51.8%) and 44 (38.6%) SiERF genes were up-regulated and down-regulated under drought stress, respectively. Among the up-regulated SiERFs, fifteen (SiERF002, 005, 016, 020, 021, 023, 033, 035, 038, 050, 077, 094, 097, 105, and 109) were highly expressed at all time points during the drought stress. Expression levels of SiERF002, SiERF003, SiERF016, and SiERF109 were maximum at 3 d after drought stress initiation. The expression levels of SiERF021, SiERF023, SiERF069, SiERF077, and SiERF097 were peaked at 7 d, and those of SiERF005 and SiERF050 at 10 d, implying their role in the sesame responses to drought stress at different times. Besides, some SiERF genes in the down-regulated group such as SiERF010, SiERF014, SiERF053, SiERF055, SiERF078, and SiERF093 exhibited a high expression at 3 d. SiERF11, SiERF34, and SiERF35 were down-regulated significantly at each time point (Fig. 4A).

Fig. 4

SiERF genes expression profiles in sesame roots under drought stress (A) and waterlogging stress (B). Transcriptome data (Reads Per Kilobase per Million mapped reads; RPKM) were used for the expression levels measurement. The colored scale for the different expression levels is shown

Three groups of SiERF genes could be distinguished under waterlogging stress (Fig. 4B). The first group constituted of 26 genes that were expressed highly at different time points. Among them, the expression of SiERF31 and SiERF54 were significantly up-regulated along with the waterlogging stress progress, indicating they might be essential for sesame survival under waterlogging conditions. The second group of SiERF genes (51 genes) was up-regulated at one, two, or three time points, except for SiERF010, SiERF053, SiERF011, and SiERF081, which were down-regulated at each time point. The third group of SiERF genes was composed of 24 genes that were expressed weakly under waterlogging stress. By integrating the results, we found that twenty-two SiERF genes, including SiERF23, SiERF35, and SiERF54, were up-regulated significantly at least once under drought and waterlogging stresses. Forty-two SiERF genes exhibited contradictory expression patterns under drought and waterlogging stress. For example, SiERF005, SiERF021, SiERF38, SiERF40, SiERF069, SiERF98, SiERF105, SiERF109, and SiERF113 were up-regulated significantly under drought and down-regulated under waterlogging, while SiERF088 was induced by waterlogging and repressed by drought.

Expression profiles of SiERF genes in response to osmotic and submerge stresses

To further investigate the potential roles of the SiERF gene family in response to multiple abiotic stresses in sesame, we selected and examined the stimulation response of eighteen SiERF genes under osmotic and submerge stresses via qRT-PCR (Fig. 5A and B). The results showed that except for SiERF004 and SiERF014, the other sixteen SiERF genes were significantly up-regulated by osmotic stress, with SiERF023 exhibiting the highest expression level (Fig. 5A). SiERF014 was significantly down-regulated, while SiERF004 expression was not significantly influenced at 6 h. SiERF023 and SiERF054 showed a steady tendency of expression profiles from 3 h (Fig. 5A). In contrast to osmotic stress, submerge stress significantly affected the expression of the selected eighteen SiERF genes except for SiERF002 and SiERF108 (Fig. 5B). SiERF004, SiERF008, SiERF014, SiERF050 and SiERF107 were significantly down-regulated while SiERF023, SiERF030, SiERF052, SiERF054, SiERF055, SiERF064, SiERF084, SiERF085, SiERF090, SiERF102, and SiERF105 were significantly up-regulated under the submerge stress (Fig. 5B).

Fig. 5

Expression profiles of eighteen SiERF genes in sesame leave subjected to osmotic stress (A) and submerge stress (B) for 6 h. Transcript abundance was quantified using quantitative real-time polymerase chain reaction (qRT-PCR), and expression levels were normalized using sesame Histone H3.3 (LOC105159325) as a reference gene. The mean expression levels from three independent biological replicates were analyzed for significance using t-tests (p < 0.01). Asterisks indicate significant expression differences

Expression profiles of SiERF genes in response to ABA and ACC treatments

Abscisic acid (ABA) is a critical plant hormone involved in various growth, developmental, as well as plant and environment interactions processes [45]. 1-aminocyclopropane-1-carboxylic acid (ACC) is the direct precursor of ethylene. It is converted into ethylene in seed plants by ACC oxidase [46]. Ethylene responses in plants are often induced via ACC treatment [47]. We investigated the expression profiles of eighteen selected SiERF genes in response to ABA and ACC treatment of sesame for 0 h, 3 h, and 6 h through qRT-PCR. As presented in Fig. 6A and B, the selected SiERF genes were up-regulated by both ABA and ACC treatments except for SiERF004, SiERF014, SiERF050, and SiERF085. SiERF105 was down-regulated by both ABA and ACC treatment. SiERF050 expression was induced by ABA treatment but was not significantly affected by ACC treatment. SiERF004 was up- and down-regulated by ABA and ACC, respectively. In contrast, SiERF085 was down- and up-regulated by ABA and ACC, respectively. The expression of SiERF023, SiERF030, SiERF052, SiERF055, SiERF061, and SiERF107 were significantly induced along with the duration of the ABA treatment, specifically at 6 h (Fig. 6A). Meanwhile, the same genes with SiERF002, SiERF008, and SiERF102 exhibited the same expression patterns under ACC (Fig. 6B).

Fig. 6

Expression profiles of eighteen SiERF genes in sesame leave treated with ABA (A) and ACC (B) for 6 h. Transcript abundance was quantified using quantitative real-time polymerase chain reaction (qRT-PCR), and expression levels were normalized using sesame Histone H3.3 (LOC105159325) as a reference gene. The mean expression levels from three independent biological replicates were analyzed for significance using t-tests (p < 0.01). Asterisks indicate significant expression differences

Discussion

Sesame is one of the most important oilseed crops supplying humans worldwide with various metabolites, including high-quality nutrients and bioactive compounds [1, 7]. The plant growth, development, survival, reproduction, and yield are usually affected by various abiotic stresses [10–12, 16]. To adapt to unfavorable environmental conditions, the plant has implemented sophisticated regulatory mechanisms involving diverse TFs [10, 48]. Among them, ERF genes have emerged as one of the key regulators of multiple stress responses in sesame [16, 17]. Therefore, in this study, we performed a comprehensive and systematic analysis of the ERF gene family in sesame and investigated the expression of SiERFs under various abiotic stresses.

The ERF gene family represents one of the largest families of plant TFs and is essential for plant species survival [23]. ERF genes have been widely identified in many plants, including Arabidopsis, rice, soybean, Brassica napus, Sorghum bicolor, Tartary buckwheat, Medicago sativa, and peanuts in which 122, 139, 323, 444, 158, 116, 159, and 63 ERFs were detected, respectively [22, 23, 28, 30, 49–51]. Herein, we identified 114 SiERFs, indicating that the ERF gene family has expanded more in many species compared with S. indicum. A similar observation was noticed by Dossa et al. [20]. The SiERFs were distributed irregularly on the sixteen LGs of the sesame genome, mostly in a cluster of two or three genes. It is shown that a subset of the ERF genes appears in clusters on the chromosomes and contributes together to regulate metabolism [51]. The interspecific variation of the number of ERF genes may be originated from differences in gene duplication events. Studies revealed that the expansion of the ERF gene family in plants might be caused by chromosomal (segmental) duplication and tandem duplication [22, 30]. We found that the SiERF gene family went through whole-genome duplication (WGD) and tandem duplication events. 52.73% of the SiERFs were derived from WGD events, indicating that WGD is essential for ERF gene family expansion in sesame.

78.94% of the SiERF genes were intron-less and contained one exon. Meanwhile, 20 SiERF genes were constituted of two exons and one intron. 60% and 38 SbERFs also had no and single intron, respectively [50]. Also, the 40 identified cis-acting elements in the promoter regions of 114 SiERFs were related to light-response, stress-response, and hormone response. These results suggest that SiERFs might play essential roles during the sesame plant growth, development, and reproduction. Particularly, SiERFs might exhibit efficient expression in swift response to environmental stresses. Phylogenetic analysis showed that SiERF family proteins were systematically classified into 11 subgroups as the previously classified AtERFs by Nakano et al., except for the group Xb-L [22]. The ERF genes in S. bicolor and Hypericum perforatum were similarly classified in 11 groups [24, 50]. The motif analysis showed that SiERFs in the same clade shared a similar motif structuring, indicating the reliability of the phylogenetic classification of the ERF proteins and the coevolution of the ERF domain with the remaining protein sequence. Most of the SiERFs conserved motifs 1–4, suggesting they might be involved in a regulation network of developmental processes and abiotic stresses response in sesame. In Arabidopsis, studies demonstrated that AP2/ERFs participate in various stress tolerance, allowing them to build an interconnected stress regulatory network [52]. Some motifs were specific to phylogenetic groups suggesting their potential contribution to the SiERF gene’s functional specialization. Taken together, these findings denote that SiERFs within the same subgroups could play similar functions. These functions could be predicted based on the reported roles of the Arabidopsis ERF genes. Indeed, it was shown that the sequences gathered in the same clade play similar physiological functions [53]. For example, GmERF135 and OsERF922 in soybean and rice, respectively, and their homologous maize ZmERF39 and ZmERF23 were both up-regulated by drought and salt stress [38, 54]. The A. thaliana ERF-VII group plays an important role in low-oxygen sensing and low-oxygen survival and root growth [55, 56]. Therefore, we speculated that the SiERF genes belonging to group VII might be involved in hypoxia response and root development [57, 58].

The sustainability of crop production requires an in-depth understanding of the stress-induced molecular mechanisms in plants and the identification of multiple stress-responsive candidate genes for targeted improvement of crop tolerance to unfavorable growth conditions. Previous studies in sesame, Arabidopsis, Panax ginseng, Triticum durum, etc., showed evidence that ERF TFs are essential for plant response to abiotic stresses [16, 17, 59–61]. Wan et al. reported that ectopic overexpression of the peanuts AhERF019 improved tolerance to drought, salt, and heat stresses in Arabidopsis [28]. Overexpression of AtERF1, AtERF019, AtERF71, and AtERF98 enhanced the Arabidopsis plant tolerance to drought, heat, salt, and osmotic stresses [33-36]. We then investigated the expression of SiERF genes under drought and waterlogging stress. We found that 59 and 26 SiERFs were significantly induced under drought and waterlogging stress, respectively, confirming their pivotal role in drought and waterlogging stresses tolerance in sesame. The up-regulated SiERF genes reached their expression peak at different time points, indicating they might be involved in different stress-responsive processes. Moreover, the qRT-PCR analysis revealed that most of the SiERFs that responded to the drought and waterlogging stresses were also induced significantly under osmotic, submerge, ABA, and ACC (an immediate precursor of ethylene) treatments. Among them, SiERF23 and SiERF54 were the most induced by both the abiotic stresses. ABA and ethylene play essential roles in various plant growth and developmental processes, including seed maturation, germination, abiotic stress responses, pathogen response, senescence, etc. [9, 62, 63]. These findings support that the ERF gene family plays a vital role during sesame growth and development, especially in the plant responses to abiotic stresses. In addition, they suggest that targeting SiERF23 and SiERF54 could help promote sesame tolerance to multiple abiotic stresses.

Conclusion

In this study, 114 SiERF genes were identified and comprehensively analyzed. Chromosomal locations, phylogenetic relationships, gene structures, conserved motifs, and cis-acting elements analyses revealed that SiERFs might be involved in networks regulation of various developmental processes, especially in stresses tolerance in sesame. Tandem duplication and mostly whole-genome duplication are the driving forces that have contributed to the ERF gene family expansion in sesame. Gene expression profiles and qRT-PCR analyses unveiled that many SiERFs are stimulated under drought, waterlogging, osmotic, and submerge stresses. Particularly, SiERF23 and SiERF54 were identified as potential candidate genes for targeted improvement of multiple abiotic stresses tolerance in sesame. This study provides reference information for exploring the SiERF gene’s functions and investigating the regulatory mechanisms involved in abiotic stresses resistance in sesame.

Materials and methods

Plant material

The sesame variety Zhongzhi No. 13 used in this study was provided by the Oil Crops Research Institute of the Chinese Academy of Agricultural Science (OCRI-CAAS, Wuhan, China).

Identification of ERF family genes in the sesame genome

Whole-genome protein sequences of Sesamum indicum were downloaded from NCBI (https://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/Sesamum_indicum/latest_assembly_versions/GCF_000512975.1_S_indicum_v1.0/). A local BLASTP alignment against all sesame proteins was established by using known ERF protein sequences from Arabidopsis as queries with a cut-off e-value of 1E-10. The Hidden Markov Model (HMM) profile of the AP2 domain (PF00847) and the B3 domain (PF02362) were downloaded from the PFAM database (http://pfam.xfam.org/) [64], and used to search against the sesame protein sequences using HMMER3.0 [65], with a threshold of E < 1E-4. The presence of the AP2 domain in the putative sesame ERF proteins was further confirmed by SMART (http://smart.embl-heidelberg.de/) [66]. After removed the proteins containing two repeated AP2 domains or B3 domains, the remaining proteins were assigned as members of the ERF family in sesame.

Chromosomal localization and gene duplication analyses

All identified ERF genes were mapped to the sesame linkage groups based on positions information using TBtools software [67]. Gene duplication analyses were performed using the One-Step MCScanX function in TBtools software, and the result was further visualized by the Circle Gene View function [67]. Genes that were located on the unassembled genomic scaffolds were excluded from analyses.

Multiple sequence alignment and phylogenetic analysis

Multiple sequence alignment of ERF proteins from sesame and Arabidopsis was performed using Clustal X [68]. Subsequently, an unrooted phylogenetic tree with 1000 bootstrap replications was constructed by the MEGA (version 5.0) program [69] using the neighbor-joining (NJ) method and based on the conserved AP2/ERF domain of ERFs from sesame and Arabidopsis.

Gene structure, conserved motifs, and cis-acting elements analyses

The gene structure of SiERFs was analyzed by TBtools software [67] based on gene’s structure annotation file in GFF3 format of sesame. Conserved motifs of SiERFs were analyzed using MEME (Multiple Em for Motif Elicitation) v5.3.3 (http://meme-suite.org/tools/meme) [70] with the default parameters. The XML file storing motif pattern information obtained from MEME was used to generate schematic diagrams of motif distribution by TBtools software [67].

To analyze the cis-acting elements in the promoter region, the 1500-bp length of the upstream DNA sequences of SiERF genes were extracted in TBtools software and submitted to the PlantCARE database (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/) [43].

Expression profiling of SiERF genes under drought and waterlogging

The expression levels of SiERF genes in response to drought and waterlogging stress were analyzed using the RNA-seq data previously developed by our group [9, 44]. The heatmap was constructed by TBtools software with Log2-based expression fold-changes [67]. The differentially expressed genes (DEGs) were identified at the criteria of false discovery rate (FDR) < 0.01 and |log2FC (fold change)| > 1.

Osmotic, submerge, ABA, and ACC treatments

The Zhongzhi No. 13 seeds were grown in a growth chamber at 28 °C (16 h light/8 h dark cycle). The different treatments were induced on two-week-old seedlings. The osmotic stress was induced as described in our previous study [71]. For the submerge stress, the seedlings were introduced into distilled water at a depth of 3 cm from the water surface. The hormone treatments were performed as per Yin et al. [72]. 0.1 mM ABA and ACC were sprayed on the surface of the seedling leaves. The leaf samples were collected after each treatment at 0 h, 3 h, and 6 h for genes expression analysis. All collected samples were frozen immediately in liquid nitrogen and stored at − 80 °C until use.

qRT-PCR

Total RNA was isolated from each sample, and first-strand cDNAs were synthesized following the methods reported by Wei et al. [73]. Quantitative real-time PCR (qRT-PCR) was performed in Roche LightCycler 480 real-time PCR system with the ChamQ SYBR qPCR Master Mix (Vazyme Biotech, China). The experiment was performed with three replicates. Relative expression levels were calculated according to the 2–ΔΔCT method and normalized to the sesame Histone H3.3 (LOC105159325) gene expression [71, 74]. The gene-specific primers are listed in Table S5.

Additional file 1: Table S1. Detailed information of Sesamun indicum ERF (SiERF) genes; Table S2. Sequence Characteristics of SiERF genes; Table S3. Number of each cis-acting element in the promoter region of SiERF genes; Table S4. Information related to the cis-acting elements identified in the SiERF genes; Table S5. List of primers used for the qRT-PCR analysis.

Additional file 2: Fig. S1. Ortholog and duplication analysis of SiERF genes; Fig. S2. The logos of 16 conserved motifs in SiERF proteins; Fig. S3. Distribution of cis-acting elements in the promoter regions of the SiERFs. The number of SiERF genes containing each cis-acting element.