Skip to main content
Download PDF

Identification and characterization of the RcTCP gene family and its expression in response to abiotic stresses in castor bean

BMC Genomics volume 25, Article number: 670 (2024) Cite this article

Abstract

Background

The TCP (teosinte branched1/cincinnata/proliferating cell factor) family plays a prominent role in plant development and stress responses. However, TCP family genes have thus far not been identified in castor bean, and therefore an understanding of the expression and functional aspects of castor bean TCP genes is lacking. To identify the potential biological functions of castor bean (RcTCP) TCP members, the composition of RcTCP family members, their basic physicochemical properties, subcellular localizations, interacting proteins, miRNA target sites, and gene expression patterns under stress were assessed.

Results

The presence of 20 RcTCP genes on the nine chromosomes of castor bean was identified, all of which possess TCP domains. Phylogenetic analysis indicated a close relationship between RcTCP genes and Arabidopsis AtTCP genes, suggesting potential functional similarity. Subcellular localization experiments confirmed that RcTC01/02/03/10/16/18 are all localized in the nucleus. Protein interaction analysis revealed that the interaction quantity of RcTCP03/06/11 proteins is the highest, indicating a cascade response in the functional genes. Furthermore, it was found that the promoter region of RcTCP genes contains a large number of stress-responsive elements and hormone-induced elements, indicating a potential link between RcTCP genes and stress response functions. qRT-PCR showed that all RcTCP genes exhibit a distinct tissue-specific expression pattern and their expression is induced by abiotic stress (including low temperature, abscisic acid, drought, and high salt). Among them, RcTCP01/03/04/08/09/10/14/15/18/19 genes may be excellent stress-responsive genes.

Conclusion

We discovered that RcTCP genes play a crucial role in various activities, including growth and development, the stress response, and transcription. This study provides a basis for studying the function of RcTCP gene in castor.

Peer Review reports

Background

Castor bean (Ricinus communis) is an important oil crop that has been used as a model plant for improving saline-alkali soil in recent years [1]. In recent years, with the occurrence of extreme weather globally, the first affected are the plants [2]. As a sessile organism, plants find it difficult to avoid environmental damage, therefore they have evolved complex protective mechanisms, including the regulation of stress response genes by recognizing adverse signals and regulating gene expression and transcription [3, 4]. Therefore, identifying and exploring the function of plant stress-regulating genes is of great significance for studying the protective mechanisms of plants in adapting to stressful environments.

The TCP (teosinte branched1/cincinnata/proliferating cell factor) gene, as a plant-specific transcription factor, plays an important role in plant growth, development, and the response to abiotic stress [5]. The name TCP originates from the initial discovery of several genes, including the TB1 (teosinte branched 1) gene from maize (Zea mays), the CYC (bycloidea) gene from snapdragon (Antirrhinum majus), and the PCF1/2 (proliferating cell factors 1/2) genes from rice (Oryza sativa) [6]. These genes all have a non-canonical helix–loop–helix (bHLH) domain consisting of 59 amino acid residues, namely the TCP domain [7]. Based on the differences in the TCP domain, previous researchers classified TCP gene family members into two classes: Class I and Class II [8]. Class I lacks four amino acid residues in the domain region compared to Class II [9], which is further divided into two sub-branches, CIN and CYC/TB1, based on protein sequence differences [10].

Research has found that TCP family genes mainly regulate the growth, development, and physiological and biochemical responses of plants in the meristematic tissues, such as the development of vascular tissue [11], seed germination [12], and the circadian rhythm [13]. In addition, TCP genes can increase plant tolerance to stress by regulating cell osmotic pressure or changing cell permeability [14,15,16]. For example, the OsNHX1 gene in rice, as a key gene regulating cell permeability, can bind specifically to OsPCF2 to activate the expression of the OsNHX1 gene and thus enhance salt tolerance [14]. Heterologous expression of the OsTCP19 gene effectively reduces water loss and the accumulation of reactive oxygen species in Arabidopsis, increasing the resistance of both seedlings and mature plants [16]. Overexpression of the OsTCP14 and OsTCP21 genes decreases the tolerance of transgenic rice to low temperature stress, while Osa-miR319b targets and regulates the OsTCP14 and OsTCP21 genes and reduces the cold tolerance of rice, indicating the involvement of TCP genes at the post-transcriptional level [17]. Furthermore, Osa-miR319a also negatively targets the OsTCP21 gene to regulate tiller number in transgenic rice, thereby reducing yield [17]. Furthermore, the TCP gene plays a significant role in controlling plant cell proliferation and leaf differentiation [18, 19]. For instance, overexpression of the LcTCP4 gene in Arabidopsis leads to transgenic plants exhibiting a smooth leaf margin phenotype [18]. The StAST1 gene in potatoes inhibits tuber proliferation by mediating plant hormone signal transduction [19].

Research indicates that redundant functionality exists in TCP proteins of the same species [20]. For example, in Arabidopsis thaliana, AtTCP5 and AtTCP17 can both bind and transcribe the PIF4 gene and also interact with the PIF4 gene to enhance the transcriptional activity of the downstream genes YUC8 and IAAI19 [21, 22]. In banana (Musa paradisiaca), MaTCP20 can form dimers with MaTCP5 and MaTCP19, regulating the transcription level of XTH10/XTH11 genes to affect plant stress resistance [23]. In Phalaenopsis equestris, PePCF10 and PeCIN8 can form homodimers, regulating ovule development in floral tissues [24].

Currently, the online website PlantTFDB (http://planttfdb.gao-lab.org/) has predicted the transcription factor members and their numbers for plants with completely sequenced genomes [25]. The number of TCP genes totals 4,187, with significant variations in the number of TCP gene family members across different species. Tobacco (Nicotiana tabacum), cultivated soybean (Glycine max), and Brassica napus var. pekinensis have the largest numbers of TCP genes, with 96, 81, and 76 genes, respectively [25]. However, castor bean TCP transcription factor family has not been identified. Thus, identifying and understanding the TCP gene in castor bean and its potential biological functions is of great significance for breeding superior castor bean varieties with resistance. In this study, we used a bioinformatics approach to screen and identify the castor bean TCP gene family. Comprehensive analysis was conducted on the chromosomal localization, physicochemical properties, potential biological functions, subcellular localization, and gene expression of these genes. The results inform a comprehensive understanding of the biological functions of the castor bean TCP gene family throughout growth and development.

Results

Identification and basic information of castor RcTCP genes

A total of 20 members of the TCP gene family were identified from the entire genome of castor bean, as revealed in Table 1. The length of the proteins encoded by these genes varied, ranging from 185 amino acids for RcTCP19 to 567 amino acids for RcTCP12. Their molecular weights also varied, ranging from 20246.68 kDa for RcTCP19 to 63947.78 kDa for RcTCP12. The theoretical isoelectric points ranged from 6.36 for RcTCP17 to 9.57 for RcTCP11. The instability index of the proteins encoded by RcTCP genes ranged from 38.45 for RcTCP11 to 67.87 for RcTCP05. The aliphatic index ranged from 53.61 for RcTCP15 to 90.02 for RcTCP20. Notably, the average hydrophilicity value of these proteins was less than 0, indicating their hydrophilic nature. Among them, RcTCP20 (− 0.115) exhibited the strongest hydrophilicity, while RcTCP07 (− 0.883) had relatively weaker hydrophilicity. Furthermore, the subcellular localization prediction results of the RcTCP proteins indicated that, 20 RcTCP proteins were all located in the nucleus,

Table 1 Analysis of the basic information of the RcTCP gene and its encoded protein
Full size table

Analysis of RcTCP gene structure and conserved motifs and domains of the encoded proteins

In Fig. 1, the 20 RcTCP proteins were categorized into three groups, namely A, B, and C (Fig. 1a). The motif composition was similar within each group. In group A, all members except RcTCP13 lacked Motif 2. In group C, all members except RcTCP09 lacked Motif 3 (Fig. 1b). Additionally, all 20 RcTCP proteins contain a conserved TCP superfamily domain at the N-terminus (Fig. 1c), indicating accurate identification. Furthermore, all RcTCP proteins possessed a conserved Motif 1 (Fig. 1b). Further analysis revealed that Motif 1 was situated within the TCP superfamily domain, suggesting its important role in RcTCP proteins (Fig. 1c). Moreover, the gene structure of RcTCP varied, with 1–7 exons and 0–4 introns detected (Fig. 1d). However, based on the evolutionary system analysis, genes within the same group exhibit similarity in gene structure, such as RcTCP01, RcTCP03, and RcTCP04 of group A (Fig. 1d).

Fig. 1
figure 1

Phylogenetic relationships, conserved protein motifs, domains, and gene structures of RcTCP genes. (a) Phylogenetic tree of 20 RcTCP proteins. (b) Motif composition analysis of castor RcTCP proteins indicated 10 conserved motifs. (c) The domain of RcTCP genes. (d) RcTCP gene structure. Black lines indicate introns; the red box represents the CDS; the black box represents the UTR

Full size image

The position and collinear relationship of castor RcTCP genes in the chromosomes

As depicted in Fig. 2, the RcTCP genes were distributed across all 10 chromosomes of castor bean. Among them, chromosomes 2 and 8 exhibited the lowest number of RcTCP genes, with one gene each, namely RcTCP04 and RcTCP15. In addition, out of the 20 genes, four pairs of genes displayed syntenic relationships: RcTCP02-RcTCP07, RcTCP03-RcTCP05, RcTCP06-RcTCP10, and RcTCP13-RcTCP19. Furthermore, the Ka/Ks values for these homologous gene pairs were all less than 1 (Table S2). This indicates that the RcTCP gene has undergone negative purifying selection in the process of evolution, and there may be functional similarity between genes.

Fig. 2
figure 2

Position and collinear relationship of castor RcTCP genes in the chromosomes. The red lines indicate collinearity between genes

Full size image

Prediction of the secondary and tertiary structure of RcTCP proteins

The analysis of the secondary and tertiary structures of RcTCP proteins can provide some basic materials for the follow-up study of protein function. The secondary structure of the RcTCP proteins indicated that alpha-helixes accounted for 15.00–37.84%, extended strands accounted for 8.80–21.41%, and random coils accounted for 44.42–72.08%, without β-turn structures (Table S3). The random coil structure was the most abundant in the tertiary structure of the RcTCP proteins, consistent with the secondary structure prediction results (Fig. 3).

Fig. 3
figure 3

Predicting the tertiary structure of RcTCP proteins

Full size image

Phylogenetic evolution, collinearity, and selection pressure analysis of the TCP gene family

Castor bean, Arabidopsis, and rice had a total of 66 TCP proteins, which were divided into two groups, Class I and Class II. There were 33 TCP proteins in each group, with 10, 11, and 12 Class II TCP proteins in castor bean, Arabidopsis, and rice (Oryza sativa), respectively, and 10, 13, and 10 Class I TCP proteins in castor bean, Arabidopsis, and rice (Oryza sativa), respectively, with similar distributions (Fig. 4a). Interestingly, 11 RcTCP genes in castor bean had 16 collinear relationships with 15 genes in Arabidopsis, and three RcTCP genes had four collinear relationships with three OsTCP genes in rice, indicating that these genes are paralogous (Fig. 4b). To better understand the evolutionary constraints on the TCP gene family, selection pressure analysis was conducted on these paralogous gene pairs (Table S2). The RcTCP genes in castor exhibited a distant evolutionary distance from eight and four TCP genes in Arabidopsis and rice, and the Ks values could not be calculated. These gene pairs, including RcTCP18-AtTCP10, RcTCP04-AtTCP22, RcTCP01-AtTCP9, RcTCP01-AtTCP19, RcTCP14-AtTCP6, RcTCP19-AtTCP11, RcTCP10-AtTCP13, RcTCP10-AtTCP5, RcTCP05-OsTCP6, RcTCP03-OsTCP6, RcTCP03-OsTCP12, and RcTCP01-OsTCP18, have extensive sequence divergence, with most of the potentially synonymous mutation sites experiencing synonymous mutations. It is hypothesized that orthologous genes in different plants may exhibit functional similarities.

Fig. 4
figure 4

Inter-species evolutionary tree and collinearity analysis of TCP proteins. (a) Inter-species evolutionary tree analysis; Rc, Os, and At represent castor bean, rice, and Arabidopsis thaliana TCP proteins. (b) Inter-species collinearity analysis; red lines indicate collinear genes

Full size image

Prediction of the cis-acting elements of RcTCP gene promoters in castor

According to the diagram in Fig. 5, the promoter region of the RcTCP gene contained a total of 26 cis-acting elements, including seven hormone-response elements, nine light-response elements, and 10 stress-response elements, totaling 290 elements. Among the hormone-response elements, ABRE was the most abundant, accounting for 35.85% of the total, and was mainly distributed in the promoters of the RcTCP10 and RcTCP19 genes. Among the light-response elements, Box 4 was the most abundant, accounting for 36.08% of the total, and was mainly distributed in the promoters of the RcTCP12 and RcTCP16 genes. Among the stress-response elements, MYB and MYC elements were relatively abundant, accounting for 46.43% and 22.14% of the total number of elements, respectively. Notably, all RcTCP gene promoters contained MYB elements except RcTCP08 and RcTCP14 gene. Among them, the promoters of the RcTCP20, RcTCP18, and RcTCP11 genes had a higher number of MYB elements, with nine, eight, and six elements, respectively. Based on these results, we speculate that RcTCP genes may be involved in plant responses to stress through the binding of MYB or MYC elements.

Fig. 5
figure 5

Prediction of the cis-acting elements of the RcTCP promoter. The numbers in the figure represent the quantity of elements

Full size image

Subcellular localization analysis of RcTCP proteins

To clarify the subcellular location of RcTCP proteins, we constructed recombinant plasmids for genes RcTC01/02/03/10/16/18, with 35 S::GFP as a control, and transformed them into Arabidopsis protoplasts. The green fluorescence of 35 S::GFP was present in the cell nucleus, cell membrane, and cytoplasm, while the green fluorescence of 35 S::RcTC01/02/03/10/16/18-GFP was mainly distributed in the cell nucleus of Arabidopsis protoplast cells (Fig. 6). This indicates that the previously predicted subcellular location of the RcTCP proteins was consistent and reliable.

Fig. 6
figure 6

Subcellular localization of RcTC01/02/03/10/16/18 proteins. Note: GFP indicates the green fluorescence field, fluorescence stands for the chloroplast autofluorescence field, and Merge stands for the superimposed field. Excitation light wavelengths: GFP field: 488 nm, fluorescence field: 488 nm. Note: the green fluorescence and chloroplast autofluorescence excitation light wavelengths were the same, and the acquisition light wavelengths were different. The fluorescent images were observed using a confocal laser scanning microscope. Scale bar = 10 μm

Full size image

Construction of the PPIs network of RcTCP and prediction of miRNA target sites on encoding genes

The PPI results (Fig. 7a) indicated that, apart from the lack of interaction between the RcTCP20 protein and other RcTCP proteins, the remaining 19 RcTCP proteins interacted. Among them, the proteins with the most interactions included RcTCP03, RcTCP06, and RcTCP11, with six, six, and five interacting proteins, respectively. This suggests that these interacting proteins may collectively participate in the regulation of growth and development as well as the stress response in castor plants.

Fig. 7
figure 7

(a) Analysis of protein-protein interaction network of RcTCP. The darker the color, the higher the node degree. (b) Prediction of miRNA targets for the RcTCP gene

Full size image

miRNAs can interact with non-coding RNAs to form ceRNA networks that participate in regulating plant physiological activities. Therefore, the miRNAs targeted by RcTCP were predicted. Among the 20 RcTCP genes, six genes were predicted to have 17 miRNAs as targets, and 38 regulatory pathways were constructed (Fig. 7b). Among them, RcTCP12 and RcTCP17 had the most miRNA target sites, with 13 and eight, respectively. In addition, miR159 could regulate five target genes RcTCP05/08/12/17/18 through cleavage. These results imply that RcTCP genes are expressed during various physiological activities in castor.

Analysis of the tissue expression patterns of the RcTCP genes

As shown in Fig. 8, the 20 RcTCP genes exhibited significant tissue-specific expression differences (P < 0.05). Among them, the expression levels of the RcTCP02/10/13/14/15/16/18/19 genes were highest in the roots; the RcTCP03/04/05/08/09/11/17/20 genes were most expressed in the cotyledons; the RcTCP01/07/12 genes exhibited the highest expression in the stems; and the RcTCP06 gene had the highest expression in the true leaves. Eleven RcTCP genes showed the lowest expression levels in the stems, including RcTCP05/06/08/10/11/13/14/15/18/19/20; six RcTCP genes had the lowest expression levels in the true leaves, including RcTCP01/02/03/04/09/17; two genes had the lowest expression levels in the cotyledons, including RcTCP07 and RcTCP16; and the RcTCP12 gene had the lowest expression level in the roots. Among these, the RcTCP20, RcTCP10, and RcTCP12 genes exhibited the greatest fold difference in tissue-specific expression, with fold differences between the extremes being 43.44, 41.54, and 21.56, respectively. By contrast, the RcTCP03, RcTCP04, and RcTCP06 genes demonstrated the smallest fold difference between tissues, with fold differences between the extremes being 1.52, 2.41, and 3.74, respectively. The results above indicate that the role played by the RcTCP gene in different tissues during the 4-leaf stage is varied.

Fig. 8
figure 8

Analysis of the tissue-specific expression pattern of RcTCP genes. From bottom to top are the root, stem, cotyledon, and true leaf tissues of castor. Darker colors indicate higher relative expression levels of the gene. The expression values are the average of three biological replicates relative to the true leaf tissue control

Full size image

Analysis of the expression patterns of RcTCP genes under low-temperature stress

To clarify the expression patterns of RcTCP genes under low-temperature treatment, the relative expression patterns of 20 RcTCP genes were analyzed using quantitative real-time (qRT)-PCR. As shown in Fig. 9, with the exception of the RcTCP06 gene, which showed no significant difference in expression level under low-temperature stress, the expression of the remaining 19 RcTCP genes was induced by low-temperature stress. The expression of the RcTCP01/02/03/05/09/14/15/16/17/18/19/20 genes was activated by low-temperature stress, and their relative expression levels at 4 h, 8 h, and 12 h were higher than at 0 h (control). Among these genes, the expression levels of RcTCP01 and RcTCP03 continued to increase; RcTCP07, RcTCP11, and RcTCP13 showed the highest expression levels at 4 h, with lower levels at 8 h and 12 h, indicating a pattern of an initial increase followed by a decrease; RcTCP08 and RcTCP12 reached their highest expression levels at 12 h, with lower levels detected at 4 h, indicating a pattern of an initial decrease and then an increase. The expression levels of the RcTCP04 and RcTCP10 genes continually decreased, indicating that their expression was suppressed at low temperature. Thus, RcTCP01, RcTCP03, RcTCP04, and RcTCP10 are key responsive genes of castor bean under low-temperature stress.

Fig. 9
figure 9

Gene expression of 20 RcTCP genes under low-temperature stress at 0 h, 4 h, 8 h and 12 h was analyzed using qRT-PCR. Error bars represent standard errors of three biological replicates. *, ** and *** denote significance at p < 0.05, p < 0.01, and p < 0.001 respectively, compared with 0 h based on Student’s t-test

Full size image

Analysis of the expression patterns of abscisic acid (ABA)-induced RcTCP genes

Due to the presence of multiple hormone-responsive cis-elements in the RcTCP promoter region, we analyzed the expression patterns of RcTCP genes under ABA stress. As shown in Fig. 10, the expression of the 20 RcTCP genes was induced by ABA, with the exception of RcTCP10, which was suppressed, while the others were activated. Interestingly, most genes, including RcTCP01/02/04/05/06/07/08/09/11/13/14/16/18/20, peaked at 8 h of stress, while RcTCP03/12/15/17 peaked at 12 h, indicating the delayed expression of RcTCP genes under ABA stress. The RcTCP10 gene may be a key responsive gene in castor bean under ABA stress.

Fig. 10
figure 10

Gene expression of 20 RcTCP genes under ABA stress at 0 h, 4 h, 8 h and 12 h was analyzed using qRT-PCR. Error bars represent standard errors of three biological replicates. *, ** and *** denote significance at p < 0.05, p < 0.01, and p < 0.001 respectively, compared with 0 h based on Student’s t-test

Full size image

Analysis of the expression patterns of RcTCP genes under drought stress

As shown in Fig. 11, the expression of the RcTCP08 and RcTCP10 genes was suppressed under drought stress. The expression values at 4 h, 8 h, and 12 h were all lower than at 0 h. The expression levels of the RcTCP01/02/09/14/15/17/18 genes continued to increase under stress, indicating activated expression. Interestingly, the expression levels of the RcTCP04/05/06/07/11/12/13/19 genes were lower at 4 h than at 0 h, and then increased after 4 h, suggesting that these genes exhibited a delayed response to drought stress. Out of the 20 genes, 14 genes showed the highest expression at 12 h, including the RcTCP01/02/05/06/07/09/12/13/14/15/16/17/18/19 genes, indicating that the RcTCP genes in castor bean exhibit a sustained response to drought stress.

Fig. 11
figure 11

Gene expression of 20 RcTCP genes under drought stress at 0 h, 4 h, 8 h and 12 h was analyzed using qRT-PCR. Error bars represent standard errors of three biological replicates. *, ** and *** denote significance at p < 0.05, p < 0.01, and p < 0.001 respectively, compared with 0 h based on Student’s t-test

Full size image

Analysis of the expression patterns of RcTCP genes under high-salt stress

The potential functions of RcTCP genes under high salt stress were explored. As shown in Fig. 12, the expression levels of the RcTCP08, RcTCP09, and RcTCP19 genes were continuously induced under salt stress, showing a gradually increasing trend. The expression of the RcTCP03/04/10/12 genes was suppressed at 4 h of salt stress, followed by an increase in expression levels. The expression of the RcTCP01/02/05/06/07/11/13/14/15/16/18/20 genes showed an initial increase followed by a decrease, and the expression levels at 4 h, 8 h, and 12 h were higher than at 0 h. In addition, the expression of 11 RcTCP genes peaked at 8 h, including RcTCP01/02/04/06/10/13/14/15/16/18/20. Therefore, RcTCP genes actively respond to high salt stress.

Fig. 12
figure 12

Gene expression of 20 RcTCP genes under high salt stress at 0 h, 4 h, 8 h and 12 h was analyzed using qRT-PCR. Error bars represent standard errors of three biological replicates. *, ** and *** denote significance at p < 0.05, p < 0.01, and p < 0.001 respectively, compared with 0 h based on Student’s t-test

Full size image

Discussion

Currently, TCP genes have been identified in many plants, including 24, 22, and 41 genes in Arabidopsis [26], rice (Oryza sativa) [26], and Solanum muricatum [27], respectively. We identified 20 castor bean RcTCP genes, further supporting the variability in the number of TCP genes among different species. Previous studies have shown that gene duplication contributes to the expansion of gene family members, and segmental duplication enhances gene function through an additive effect [28]. RcTCP genes have undergone segmental duplication, resulting in similar gene structures and compositions in deduced protein motifs. Additionally, phylogenetic evolutionary trees constructed for RcTCP genes in Arabidopsis and rice (Oryza sativa) revealed two gene classes, with high homology between RcTCP and AtTCP genes and significant collinearity. Genes within the same class exhibit functional redundancy [29], suggesting similar biological functions for these homologous genes. Analysis of the selection pressure between genes can significantly contribute to the understanding of gene evolution. RcTCP genes exhibit abnormal Ks values compared to OsTCP genes, while the Ka/Ks ratio of AtTCP genes is less than 1, indicating purifying selection and implying similar functions between RcTCP and AtTCP genes. For example, the AtTCP12 gene affects Arabidopsis branching development [30], suggesting that the RcTCP07 gene may be involved in castor bean growth and development. AtTCP14/15/23 are involved in plant responses to biotic and abiotic stress [30,31,32], implying potential roles for the RcTCP03 and RcTCP05 genes in castor bean stress regulation. Additionally, AtTCP14 and AtTCP15 are involved in hormone signaling pathways [30, 31], suggesting that the RcTCP03, RcTCP05, and RcTCP01 genes may be involved in hormone signaling transduction. The promoter regions of these three genes all contain ABRE elements, indicating that they may be regulated by ABA hormone. This hypothesis was confirmed by qRT-PCR results.

At the transcriptional level, TCP genes can regulate the expression of downstream genes in multiple ways, which also influences their own expression [33, 34]. For example, in rice, the IPA1 (IDEAL PLANT ARCHITECTURE 1) protein has been shown to directly inhibit the transcription of OsTB1, thus affecting rice tillering [34]. At the post-transcriptional level, miRNA-mediated mRNA degradation is also an important regulatory mechanism [35]. miR319, as a star target site of TCP genes, participates in the transcription of TCP genes [35]. For example, in cotton fiber, miR319 serves as a target site for the mRNA of GhTCP2/3/4/10 genes, regulating the elongation of fiber cells and the thickening of cell walls [36]. miR319a2 reduces the transcription level of Chinese cabbage (Brassica rapa ssp.) BrpTCP2/3/4 genes, affecting the development of cabbage head shape [37]. miR319 targeting is associated with reduced disease resistance in plants with BrpTCP2/3/10 genes. We predicted four homologous miRNAs of miR319, namely miR319a to miR319d, and all of these miRNAs target the mRNA of RcTCP genes, specifically RcTCP08/12/17/18. This suggests that RcTCP08/12/17/18 genes may have similar functions to Class II AtTCP1/2/3/4 genes and that their transcription is influenced by miR319.

Studies have shown that TCP genes do not act alone in the development and stress response of plants, but interact with homologous TCP genes or other transcription factors to function together [26,27,28,29,30]. AtTCP21, as an important component of the Arabidopsis circadian rhythm network, can specifically bind to the promoter region of the CCA1 (circadian clock associated 1) gene, suppressing the expression of the AtTCP21 gene to mitigate the effect of environmental stress on plants [13, 38]. Related research has also found interactions between AtTCP2/3/11/15 proteins, regulating circadian rhythm in plants [39]. It was found that RcTCP03/06/11 proteins have the most interactions, while AtTCP3/17/7, as homologous proteins of RcTCP, mainly function in Arabidopsis cell proliferation and leaf development [40], indicating a possible functional redundancy and influence on castor leaf development. The tissue expression of RcTCP03/06/11 genes provides strong evidence for this inference.

The expression patterns of genes are important manifestations of their function [41]. Numerous studies have shown that the expression of TCP genes is influenced by abiotic stress [42,43,44]. For example, under salt stress, the PeTCP10 gene in bamboo is significantly expressed in multiple organs (mature leaves, roots, and stems), and the heterologous expression of the PeTCP10 gene in Arabidopsis enhances salt tolerance [15]. The expression of maize ZmTCP32 and ZmTCP42 genes is activated by ABA and polyethylene glycol (PEG) stress, and through the ABA signaling pathway, enhances the drought tolerance of transgenic Arabidopsis [43]. The genes CnTCP2/4/14 in Chrysanthemum nankingense are suppressed by low-temperature stress, and overexpression of the CnTCP2 gene in Arabidopsis results in a hypersensitive response to low temperature [44]. The expression of RcTCP genes in castor bean is affected by low temperature, ABA, PEG, and salt stress. The RcTCP01 and RcTCP03 genes were continuously upregulated under low temperature, and their expression levels in the cotyledons were relatively high, which is consistent with the role of the AtTCP9 and AtTCP15 genes in Arabidopsis leaves. The RcTCP04 and RcTCP10 genes were downregulated under stress conditions, suggesting that they may be negative regulators in castor bean under low-temperature conditions. In addition, the genes RcTCP09/14/15/18 were continuously activated by PEG, and it is speculated that these genes regulate the impact of drought stress on castor bean in the root and cotyledon tissues. Finally, potential key genes under high salt stress in castor bean, such as RcTCP08/09/19, were continuously induced by high salt stress and may regulate plant stress resistance through the ABA pathway. In conclusion, this study found that RcTCP genes are likely playing a positive role in the response of castor bean to abiotic stress, providing a foundation for the further analysis of RcTCP gene function and mechanisms.

Conclusion

This study identified 20 members of the RcTCP gene family in castor and analyzed their evolutionary relationships with other species, subcellular localizations, and relative expression patterns. All RcTCP gene members were found to possess a TCP domain. The RcTC01/02/03/10/16/18 proteins were all localized in the cell nucleus, and RcTCP family members possessed multiple miRNA target sites. Interaction was detected between the encoded proteins. In addition, the expression of these genes was induced by various abiotic stresses, and potential functional genes, namely RcTCP01/03/04/08/09/10/14/15/18/19, were identified. This study provides a basis for the future exploration of the function of RcTCP genes.

Materials and methods

Identification and basic information of castor RcTCP genes

First, the pfam (PF03634) file of the TCP gene family was downloaded from the Pfam (https://pfam.xfam.org) database. Second, we downloaded the castor bean CDS sequence file, genome and annotation files, as well as the protein sequence file from the oil plant database (http://oilplants.iflora.cn), which was generated by Wei et al. [45] assembled the whole genome of wild castor bean ‘Rc039’ (accessions PRJNA706790). The RcTCP gene family members of castor were screened using the local HMMER program, and the sequences with missing domains were manually removed. In addition, Arabidopsis TCP family proteins were downloaded from the TAIR (https://www.arabidopsis.org) website [46], and the RcTCP proteins of castor were screened using the local Blast program and then integrated with the HMMER results. Finally, a total of 20 RcTCP gene family members were screened in castor. The basic physicochemical properties and subcellular locations of the proteins were predicted using the ExPASy (https://www.expasy.org) and WoLF PSORT (https://wolfpsort.hgc.jp/) tools, respectively.

Evolutionary relationships and gene structure analysis of castor RcTCP genes

Phylogenetic trees of the 20 RcTCP proteins in castor were reconstructed and visualized in MEGA 11.0 software. The bootstrap replicates were set to 1000, and the other parameters remained at default values. The 20 protein sequences were submitted to the MEME (https://meme-suite.org/meme/doc/meme.html) website to predict the conserved motifs, with the number of motifs set to 10 and the other parameters kept at default values [47]. The XML files were saved and submitted to Tbtools for visualization. The domain files of the family members were obtained by NCBI-CD Search (https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi) and were manually adjusted and submitted to Tbtools for visualization. Finally, Tbtools [48] was used to display the structural regions of the RcTCP family members, including the CDS region and UTR region, conserved motifs, and domains.

Secondary and tertiary structure prediction of castor RcTCP proteins

The secondary structure of the RcTCP proteins was predicted by SOPMA (http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_sopma.html) [49]. The protein sequences of the RcTCP gene family members were submitted to SWISS-MODEL (https://www.swissmodel.expasy.org/) to predict the tertiary structure of the RcTCP proteins [50].

The position and collinear relationship of castor RcTCP genes in the chromosomes

Tbtools was used to extract the location and common relationship information of the RcTCP family members in the castor gene annotation files, and Advanced Circos was used to visualize the results.

Analysis of the systematic evolution and selection pressure of the TCP gene family

Integrated the protein sequences of 20 castor bean, 24 Arabidopsis, and 22 rice TCP genes into one file. A phylogenetic tree was reconstructed using the neighbor-joining method with 1000 bootstrap replicates in MEGA 11.0 software. The tree was edited using the iTol (https://itol.embl.de) website [51]. The homologous gene pairs with the RcTCP gene in castor bean were filtered and plotted using the One Step MCScanX-Super Fast feature in TBtools software. The selection pressure value of the homologous gene pairs was calculated using the Simple Ka/Ks Calculator program.

Prediction of the cis-acting elements of RcTCP gene promoters in castor

The 1000-bp promoter sequence upstream of the translation initiation site of the 20 family members was obtained using the gene annotation file of castor and submitted to the PlantCare (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/) website [52]. The interactive information obtained by manual collation only retained the response and regulation components, and the prediction results were visualized using Tbtools and Excel software.

Analyzing PPIs of RcTCP and predicting miRNA target sites in the coding genes

The STRING website (https://cn.string-db.org/) was used to predict the interaction between RcTCP proteins, and Cytoscape 3.7.4 software was used to construct a network of interactions between RcTCP genes [53]. The online website psRNATarget (http://plantgrn.noble.org/psRNATarget/) was used to predict miRNAs related to RcTCP, and the miRNA network was visualized using the OmicShare tool (http://www.omicshare.com/tools) [54].

Subcellular localization analysis of RcTCP proteins

The subcellular localization of the RcTCP01/02/03/10/16/18 proteins was determined using specific primers designed without stop codon (Table S4, Fig. S1). To construct the subcellular localization vector 35 S::RcTCP-GFP, the fragments were subcloned into the pCAMBIA2300-GFP vector (35 S::GFP) using the Hieff Clone® One Step Cloning Kit (Yeasen, Shenyang, China). Arabidopsis protoplasts were isolated using the Plant Protoplasts Isolation Kit (Beyotime, Shenyang, China), and the empty vector and fusion expression vector were separately transformed into the protoplasts according to the instructions of the Plant Protoplasts Transfection Kit (Beyotime, Shenyang, China). Then, the protoplasts, cultured at 22 °C in a growth chamber for 16 h, were observed using a confocal laser scanning microscope.

Castor material processing and expression pattern analysis of RcTCP genes

‘Tongbi No.5’ was used as the experimental material was generously provided by the Tongliao Academy of Agriculture Sciences, China. Ricinus seeds were sterilized with 75% alcohol for 30 s and then germinated at 28 °C. After 4 days, uniformly germinated seeds were selected and placed in three germination boxes measuring 32 × 25.5 × 12 cm. The seedlings were cultured in an incubator at 25 °C with 16 h of light (light intensity 450 µmol m− 2s− 1) and 70–75% relative humidity. Once the two cotyledons had opened, the plants were inundated with 1/2 Hoagland’s nutrient solution. Seedlings at the 4-leaf stage were subjected to low temperature (4 °C) stress, ABA (150 µmol·L− 1) stress, drought (10% PEG6000 simulated drought) stress, and high salt (300 mmol·L− 1) stress. Tissues (roots, stems, cotyledons, and true leaves) were harvested at time points of 0 h, 4 h, 8 h, and 12 h, and each treatment was repeated three times. Total RNA was extracted from the plants using the Total RNA Extractor (Sangon) Kit (Fig. S2), and the RNA concentration and purity were detected on a Qubit2.0 fluorometer (Invitrogen). The PrimeScript™ RT reagent Kit (Perfect Real Time) (Takara, Shanghai, China) was used to remove genomic DNA, and qRT-PCR reactions were performed on a qTOWER3G (Analytik Jena, Germany) instrument using 2XRealStar Fast SYBR gPCR Mix (Genstar, Shenyang, China) according to the manufacturer’s instructions. Each reaction consisted of three technical replicates, using actin as the reference gene, and primers were designed using Snap Gene 4.3.6 software (Table S1). The relative expression levels of genes at different time points were calculated using the 2−ΔΔCT method, and graphs were generated using TBtools and GraphPad Prism 9.5.1 software.

Data availability

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

References

  1. Deng X, Ma Y, Cheng S, Jin Z, Shi C, Liu J, Lin J, Yan X. Castor plant adaptation to salinity stress during early seedling stage by physiological and transcriptomic methods. Agronomy. 2023;13(3):693.

    Article  CAS  Google Scholar 

  2. Janni M, Maestri E, Gullì M, Marmiroli M, Marmiroli N. Plant responses to climate change, how global warming may impact on food security: a critical review. Front Plant Sci. 2024;14:1297569.

    Article  PubMed  PubMed Central  Google Scholar 

  3. Fan M, Li Q. The metabolism, detrimental effects, and Signal Transduction Mechanism of Reactive Oxygen Species in plants under abiotic stress. J Biobased Mater Bioenergy. 2024;18(3):359–76.

    Article  Google Scholar 

  4. Mahmoud RM. MS Fouad 2024 Approaches to antioxidant Defence System: an Overview of Coping Mechanism against Lithium/Nickel Exposure in Plants. Lithium Nickel Contam Plants Environ 95 138.

    Google Scholar 

  5. Wang J, Wang Z, Jia C, Miao H, Zhang J, Liu J, Xu B, Jin Z. Genome-wide identification and transcript analysis of TCP gene family in Banana (Musa acuminata L). Biochem Genet. 2022;60(1):204–22.

    Article  CAS  PubMed  Google Scholar 

  6. Doebley J, Stec A, Hubbard L. The evolution of apical dominance in maize. Nature. 1997;386(6624):485–8.

    Article  CAS  PubMed  Google Scholar 

  7. Luo D, Carpenter R, Copsey L, Vincent C, Clark J, Coen E. Control of organ asymmetry in flowers of Antirrhinum. Cell. 1999;99(4):367–76.

    Article  CAS  PubMed  Google Scholar 

  8. Nicolas M, Cubas P. TCP factors: new kids on the signaling block. Curr Opin Plant Biol. 2016;33:33–41.

    Article  CAS  PubMed  Google Scholar 

  9. Murre C, McCaw PS, Baltimore D. A new DNA binding and dimerization motif in immunoglobulin enhancer binding, daughterless, MyoD, and myc proteins. Cell. 1989;56(5):777–83.

    Article  CAS  PubMed  Google Scholar 

  10. Martín-Trillo M, Cubas P. TCP genes: a family snapshot ten years later. Trends Plant Sci. 2010;15(1):31–9.

    Article  PubMed  Google Scholar 

  11. Baulies JL, Bresso EG, Goldy C, Palatnik JF, Schommer C. Potent inhibition of TCP transcription factors by miR319 ensures proper root growth in Arabidopsis. Plant Mol Biol. 2022;108(1–2):93–103.

    Article  CAS  PubMed  Google Scholar 

  12. Tatematsu K, Nakabayashi K, Kamiya Y, Nambara E. Transcription factor AtTCP14 regulates embryonic growth potential during seed germination in Arabidopsis thaliana. Plant J. 2008;53(1):42–52.

    Article  CAS  PubMed  Google Scholar 

  13. Pruneda-Paz JL, Breton G, Para A, Kay SA. A functional genomics approach reveals CHE as a component of the Arabidopsis circadian clock. Science. 2009;323(5920):1481–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Almeida DM, Gregorio GB, Oliveira MM, Saibo NJ. Five novel transcription factors as potential regulators of OsNHX1 gene expression in a salt tolerant rice genotype. Plant Mol Biol. 2017;93:61–77.

    Article  CAS  PubMed  Google Scholar 

  15. Xu Y, Liu H, Gao Y, Xiong R, Wu M, Zhang K, Xiang Y. The TCP transcription factor PeTCP10 modulates salt tolerance in transgenic Arabidopsis. Plant Cell Rep. 2021;40(10):1971–87.

    Article  CAS  PubMed  Google Scholar 

  16. Mukhopadhyay P, Tyagi AK. OsTCP19 influences developmental and abiotic stress signaling by modulatingABI4-mediated pathways. Sci Rep. 2015;5(1):9998.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Wang S-t, Sun X-l, Hoshino Y, Yu Y, Jia B, Sun Z-w, Sun M-z. Duan X-b, Zhu Y-m: MicroRNA319 positively regulates cold tolerance by targeting OsPCF6 and OsTCP21 in rice (Oryza sativa L). PLoS ONE. 2014;9(3):e91357.

    Article  PubMed  PubMed Central  Google Scholar 

  18. Wang M, Tu Z, Wang J, Zhang Y, Hu Q, Li H. Genomic survey, bioinformatics analysis, and expression profiles of TCP genes in Liriodendron chinense and functional characterization of LcTCP4. Trees 2024:1–16.

  19. Sun X, Wang E, Yu L, Liu S, Liu T, Qin J, Jiang P, He S, Cai X, Jing S. TCP transcription factor StAST1 represses potato tuberization by regulating tuberigen complex activity. Plant Physiol 2024:kiae138.

  20. Wang X, Gao J, Zhu Z, Dong X, Wang X, Ren G, Zhou X, Kuai B. TCP transcription factors are critical for the coordinated regulation of isochorismate synthase 1 expression in Arabidopsis thaliana. Plant J. 2015;82(1):151–62.

    Article  CAS  PubMed  Google Scholar 

  21. Han X, Yu H, Yuan R, Yang Y, An F, Qin G. Arabidopsis transcription factor TCP5 controls plant thermomorphogenesis by positively regulating PIF4 activity. Iscience. 2019;15:611–22.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Zhou Y, Xun Q, Zhang D, Lv M, Ou Y, Li J. TCP transcription factors associate with PHYTOCHROME INTERACTING FACTOR 4 and CRYPTOCHROME 1 to regulate thermomorphogenesis in Arabidopsis thaliana. Iscience. 2019;15:600–10.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Song C-B, Shan W, Yang Y-Y, Tan X-L, Fan Z-Q, Chen J-Y, Lu W-J, Kuang J-F. Heterodimerization of MaTCP proteins modulates the transcription of MaXTH10/11 genes during banana fruit ripening. Biochim et Biophys Acta (BBA)-Gene Regul Mech. 2018;1861(7):613–22.

    Article  CAS  Google Scholar 

  24. Lin Y-F, Chen Y-Y, Hsiao Y-Y, Shen C-Y, Hsu J-L, Yeh C-M, Mitsuda N, Ohme-Takagi M, Liu Z-J, Tsai W-C. Genome-wide identification and characterization of TCP genes involved in ovule development of Phalaenopsis Equestris. J Exp Bot. 2016;67(17):5051–66.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Tian F, Yang D-C, Meng Y-Q, Jin J, Gao G. PlantRegMap: charting functional regulatory maps in plants. Nucleic Acids Res. 2020;48(D1):D1104–13.

    CAS  PubMed  Google Scholar 

  26. Yao X, Ma H, Wang J, Zhang D. Genome-wide comparative analysis and expression pattern of TCP gene families in Arabidopsis thaliana and Oryza sativa. J Integr Plant Biol. 2007;49(6):885–97.

    Article  CAS  Google Scholar 

  27. Si C, Zhan D, Wang L, Sun X, Zhong Q, Yang S. Systematic investigation of TCP Gene Family: genome-wide identification and light-regulated gene expression analysis in Pepino (Solanum Muricatum). Cells. 2023;12(7):1015.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Flagel LE, Wendel JF. Gene duplication and evolutionary novelty in plants. New Phytol. 2009;183(3):557–64.

    Article  PubMed  Google Scholar 

  29. Love AC. Functional homology and homology of function: Biological concepts and philosophical consequences. Biology Philos. 2007;22:691–708.

    Article  Google Scholar 

  30. Aguilar-Martínez JA, Poza-Carrión C, Cubas P. Arabidopsis BRANCHED1 acts as an integrator of branching signals within axillary buds. Plant Cell. 2007;19(2):458–72.

    Article  PubMed  PubMed Central  Google Scholar 

  31. Rueda-Romero P, Barrero-Sicilia C, Gomez-Cadenas A, Carbonero P, Onate-Sanchez L. Arabidopsis thaliana DOF6 negatively affects germination in non-after-ripened seeds and interacts with TCP14. J Exp Bot. 2012;63(5):1937–49.

    Article  CAS  PubMed  Google Scholar 

  32. Weßling R, Epple P, Altmann S, He Y, Yang L, Henz SR, McDonald N, Wiley K, Bader KC, Gläßer C. Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life. Cell Host Microbe. 2014;16(3):364–75.

    Article  PubMed  PubMed Central  Google Scholar 

  33. Parapunova V, Busscher M, Busscher-Lange J, Lammers M, Karlova R, Bovy AG, Angenent GC, de Maagd RA. Identification, cloning and characterization of the tomato TCP transcription factor family. BMC Plant Biol. 2014;14(1):1–17.

    Article  Google Scholar 

  34. Wang F, Han T, Song Q, Ye W, Song X, Chu J, Li J, Chen ZJ. The rice circadian clock regulates tiller growth and panicle development through strigolactone signaling and sugar sensing. Plant Cell. 2020;32(10):3124–38.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Schommer C, Palatnik JF, Aggarwal P, Chételat A, Cubas P, Farmer EE, Nath U, Weigel D. Control of jasmonate biosynthesis and senescence by miR319 targets. PLoS Biol. 2008;6(9):e230.

    Article  PubMed  PubMed Central  Google Scholar 

  36. Cao J-F, Zhao B, Huang C-C, Chen Z-W, Zhao T, Liu H-R, Hu G-J, Shangguan X-X, Shan C-M, Wang L-J. The miR319-targeted GhTCP4 promotes the transition from cell elongation to wall thickening in cotton fiber. Mol Plant. 2020;13(7):1063–77.

    Article  CAS  PubMed  Google Scholar 

  37. Mao Y, Wu F, Yu X, Bai J, Zhong W, He Y. MicroRNA319a-targeted Brassica rapa ssp. pekinensis TCP genes modulate head shape in Chinese cabbage by differential cell division arrest in leaf regions. Plant Physiol. 2014;164(2):710–20.

    Article  CAS  PubMed  Google Scholar 

  38. Pruneda-Paz JL, Kay SA. An expanding universe of circadian networks in higher plants. Trends Plant Sci. 2010;15(5):259–65.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Giraud E, Ng S, Carrie C, Duncan O, Low J, Lee CP, Van Aken O, Millar AH, Murcha M, Whelan J. TCP transcription factors link the regulation of genes encoding mitochondrial proteins with the circadian clock in Arabidopsis thaliana. Plant Cell. 2010;22(12):3921–34.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Aguilar-Martínez JA, Sinha N. Analysis of the role of Arabidopsis class I TCP genes At TCP7, At TCP8, At TCP22, and At TCP23 in leaf development. Frontiers in plant science 2013, 4:406.

  41. Dhaka N, Bhardwaj V, Sharma MK, Sharma R. Evolving tale of TCPs: new paradigms and old lacunae. Front Plant Sci. 2017;8:479.

    Article  PubMed  PubMed Central  Google Scholar 

  42. Liu M-M, Wang M-M, Yang J, Wen J, Guo P-C, Wu Y-W, Ke Y-Z, Li P-F, Li J-N, Du H. Evolutionary and comparative expression analyses of TCP transcription factor gene family in land plants. Int J Mol Sci. 2019;20(14):3591.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Ding S, Cai Z, Du H, Wang H. Genome-wide analysis of TCP family genes in Zea mays L. identified a role for ZmTCP42 in drought tolerance. Int J Mol Sci. 2019;20(11):2762.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Tian C, Zhai L, Zhu W, Qi X, Yu Z, Wang H, Chen F, Wang L, Chen S. Characterization of the TCP gene family in Chrysanthemum nankingense and the role of CnTCP4 in cold tolerance. Plants. 2022;11(7):936.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Xu W, Wu D, Yang T, Sun C, Wang Z, Han B, Wu S, Yu A, Chapman MA, Muraguri S. Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean. Genome Biol. 2021;22:1–27.

    Article  Google Scholar 

  46. Reiser L, Bakker E, Subramaniam S, Chen X, Sawant S, Khosa K, Prithvi T, Berardini TZ. The Arabidopsis Information Resource in 2024. Genetics; 2024.

  47. Bailey TL, Johnson J, Grant CE, Noble WS. The MEME suite. Nucleic Acids Res. 2015;43(W1):W39–49.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Chen C, Wu Y, Li J, Wang X, Zeng Z, Xu J, Liu Y, Feng J, Chen H, He Y. TBtools-II: a one for all, all for one bioinformatics platform for biological big-data mining. Mol Plant 2023.

  49. Geourjon C, Deleage G. SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Bioinformatics. 1995;11(6):681–4.

    Article  CAS  Google Scholar 

  50. Bienert S, Waterhouse A, De Beer TA, Tauriello G, Studer G, Bordoli L, Schwede T. The SWISS-MODEL Repository—new features and functionality. Nucleic Acids Res. 2017;45(D1):D313–9.

    Article  CAS  PubMed  Google Scholar 

  51. Letunic I, Bork P. Interactive tree of life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021;49(W1):W293–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouzé P, Rombauts S. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 2002;30(1):325–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M. STRING 8—a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res. 2009;37(suppl1):D412–6.

    Article  CAS  PubMed  Google Scholar 

  54. Dai X, Zhuang Z, Zhao PX. psRNATarget: a plant small RNA target analysis server (2017 release). Nucleic Acids Res. 2018;46(W1):W49–54.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We appreciate the contributions and support from the lab members. We extend our sincere gratitude to the editor and reviewers for their thorough evaluation of this manuscript and for providing valuable feedback for its enhancement. We thank LetPub (www.letpub.com) for its linguistic assistance during the preparation of this manuscript.

Funding

This research was funded by the National Natural Science Foundation of China (31860389; 32060492), the Natural Science Foundation Project of the Inner Mongolia Autonomous Region (2022MS03057; 2023MS03032), the Basic Scientific Research Business Fee Items of Universities in Inner Mongolia Autonomous Region (GXKY23Z047) and the 2023 castor industry technology innovation Inner Mongolia Autonomous Region Engineering Research Center open project (MDK2023010; MDK2023081).

Author information

Author notes

  1. Yanxiao Li, Xingyang Liu and Xingyuan Xu contributed equally to this work.

Authors and Affiliations

  1. College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China

    Yanxiao Li, Xingyang Liu, Xingyuan Xu, Guishuang Zhu, Dianjun Xiang & Peng Liu

Authors
  1. Yanxiao Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xingyang Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xingyuan Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Guishuang Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Dianjun Xiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Peng Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

YL, XL and XX performed data collection, data processing and performed experiments. GZ participated in some of the experiments and data collection. DX and GZ participated in study design and interpretation of the results. XL, XX and PL assisted in the interpretation of the results and wrote and revised the manuscript. PL and DX are responsible for the completeness of the data and accuracy of the data analysis. All authors edited and approved the final manuscript.

Corresponding authors

Correspondence to Dianjun Xiang or Peng Liu.

Ethics declarations

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Material 1

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Li, Y., Liu, X., Xu, X. et al. Identification and characterization of the RcTCP gene family and its expression in response to abiotic stresses in castor bean. BMC Genomics 25, 670 (2024). https://doi.org/10.1186/s12864-024-10347-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1186/s12864-024-10347-6

Keywords

BMC Genomics

ISSN: 1471-2164

Contact us