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Genome-wide identification and expression characterization of the GH3 gene family of tea plant (Camellia sinensis)

BMC Genomics volume 25, Article number: 120 (2024) Cite this article

Abstract

To comprehensively understand the characteristics of the GH3 gene family in tea plants (Camellia sinensis), we identified 17 CsGH3 genes and analyzed their physicochemical properties, phylogenetic relationships, gene structures, promoters, and expression patterns in different tissues. The study showed that the 17 CsGH3 genes are distributed on 9 chromosomes, and based on evolutionary analysis, the CsGH3 members were divided into three subgroups. Gene duplication analysis revealed that segmental duplications have a significant impact on the amplification of CsGH3 genes. In addition, we identified and classified cis-elements in the CsGH3 gene promoters and detected elements related to plant hormone responses and non-biotic stress responses. Through expression pattern analysis, we observed tissue-specific expression of CsGH3.3 and CsGH3.10 in flower buds and roots. Moreover, based on predictive analysis of upstream regulatory transcription factors of CsGH3, we identified the potential transcriptional regulatory role of gibberellin response factor CsDELLA in CsGH3.14 and CsGH3.15. In this study, we found that CsGH3 genes are involved in a wide range of activities, such as growth and development, stress response, and transcription. This is the first report on CsGH3 genes and their potential roles in tea plants. In conclusion, these results provide a theoretical basis for elucidating the role of GH3 genes in the development of perennial woody plants and offer new insights into the synergistic effects of multiple hormones on plant growth and development in tea plants.

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Background

Tea plant (Camellia sinensis (L.) O. Kuntze) is an extremely important economic crop in the world, widely loved by consumers due to its good health benefits, such as weight loss, blood glucose reduction, antioxidant properties [1, 2], and alleviating hypercholesterolemia [3, 4]. Tea plant leaves are the main processing material [5], and the formation of plant leaf morphological characteristics is usually a very complex physiological and biochemical mechanism [6]. Understanding the mechanism and mechanism of tea leaf growth and development is of great significance for the picking, storage, and processing of tea leaves, and can also increase their economic value. Plant hormones play a vital role in the growth and development of plant leaves [7,8,9], including controlling the growth and differentiation of leaf primordia [10], controlling the differentiation of vasculature [11], cell division of leaves [12], and cell expansion of leaves [13].

Plant hormones include auxins, gibberellins, cytokinins, abscisic acid, ethylene, brassinosteroids, etc. Among them, auxin, as one of the important hormones in the plant life cycle, regulates cell division, elongation, and differentiation [14, 15]. It mainly controls plant growth and development by regulating the expression of the auxin-responsive gene families, including GH3, SAURs, AUX/IAA, and ARF [16, 17]. GH3 family proteins play important roles in the regulation of plant hormone homeostasis and signaling pathways [18]. The IAA-amido synthetase encoded by the GH3 gene family catalyzes the conjugation of auxin and the binding of free IAA to amino acids to maintain auxin homeostasis [19, 20]. GH3 proteins, as enzymes, are also involved in the synthesis of IAA and JA [21], and they possess amino acid synthetase activity. By regulating hormone and stress-related signaling pathways, they bind excess IAA, SA, and JAS to amino acids to maintain hormone homeostasis [22,23,24]. In addition, some GH3 genes are associated with developmental regulation and stress response. Overexpression of GH3 can enhance plant disease resistance by inhibiting cell wall loosening and reducing auxin levels [25]. GH3 can also reduce endogenous auxin levels to enhance plant drought tolerance [26] and regulate ABA levels to influence plant drought and cold resistance [27].

Currently, the GH3 family has been identified in many plant species. For example, 19 family members in Arabidopsis thaliana (L.) Heynh [28], 13 in rice (Oryza sativa) [29], 12 in maize [30], 15 in tomato (Solanum lycopersicum) [31], 2 in longan (Dimocarpus longan L.) [32], 9 in grape (Vitis vinifera L.) [33], 15 in apple (Malus × domestica) [24], and 11 in citrus (Citrus sinensis L.) [34]. Although GH3 has been identified in these species, little is known about the GH3 gene family in tea plants, and its evolution, function, and classification in tea plants have not been systematically studied. The identification of the GH3 gene family in tea plants will be important for the picking, storage, and processing of tea leaves. Therefore, based on the genomic data of tea plants, this study aims to identify the GH3 family members and analyze their chromosomal localization, collinearity analysis, evolutionary relationships, promoter cis-acting elements, codon preferences, etc. The GH3 gene family will be validated using qRT-PCR and yeast one-hybrid techniques. The results of this study will provide insights into the function of the GH3 gene family in tea plants and lay a theoretical foundation for further research on tea leaf growth and development.

Materials and methods

Plant materials

The tea plant variety selected for this experiment is ‘Fuding Dabai’ (Plants were cultivated in the greenhouse of Guizhou University East Campus in Guiyang at a room temperature of 25 °C and a light cycle of 16 h/20°C.). In May 2023, well-grown and healthy shoots with one bud and two leaves were harvested. After sampling, the plant materials were snap-frozen in liquid nitrogen and stored at -80℃ for future use. Each treatment was replicated three times for biological analysis.

Identification and characteristic analysis of CsGH3 gene family members

The complete genome sequence, proteome data, and genome annotation files of the ‘Tieguanyin’ tea plant were downloaded from the Tea Plant Information Archive (TPIA): A comprehensive knowledge database for tea plants (teaplants.cn) [35]. The hidden Markov model (PF03321) of GH3 from the Pfam database (http://pfam.Xfam.org/) was used to screen the protein sequences of the tea plant [36]. The amino acid sequences of GH3 gene family in Arabidopsis thaliana were used as a reference to retrieve homologous genes in the tea plant through BLAST in TBtools (https://github.com/CJ-Chen/TBtools) [37]. The results of the two search methods were combined, redundant sequences were removed, and the amino acid sequences of candidate members were submitted to the NCBI’s CDD database (https://www.ncbi.nlm.nih.gov/cdd/) to manually delete members with incomplete N/C terminals [38]. Finally, the GH3 gene family members of the ‘Tieguanyin’ tea plant were obtained.

The protein physicochemical properties of CsGH3 were analyzed using the online website ExPASy (https://web.expasy.org/protparam) [39], and subcellular localization prediction of CsGH3 was conducted using the online website wolf-psort (https://www.genscript.com/wolf-psort.html) [40].

Construction of the CsGH3 phylogenetic tree

The GH3 protein sequences of the tea plant, Arabidopsis thaliana, maize (Zea mays), and woodland strawberry (Fragaria vesca L.) were aligned using MEGA 7.0 [41]. The neighbor-joining method was used to construct the phylogenetic tree of the GH3, with a bootstrap value set to 1000 and other parameters set to default values [42].

Chromosomal localization and collinearity analysis of CsGH3 gene family

The chromosome location information of CsGH3 gene family members was extracted from the tea plant genome gff file using the TBtools [43] software, and visualizations were generated.

The TBtools software’s Advanced Circos function was utilized to perform intraspecific and interspecific collinearity analysis of the CsGH3 gene family.

Analysis of CsGH3 conserved motif, gene structure, promoter Cis-acting element, and codon preference

The full-length protein sequences of the identified CsGH3 genes were subjected to conservation sequence analysis, identification of important functional sites, and motif analysis using the online software MEME (https://meme-suite.org/meme/tools/meme) with default parameters [44]. The gene structures of CsGH3 were visualized and analyzed using the TBtools software. The upstream 2000 bp sequences of CsGH3 gene family members were extracted using the TBtools software [45, 46]. Plant CARE (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/) online software was employed to predict cis-acting elements in these sequences [47]. Codon W 1.4.4 software (https://codonw.sourceforge.net/culong.html#CodonW) were utilized to obtain the major parameters of codons and the relative synonymous codon usage (RSCU) for the tea plant GH3 gene family members.

Prediction and validation of upstream regulatory transcription factors of CsGH3

The upstream 2000 bp sequences of CsGH3 gene family members were submitted to the PlantTFDB database Regulation Prediction (http://plantregmap.gao-lab.org/regulation_prediction.php) [48]. The submission criteria were set as p-value ≤ e-7, with Arabidopsis thaliana as the reference species, to predict the upstream regulatory transcription factors of CsGH3. The tea plant gene sequence IDs were obtained by performing BLASTP in the TPIA database against Arabidopsis thaliana homologous genes.

Selected predicted transcription factors such as CsDELLA, CsSOC, CsBBR, and CsREM, together with CsGH3.14Pro and CsGH3.15Pro, were validated using yeast one-hybrid (Y1H) assay. Primers were designed based on the gene promoter and coding region sequences (Table S1). The Hind III and Xho I restriction sites were used for pAbAi vector digestion, while the EcoR I and BamH I restriction sites were used for pGADT7 vector digestion. All the required recombinant vectors were constructed using the ClonExpress II One Step Cloning Kit (Nanjing Novogene Bioinformatics Technology Co., Ltd.).

The recombinant vectors pAbAi-P53, pAbAi-CsGH3.14Pro, and pAbAi-CsGH3.15Pro were digested with BstB I and transformed into yeast Y1H competent cells using the PEG/LiAc method. To screen for the appropriate concentration of aureobasidin A (AbA) that inhibits the growth of Y1H(CsGH3.14Pro) and Y1H(CsGH3.15Pro), pAbAi-P53 was used as a positive control. The transformed cells were cultured on SD/-URA plates containing different concentrations of AbA (0, 50, 150, 300, 500 ng·mL− 1) for 3–5 days, and colony formation was observed. After determining the inhibitory concentration of AbA, the one-step yeast transformation kit (Wuhan Puner Biotechnology Co., Ltd.) was used to transform pGADT7 and the corresponding pGADT7-DELLA (TGY052266), pGADT7-SOC (TGY105712), pGADT7-BBR (TGY100531), pGADT7-REM (TGY021590) into Y1H(CsGH3.14Pro) and Y1H(CsGH3.15Pro) competent cells. This resulted in yeast recombinant strains, including Y1H(CsGH3.14Pro + pGADT7), Y1H(CsGH3.14Pro + CsDELLA), Y1H(CsGH3.14Pro + CsBBR), Y1H(CsGH3.14Pro + CsSOC), Y1H(CsGH3.15Pro + pGADT7), Y1H(CsGH3.15Pro + CsDELLA), Y1H(CsGH3.15Pro + CsSOC), and Y1H(CsGH3.15Pro + CsREM). The strains were cultured on SD/-Leu and SD/-Leu/AbA50 plates for 3–5 days. Y1H(CsGH3.14Pro + pGADT7) and Y1H(CsGH3.15Pro + pGADT7) strains were used as negative controls, and colony formation was observed.

Results

Identification and physicochemical analysis of the CsGH3 gene family

Through HMMER and BLAST searches, a total of 17 GH3 genes were identified in the ‘Tieguanyin’ tea plant genome. Based on their chromosomal distribution, they were named CsGH3.1-CsGH3.17. The molecular weights ranging from 53.7 kDa to 73.7 kDa. The isoelectric points (pI) of these gene family members were all below 7, indicating that they are acidic hydrophilic proteins. The hydrophilicities were all below 0, indicating a strong hydrophilic nature. The protein instability index values were all below 40, suggesting that they are stable proteins. Among them, CsGH3.8, CsGH3.11, CsGH3.12, and CsGH3.16 were identified as stable proteins, while the rest were classified as unstable proteins. Subcellular localization prediction results showed that the 17 GH3 proteins were distributed widely in the cell nucleus, cytoplasm, and chloroplasts (Table S2).

The 17 CsGH3 genes were distributed on 9 chromosomes (Chr 01, Chr 02, Chr 03, Chr 05, Chr 06, Chr 07, Chr 10, Chr 11, Chr 13). Among these chromosomes, Chr 03 had the highest number of CsGH3 genes with 4 members, including CsGH3.5, CsGH3.6, CsGH3.7, and CsGH3.8. Following that, Chr 02 had 3 members, while Chr 05, Chr 06, and Chr 07 each had 2 members. The remaining chromosomes each had only 1 CsGH3 gene (Fig. 1).

Fig. 1
figure 1

The distribution of 17 CsGH3 genes on the chromosomes. 0 Mb to 300 Mb represents the position range of gene family on a chromosome. This range is measured in physical distance on the chromosome and is typically expressed in megabase pairs (Mb). Specifically, 0 Mb represents the starting position of the gene, while 300 Mb represents the ending position

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Collinearity analysis of the CsGH3 gene family

Gene duplication events play an important role in the amplification of gene family members during plant evolution. Intraspecific collinearity analysis revealed the presence of 5 pairs of collinear genes in the ‘Tieguanyin’ tea plant (CsGH3.1-CsGH3.5, CsGH3.1-CsGH3.9, CsGH3.5-CsGH3.17, CsGH3.8-CsGH3.12, CsGH3.10-CsGH3.13), all of which were attributed to segmental duplication (Fig. 2A). No tandem duplication events were identified, indicating that segmental duplication was the primary mode of expansion for the CsGH3 gene family.

The collinearity analysis between ‘Tieguanyin’ and ‘Shuchazao’ and ‘Huangdan’ tea plant varieties revealed the presence of 22 pairs and 24 pairs of paralogous genes, respectively, indicating a high degree of conservation in the evolution of the CsGH3 gene family (Fig. 2B).

In the collinearity analysis between the ‘Tieguanyin’ tea plant and the Arabidopsis thaliana genome, it was found that there were 11 pairs of collinear GH3 genes between the two species (Fig. 2C, Table S4). It was observed that a single gene had multiple collinear counterparts, such as CsGH3.1-AtGH3.2/AtGH3.3, CsGH3.9-AtGH3.2/AtGH3.3, and CsGH3.13-AtGH3.5/AtGH3.6. This indicates the conservation of duplicated genes and the existence of ancient gene pairs before the divergence of Arabidopsis thaliana and the tea plant. The high conservation between GH3 proteins of different species suggests the functional similarity between the GH3 proteins of the tea plant and those of other species.

Fig. 2
figure 2

Collinearity Analysis of the Tea Plant GH3 Gene Family. (A) Chromosomal distribution of CsGH3 genes in tea plants. (B) Colinearity analysis of CsGH3 in three tea plant varieties, included Shuchazao (CSS), Tieguanyin (TGY), and Huangdan (HD). (C) Colinearity analysis of CsGH3 between Tieguanyin of tea plants and Arabidopsis

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GH3 evolutionary analysis in tea plants

In order to deeply understand the evolutionary patterns of GH3 in different species, the MEGAX software was used to perform multiple sequence alignment on 58 GH3 proteins from four species: tea plants (Camellia sinensis), Arabidopsis thaliana, maize (Zea mays), and woodland strawberry (Fragaria vesca) (Fig. 3). The results showed that all GH3 proteins were mainly classified into three groups: Group A, Group B, and Group C. Among them, Group B did not contain any distribution of CsGH3 members from tea plants but only included AtGH3 members from Arabidopsis. Group A contained 10 CsGH3 members, and Group C contained 7 members. In addition, the affinity between GH3 proteins of tea plants and woodland strawberry was the closest, indicating a certain functional similarity between GH3 proteins in tea plants and woodland strawberry.

Fig. 3
figure 3

Phylogenetic tree of the GH3 family proteins in Camellia sinensis, Fragaria vesca, Zea mays, and Arabidopsis thaliana

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Codon usage bias and selection pressure analysis in CsGH3 gene family

The analysis of codon usage bias in the CsGH3 gene family revealed that the GC content ranged from 0.417 to 0.519, with an average of 0.47. The frequency of G or C in the third codon position (GC3s) ranged from 0.343 to 0.606, with a mean of 0.49. The frequencies of A, T, G, and C in the third codon position (A3s, T3s, C3s, G3s) were 0.29, 0.34, 0.33, and 0.30, respectively.

The effective number of codons (ENc) reflects the degree of codon usage bias in genes, and it ranged from 21 to 60. The closer the ENc value is to 20, the stronger the codon preference. The mean ENc value for the CsGH3 gene family was 55.28. The codon adaptation index (CAI) is another important parameter for measuring codon usage bias, and the mean CAI value for the CsGH3 gene family was 0.21. Overall, the CsGH3 gene family showed a weak codon usage bias, and the gene expression level was relatively low.

The Ka/Ks ratio can be used to determine whether there is selection pressure on the protein-coding genes. It plays an important role in the evolutionary analysis of gene families. The Ka/Ks analysis was performed on CsGH3 genes (Table S3). The results showed that the Ka/Ks values for gene duplication events ranged from 0.079 to 0.140. All duplicated genes had Ka/Ks values less than 1, indicating that these genes evolved under purifying selection pressure.

Gene structure and conserved motif analysis of the tea plant GH3 gene family

The number of exons in CsGH3 gene members ranges from 2 to 4, with most members consisting of 3 exons. The analysis of conserved motifs showed that the number of conserved motifs in most CsGH3 gene members was consistent (Fig. 4). CsGH3.4 only had 6 conserved motifs, lacking motifs 10, 9, 8, and 5. CsGH3.2 and CsGH3.3 contained 9 conserved motifs, including motif 5.

Fig. 4
figure 4

Phylogenetic tree, core motif, and protein domain of tea plants GH3 proteins. The scales in motif and domain analyses represent the relative positions of specific motifs or different domains, respectively

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Analysis of Cis-acting elements in the promoter region of the CsGH3 gene family

The TBtools software was used to extract the 2000 bp upstream gene sequence of the CsGH3 gene as the promoter sequence of CsGH3. The results showed that the cis-acting elements of the 17 CsGH3 members can be divided into five categories: phytohormone-responsive elements, light-responsive elements, plant growth and development-related elements, abiotic stress-responsive elements, and transcription factor recognition and binding sites (Fig. 5). Among them, light-responsive elements accounted for the highest proportion, followed by phytohormone-responsive elements. Phytohormone-responsive elements include auxin-responsive elements (AuxRE, TGA-box) and gibberellin-responsive elements (GARE-motif, P-box). The promoter regions of CsGH3.1 and CsGH3.2 respectively contain 7 and 13 abscisic acid responsiveness elements (ABRE), suggesting their main involvement in ABA response. In addition, anaerobic induction responsive elements are an important part of the stress-responsive elements, and CsGH3.9, CsGH3.10, CsGH3.11, and CsGH3.16 contain a higher number of anaerobic induction responsive elements, suggesting their important roles in plant anaerobic response. In conclusion, CsGH3 not only performs normal transcription activities, but also participates in plant light response, hormone response, stress response, and growth and development activities.

Fig. 5
figure 5

Analysis of cis-acting elements in the promoter region of the CsGH3 gene family. The dots, from small to large and from blue to red, represent increasing quantity

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qRT-PCR analysis of the CsGH3 gene family

The qRT-PCR analysis was performed to investigate the expression patterns of the CsGH3 gene family. Total RNA was extracted from various tissues including leaves, stems, roots, and flowers. Reverse transcription was carried out to synthesize cDNA, and qPCR was conducted to quantify the expression levels of the CsGH3 genes. The results showed differential expression patterns among the CsGH3 gene family members in different tissues (Fig. 6). Most GH3 genes are expressed in different tissues, while CsGH3.15 is expressed at a low level in various tissue parts. Among the gene family members, four genes (CsGH3.3, CsGH3.10, CsGH3.5, CsGH3.16) are highly expressed in roots, suggesting their potentially important role in tea tree roots. CsGH3.3 and CsGH3.10 are expressed higher in flower buds compared to other tissues, indicating their involvement in flower bud differentiation.

Fig. 6
figure 6

qRT-PCR analysis of the CsGH3 gene family. The dots, from small to large and from blue to red, represent increasing abundance

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Prediction and validation of upstream regulatory factors of the CsGH3 gene family

Using the model plant Arabidopsis thaliana as a reference, transcription factors that potentially bind to the promoter regions of the CsGH3 gene family were predicted through the PlantTFDB website, followed by homology comparison in the tea plant. A total of 32 transcription factors were identified, mainly including AP2/ERF, DOF, ZIP, and other transcription factors (Fig. 7A, Tables S6 and S8).

The predicted results of transcriptional regulation were validated in vitro. Yeast one-hybrid (Y1H) assays showed that both pAbAi + CsGH3.14Pro and pAbAi + CsGH3.15Pro strains could grow normally on SD/-URA medium. By screening with different concentrations of AbA, it was found that both pAbAi + CsGH3.14Pro and pAbAi + CsGH3.15Pro strains stopped growing at a concentration of 50 ng·mL− 1 AbA. Therefore, the self-activation of CsGH3.14Pro and CsGH3.15Pro occurred at a concentration of 50 ng·mL− 1 AbA (Fig. 7B). Furthermore, the predicted CsDELLA (CsGRAS), CsSOC, CsBBR, and CsREM transcription factors were tested for their interaction with CsGH3.14Pro and CsGH3.15Pro in the yeast one-hybrid assay. The results showed that all yeast strains co-transformed with the bait and pGADT7 plasmids could grow normally on the SD/-Leu medium. On SD/-Leu medium supplemented with 50 ng·mL− 1 AbA, the CsGH3.14Pro + CsDELLA and CsGH3.15Pro + CsDELLA strains could grow, indicating the interaction between the CsDELLA transcription factor and CsGH3.14Pro, CsGH3.15Pro promoters.

Fig. 7
figure 7

Prediction (A) and validation (B) of upstream regulatory factors of the CsGH3 gene family

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Discussion

The GH3 gene family was first discovered and named by Gretchen Hagen in soybean (Glycine max). Currently, there have been reports of the genome-wide identification of the GH3 gene family, not only in model plants such as Arabidopsis [28] and tobacco, but also in various other plant species, including cucumber [49], cabbage [50], walnut [51], and kiwifruit [52]. Indole-3-acetic acid (IAA) is of crucial importance for plant growth and development. Research has shown that GH3 proteins conjugate IAA with amino acids such as leucine, alanine, and phenylalanine to form conjugated IAA, serving as a storage form of IAA [19, 53]. This process is reversible and is a vital prerequisite for maintaining the homeostasis of plant growth hormone [54,55,56]. GH3 family proteins can catalyze the conjugation of jasmonic acid, salicylic acid, and other small molecule substrates (such as amino acids) to form conjugated hormones, thereby participating in hormone regulation in plants. Moreover, GH3 proteins are involved in plant stress responses. Silencing the expression of six GH3 genes in apple has been found to contribute to better drought tolerance in transgenic plants, enhancing their adaptability to prolonged drought conditions [57]. GH3 genes play a role not only in plant growth and development processes but also in influencing plant resistance. Therefore, the study of GH3 genes holds significant importance in plant research. In this study, using bioinformatics methods, 17 GH3 genes were identified in ‘Tieguanyin’ tea plants and named as CsGH3.1-CsGH3.17. They all had isoelectric points below 7. Bioinformatics analysis indicated that CsGH3 genes exhibited high similarities in terms of amino acid sequences, gene structures, and conserved motifs, suggesting that although there are certain differences among the members of the GH3 gene family, they remain relatively conserved during evolutionary processes. This implies the presence of both functional similarity and differentiation among CsGH3 genes, indicating their synergistic roles in regulating plant growth and development.

Based on protein sequence homology and substrate specificity differences, GH3 members in plants can be classified into three groups, mainly catalyzing the conjugation of JA, IAA, and SA with amino acids. The evolutionary tree results show that Group C contains AtGH3.10/DWARF IN LIGHT2 (DFL2) and AtGH3.11/AtJAR1. These two genes have been proven to be mainly involved in the biosynthesis of JA-amino acids [21, 58, 59]. The functionalities of Group B members have not been fully confirmed, and they have only been found in Arabidopsis and cruciferous plants [60,61,62]. Only AtGH3.12 has been discovered to participate in the SA signaling pathway. In Group B, genes play important roles in IAA adenylation or amino acid conjugation reactions [19, 63]. Studies have found that members of Group A in Arabidopsis have undergone gene duplication events [61]. These newly duplicated members are mostly redundant in Arabidopsis. Based on the distribution of GH3 members in different evolutionary branches and collinearity analysis in tea plants, GH3 members in tea plants are also enriched in Group A. Gene fragment duplication events have occurred four times in Group A: CsGH3.1-CsGH3.5, CsGH3.1-CsGH3.9, CsGH3.5-CsGH3.17, CsGH3.10-CsGH3.13. Collinearity analysis between Arabidopsis and ‘Tieguanyin’ tea plants shows that gene family expansion has led to more collinear genes between Arabidopsis and tea plants. Based on the results of intra-species and inter-species collinearity, it is inferred that the gene duplication events of CsGH3.5 and CsGH3.1 occurred earlier and underwent more evolution, resulting in different collinear genes compared to Arabidopsis. After continuous evolution and selection in tea plants, CsGH3.5 and CsGH3.1 were duplicated into CsGH3.17 and CsGH3.9, respectively. Therefore, the collinear genes of CsGH3.1-CsGH3.9 and CsGH3.5-CsGH3.17 are consistent with Arabidopsis.

Through the analysis of gene promoter regions, it is beneficial to understand and predict the potential cis-acting elements that they may contain, which is of great significance for further research on gene function. In this study, the upstream 2000 bp sequence of CsGH3 was analyzed, and it was found that the promoter region of the CsGH3 gene contains various elements related to hormone response and light response. Light is one of the necessary conditions for plant growth and development, and as a key factor in auxin response, auxin-responsive elements (AuxRE, TGA-box) were found in the promoter regions of genes CsGH3.1, CsGH3.4, CsGH3.6, CsGH3.7, CsGH3.11, and CsGH3.16. SA response elements were only found in CsGH3.12, and CsGH3.11 only contained six elements related to ethylene response. Additionally, a significant number of ABA response elements (ABRE) were found in the upstream regions of most members (11 genes). This suggests that the function of the CsGH3 gene family is primarily involved in the JA, SA, ABA, and ethylene signaling pathways. Auxin is crucial for the morphogenesis of plants, including nutrient growth, root differentiation, vascular tissue differentiation, axillary bud differentiation, and flower organ formation [64]. The roles of GH3 vary in different species, growth stages, and tissue types. In Arabidopsis, AtGH3.3 and AtGH3.5 played important roles in root development [28, 65]. Similar to these, CsGH3.3, CsGH3.5, CsGH3.10, and CsGH3.16 in tea plants are mainly expressed in roots, suggesting the involvement of GH3 in regulating root development in tea plants. Additionally, CsGH3.3 and CsGH3.10 are highly expressed in flower tissues of tea plants. In rice, OsGH3.1, OsGH3.4, OsGH3.5, OsGH3.8, and OsGH3.11 exhibited the highest expression in flowers [29]. Moreover, as a target of the MADS-box, OsGH3.8 is involved in the differentiation of floral organs in rice [66]. In chickpeas, CaGH3.10 played an important role in regulating the steady state of auxin during early flower organ development [67]. These results suggested that CsGH3 played an important role in both the growth and reproductive development of tea plants.

Through previous predictions, it was found that the promoter region of the CsGH3 gene is enriched with several transcription factors. AP2/ERF transcription factors have been proven to participate in plant responses to abiotic stress [68]. Additionally, studies have shown that members of the ERF subfamily can bind to ethylene-responsive elements (EREs) in gene promoter regions, mediating ethylene biosynthesis [69]. SOC transcription factors, as important members of the MADS-box family, were widely involved in flower organ formation, development, and flowering time regulation [70]. Therefore, we speculated that the formation of the IAA-conjugate mediated by CsGH3 is likely closely related to ethylene biosynthesis and may also be involved in the growth and development of flower organs. The expression of GH3 genes is not only influenced by hormones and various biotic and abiotic stresses but also regulated by upstream transcription factors. Transcription factors such as ARF [71], bZIP [72], and R2R3-MYB [73] have been proven to regulate the expression of GH3 genes by binding to cis-acting elements in the GH3 gene promoter region. In this study, the potential regulatory role of the transcription factor CsDELLA on CsGH3.14 and CsGH3.15 was predicted and verified through yeast one-hybrid assays. DELLA proteins are essential components in the GA signaling pathway, and research has shown that environmental and hormonal signals, such as auxin and abscisic acid, can regulate plant growth by affecting the stability of DELLA proteins [74, 75]. Growth hormone enhances the instability of DELLA proteins, leading to the promotion of root growth. In poplar, AUXIN RESPONSE FACTOR 7 (ARF7) forms a ternary complex with Aux/INDOLE-3-ACETIC ACID 9 (IAA9) and DELLA, mediating cross-talk between the auxin and GA signaling pathways during cambium development [76]. In the growth and development processes of plants, multiple hormone signals and transcription factors form a complex and precise regulatory network, orchestrating various life processes in plants. This experiment, for the first time, identified the transcriptional regulation of key IAA metabolism gene CsGH3 by the GA signaling-related factor CsDELLA in tea plants, providing new insights into the interplay between GA and auxin signaling in tea plants.

Conclusion

It was deduced that the GH3 gene family plays important roles in plants. They are involved in hormone regulation, stress responses, and growth and development activities. Different GH3 members exhibit regulatory mechanisms, with their expression being regulated by various hormones and external environmental factors. The promoter regions of CsGH3 genes contain multiple cis-acting elements that can be regulated by transcription factors. In tea plants, CsGH3 genes have undergone evolution and duplication events, leading to diverse gene compositions and regulatory patterns. Further research on the functions and regulatory mechanisms of the GH3 gene family is of great significance in unraveling the molecular mechanisms underlying plant growth, development, and responses to stress.

Data availability

The datasets analysed and all the accession numbers of the sequences during the current study are provided in supplementary Tables S1 (Primer sequences used in PCR), S2 (Physicochemical properties of CsGH3), S3 (Evolutionary analysis of the CsGH3 gene family), S4 (Co-linear genes of GH3 in tea plants and Arabidopsis), S5 (Physical and chemical properties of the CsGH3 gene family), S6(Binding Site Prediction Results), S7 (Relative expression for CsGH3 in flower bud, flower,young leaf,old leaf, stem, and rootin Camellia sinensis using qRT-PCR), and S8 (Prediction results of screened binding siteswhich can also be downloaded fromTea Plant Information Archive (http://tpia.teaplants.cn/index.html) and Arabidopsis database (http://www.arabidopsis.org/).

References

  1. Cao Y, Zhao M, Zhao T, Cui C, Zhao Q, Feng Y. Functional Components and activities of different dark tea extracts. Food Sci. 2017;38(18):54–9. (In Chinese).

    Google Scholar 

  2. Lv H-p, Zhang Y, Shi J, Lin Z. Phytochemical profiles and antioxidant activities of Chinese dark teas obtained by different processing technologies. Food Res Int. 2017;100:486–93.

    Article  PubMed  CAS  Google Scholar 

  3. Mo L, Zeng Z, Li Y, Li D, Yan C-y, Xiao S, Huang Y. -h. animal study of the anti-diarrhea effect and microbial diversity of dark tea produced by the Yao population of Guangxi. Food Funct. 2019;10(4):1999–2009.

    Article  PubMed  CAS  Google Scholar 

  4. Zhang L, Zhang Z, Zhou Y, Ling T, Wan X. Chinese dark teas: Postfermentation, chemistry and biological activities. Food Res Int. 2013;53(2):600–7.

    Article  CAS  Google Scholar 

  5. Li H, Liu ZW, Wu ZJ, Wang YX, Teng RM, Zhuang J. Differentially expressed protein and gene analysis revealed the effects of temperature on changes in ascorbic acid metabolism in harvested tea leaves. Hortic Res. 2018;5:13.

    Article  PubMed  PubMed Central  Google Scholar 

  6. Gonzalez N, Vanhaeren H, Inze D. Leaf size control: complex coordination of cell division and expansion. Trends Plant Sci. 2012;17(6):332–40.

    Article  PubMed  CAS  Google Scholar 

  7. Rosquete MR, Barbez E, Kleine-Vehn J. Cellular Auxin Homeostasis: gatekeeping is housekeeping. Mol Plant. 2012;5(4):772–86.

    Article  PubMed  Google Scholar 

  8. Luo J, Zhou JJ, Zhang JZ. Aux/IAA Gene Family in plants: molecular structure, regulation, and function. Int J Mol Sci. 2018;19(1):17.

    Article  Google Scholar 

  9. Kunkel BN, Johnson JMB. Auxin Plays multiple roles during Plant-Pathogen interactions. Cold Spring Harbor Perspect Biol. 2021;13(9):11.

    Article  Google Scholar 

  10. Reinhardt D, Mandel T, Kuhlemeier C. Auxin regulates the initiation and radial position of plant lateral organs. Plant Cell. 2000;12(4):507–18.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  11. Sieburth LE. Auxin is required for leaf vein pattern in Arabidopsis. Plant Physiol. 1999;121(4):1179–90.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  12. Ljung K, Bhalerao RP, Sandberg G. Sites and homeostatic control of auxin biosynthesis in Arabidopsis during vegetative growth. Plant J. 2001;28(4):465–74.

    Article  PubMed  CAS  Google Scholar 

  13. Braun N, Wyrzykowska J, Muller P, David K, Couch D, Perrot-Rechenmann C, Fleming AJ. Conditional repression of AUXIN BINDING PROTEIN1 reveals that it coordinates Cell Division and Cell Expansion during Postembryonic shoot Development in Arabidopsis and Tobacco. Plant Cell. 2008;20(10):2746–62.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  14. AW W. Auxin: regulation, action, and interaction. Ann Bot. 2005;95(5):707–35.

    Article  Google Scholar 

  15. Teale WD, Paponov IA, Palme K. Auxin in action: signalling, transport and the control of plant growth and development. Nat Rev Mol Cell Biol. 2006;7(11):847–59.

    Article  PubMed  CAS  Google Scholar 

  16. Abel S, Theologis A. Early genes and auxin action. Plant Physiol. 1996;111(1):9–17.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  17. Chen YZ, Hao X, Cao J. Small auxin upregulated RNA (SAUR) gene family in maize: identification, evolution, and its phylogenetic comparison with Arabidopsis, rice, and sorghum. J Integr Plant Biol. 2014;56(2):133–50.

    Article  PubMed  CAS  Google Scholar 

  18. Chapman EJ, Estelle M. Mechanism of Auxin-regulated gene expression in plants. Annu Rev Genet. 2009;43(1):265–85.

    Article  PubMed  CAS  Google Scholar 

  19. Staswick PE, Serban B, Rowe M, Tiryaki I, Maldonado MT, Maldonado MC, Suza W. Characterization of an Arabidopsis enzyme family that conjugates amino acids to indole-3-acetic acid. Plant Cell. 2005;17(2):616–27.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  20. Feng SG, Yue RQ, Tao S, Yang YJ, Zhang L, Xu MF, Wang HZ, Shen CJ. Genome-wide identification, expression analysis of auxin-responsive GH3 family genes in maize (Zea mays L.) under abiotic stresses. J Integr Plant Biol. 2015;57(9):783–95.

    Article  PubMed  CAS  Google Scholar 

  21. Delfin JC, Kanno Y, Seo M, Kitaoka N, Matsuura H, Tohge T, Shimizu T. AtGH3.10 is another jasmonic acid-amido synthetase in Arabidopsis thaliana. Plant J. 2022;110(4):1082–96.

    Article  PubMed  CAS  Google Scholar 

  22. Casanova-Saez R, Voss U. Auxin Metabolism controls Developmental decisions in land plants. Trends Plant Sci. 2019;24(8):741–54.

    Article  PubMed  CAS  Google Scholar 

  23. Westfall CS, Zubieta C, Herrmann J, Kapp U, Nanao MH, Jez JM. Structural basis for Prereceptor Modulation of Plant hormones by GH3 proteins. Science. 2012;336(6089):1708–11.

    Article  PubMed  CAS  Google Scholar 

  24. Yuan HZ, Zhao K, Lei HJ, Shen XJ, Liu Y, Liao X, Li TH. Genome-wide analysis of the GH3 family in apple (Malus x Domestica). BMC Genomics. 2013;14:14.

    Article  Google Scholar 

  25. Domingo C, Andres F, Tharreau D, Iglesias DJ, Talon M. Constitutive expression of OsGH3.1 reduces Auxin Content and enhances Defense Response and Resistance to a Fungal Pathogen in Rice. Mol Plant-Microbe Interact. 2009;22(2):201–10.

    Article  PubMed  CAS  Google Scholar 

  26. Zhang SW, Li CH, Cao J, Zhang YC, Zhang SQ, Xia YF, Sun DY, Sun Y. Altered Architecture and enhanced Drought Tolerance in Rice via the down-regulation of Indole-3-Acetic acid by TLD1/OsGH3.13 activation. Plant Physiol. 2009;151(4):1889–901.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  27. Du H, Wu N, Fu J, Wang SP, Li XH, Xiao JH, Xiong LZ. A GH3 family member, OsGH3-2, modulates auxin and abscisic acid levels and differentially affects drought and cold tolerance in rice. J Exp Bot. 2012;63(18):6467–80.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  28. Takase T, Nakazawa M, Ishikawa A, Kawashima M, Ichikawa T, Takahashi N, Shimada H, Manabe K, Matsui M. ydk1-D, an auxin-responsive GH3 mutant that is involved in hypocotyl and root elongation. Plant J. 2004;37(4):471–83.

    Article  PubMed  CAS  Google Scholar 

  29. Jain M, Kaur N, Tyagi AK, Khurana JP. The auxin-responsive GH3 gene family in rice (Oryza sativa). Funct Integr Genom. 2006;6(1):36–46.

    Article  CAS  Google Scholar 

  30. Zhang DF, Zhang N, Zhong T, Wang C, Xu ML, Ye JR. Identification and characterization of the GH3 gene family in maize. J Integr Agric. 2016;15(2):249–61.

    Article  CAS  Google Scholar 

  31. Kumar R, Agarwal P, Tyagi AK, Sharma AK. Genome-wide investigation and expression analysis suggest diverse roles of auxin-responsive GH3 genes during development and response to different stimuli in tomato (Solanum lycopersicum). Mol Genet Genomics. 2012;287(3):221–35.

    Article  PubMed  CAS  Google Scholar 

  32. Kuang JF, Zhang Y, Chen JY, Chen QJ, Jiang YM, Lin HT, Xu SJ, Lu WJ. Two GH3 genes from longan are differentially regulated during fruit growth and development. Gene. 2011;485(1):1–6.

    Article  PubMed  CAS  Google Scholar 

  33. Bottcher C, Boss PK, Davies C. Acyl substrate preferences of an IAA-amido synthetase account for variations in grape (Vitis vinifera L.) berry ripening caused by different auxinic compounds indicating the importance of auxin conjugation in plant development. J Exp Bot. 2011;62(12):4267–80.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  34. Xie RJ, Pang SP, Ma YY, Deng L, He SL, Yi SL, Lv Q, Zheng YQ. The ARF, AUX/IAA and GH3 gene families in citrus: genome-wide identification and expression analysis during fruitlet drop from abscission zone A. Mol Genet Genomics. 2015;290(6):2089–105.

    Article  PubMed  CAS  Google Scholar 

  35. Xia EH, Li FD, Tong W, Li PH, Wu Q, Zhao HJ, Ge RH, Li RP, Li YY, Zhang ZZ, et al. Tea Plant Information Archive: a comprehensive genomics and bioinformatics platform for tea plant. Plant Biotechnol J. 2019;17(10):1938–53.

    Article  PubMed  PubMed Central  Google Scholar 

  36. Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, Sonnhammer ELL, Tosatto SCE, Paladin L, Raj S, Richardson LJ et al. Pfam: The protein families database in 2021. Nucleic Acids Res. 2021;49(D1):D412-D419.

  37. Chen CJ, Wu Y, Li JW, Wang X, Zeng ZH, Xu J, Liu YL, Feng JT, Chen H, He YH, et al. TBtools-II: a one for all, all for onebioinformatics platform for biological big-data mining. Mol Plant. 2023;16(11):1733–42.

    Article  PubMed  CAS  Google Scholar 

  38. Marchler-Bauer A, Bo Y, Han LY, He JE, Lanczycki CJ, Lu SN, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR, et al. CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res. 2017;45(D1):D200–3.

    Article  PubMed  CAS  Google Scholar 

  39. Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A. ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 2003;31(13):3784–8.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  40. Horton P, Park K-J, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K. WoLF PSORT: protein localization predictor. Nucleic Acids Res. 2007;35:W585–587.

    Article  PubMed  PubMed Central  Google Scholar 

  41. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for bigger datasets. Mol Biol Evol. 2016;33(7):1870–4.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  42. Duan L, Liu R. Genome-wide identification and analysis of YABBY gene family of Nicotiana tabacum. J Mountain Agric Biology. 2023;42(04):38–44. (In Chinese).

    Google Scholar 

  43. Chen CJ, Chen H, Zhang Y, Thomas HR, Frank MH, He YH, Xia R. TBtools: an integrative Toolkit developed for interactive analyses of big Biological Data. Mol Plant. 2020;13(8):1194–202.

    Article  PubMed  CAS  Google Scholar 

  44. Bailey TL, Johnson J, Grant CE, Noble WS. The MEME suite. Nucleic Acids Res. 2015;43(W1):W39–W49.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  45. Wang Q, Zhao XB, Sun QX, Mou YF, Wang J, Yan CX, Yuan CL, Li CJ, Shan SH. Genome-wide identification of the LRR-RLK gene family in peanut and functional characterization of AhLRR-RLK265 in salt and drought stresses. Int J Biol Macromol. 2024;254:16.

    Article  Google Scholar 

  46. Zhang ZJ, Yu PY, Bing H, Ma RF, Vinod KK, Ramakrishnan M. Genome-wide identification and expression characterization of the DoG gene family of moso bamboo (Phyllostachys edulis). BMC Genomics. 2022;23(1):22.

    Article  Google Scholar 

  47. Lescot M, Dehais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouze 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  PubMed  PubMed Central  CAS  Google Scholar 

  48. Tian F, Yang DC, Meng YQ, Jin JP, Gao G. PlantRegMap: charting functional regulatory maps in plants. Nucleic Acids Res. 2020;48(D1):D1104–13.

    PubMed  CAS  Google Scholar 

  49. Chen S, Zhong KQ, Li YY, Bai CH, Xue ZZ, Wu YF. Evolutionary analysis of the melon (Cucumis melo L.) GH3 gene family and identification of GH3 genes related to Fruit Growth and Development. Plants-Basel. 2023;12(6):16.

    Google Scholar 

  50. Jeong J, Park S, Im JH, Yi H. Genome-wide identification of GH3 genes in Brassica oleracea and identification of a promoter region for anther-specific expression of a GH3 gene. BMC Genomics. 2021;22(1):14.

    Article  Google Scholar 

  51. Xu DB, Yang Y, Tao SC, Wang YL, Yuan HW, Sharma A, Wang XF, Shen CJ, Yan DL, Zheng BS. Identification and expression analysis of auxin-responsive GH3 family genes in Chinese hickory (Carya cathayensis) during grafting. Mol Biol Rep. 2020;47(6):4495–506.

    Article  PubMed  CAS  Google Scholar 

  52. Gan ZY, Fei LY, Shan N, Fu YQ, Chen JY. Identification and expression analysis of Gretchen Hagen 3 (GH3) in Kiwifruit (Actinidia chinensis) during postharvest process. Plants-Basel. 2019;8(11):13.

    Google Scholar 

  53. Mellor N, Band LR, Pencik A, Novak O, Rashed A, Holman T, Wilson MH, Voss U, Bishopp A, King JR, et al. Dynamic regulation of auxin oxidase and conjugating enzymes AtDAO1 and GH3 modulates auxin homeostasis. PNAS. 2016;113(39):11022–7.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  54. Brunoni F, Collani S, Casanova-Saez R, Simura J, Karady M, Schmid M, Ljung K, Bellini C. Conifers exhibit a characteristic inactivation of auxin to maintain tissue homeostasis. New Phytol. 2020;226(6):1753–65.

    Article  PubMed  CAS  Google Scholar 

  55. Kowalczyk M, Sandberg G. Quantitative analysis of indole-3-acetic acid metabolites in Arabidopsis. Plant Physiol. 2001;127(4):1845–53.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  56. LeClere S, Tellez R, Rampey RA, Matsuda SPT, Bartel B. Characterization of a family of IAA-amino acid conjugate hydrolases from Arabidopsis. J Biol Chem. 2002;277(23):20446–52.

    Article  PubMed  CAS  Google Scholar 

  57. Jiang LJ, Shen WY, Liu C, Tahir MM, Li XW, Zhou SX, Ma FW, Guan QM. Engineering drought-tolerant apple by knocking down six GH3 genes and potential application of transgenic apple as a rootstock. Hortic Res. 2022;9:12.

    Article  Google Scholar 

  58. Howlader P, Bose SK, Jia XC, Zhang CL, Wang WX, Yin H. Oligogalacturonides induce resistance in Arabidopsis thaliana by triggering salicylic acid and jasmonic acid pathways against pst DC3000. Int J Biol Macromol. 2020;164:4054–64.

    Article  PubMed  CAS  Google Scholar 

  59. Meesters C, Monig T, Oeljeklaus J, Krahn D, Westfall CS, Hause B, Jez JM, Kaiser M, Kombrink E. A chemical inhibitor of jasmonate signaling targets JAR1 in Arabidopsis thaliana. Nat Chem Biol. 2014;10(10):830–.

    Article  PubMed  CAS  Google Scholar 

  60. Terol J, Domingo C, Talon M. The GH3 family in plants: genome wide analysis in rice and evolutionary history based on EST analysis. Gene. 2006;371(2):279–90.

    Article  PubMed  CAS  Google Scholar 

  61. Okrent RA, Wildermuth MC. Evolutionary history of the GH3 family of acyl adenylases in rosids. Plant MolBiol. 2011;76(6):489–505.

    CAS  Google Scholar 

  62. Zhao YD. Essential roles of local Auxin Biosynthesis in Plant Development and in adaptation to environmental changes. Annu Rev Plant Biol. 2018;69:417–35.

    Article  PubMed  CAS  Google Scholar 

  63. Staswick PE, Tiryaki I, Rowe ML. Jasmonate response locus JAR1 and several related Arabidopsis genes encode enzymes of the firefly luciferase superfamily that show activity on jasmonic, salicylic, and indole-3-acetic acids in an assay for adenylation. Plant Cell. 2002;14(6):1405–15.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  64. Zhao YD. Auxin Biosynthesis and its role in Plant Development. Annu Rev Plant Biol. 2010;61:49–64.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  65. Nakazawa M, Yabe N, Ichikawa T, Yamamoto YY, Yoshizumi T, Hasunuma K, Matsui M. DFL1, an auxin-responsive GH3 gene homologue, negatively regulates shoot cell elongation and lateral root formation, and positively regulates the light response of hypocotyl length. Plant J. 2001;25(2):213–21.

    PubMed  CAS  Google Scholar 

  66. Prasad K, Parameswaran S, Vijayraghavan U. OsMADS1, a rice MADS-box factor, controls differentiation of specific cell types in the lemma and palea and is an early-acting regulator of inner floral organs. Plant J. 2005;43(6):915–28.

    Article  PubMed  CAS  Google Scholar 

  67. Singh VK, Jain M, Garg R. Genome-wide analysis and expression profiling suggest diverse roles of GH3 genes during development and abiotic stress responses in legumes. Front Plant Sci. 2015;5:13.

    Article  Google Scholar 

  68. Gehan MA, Park S, Gilmour SJ, An CF, Lee CM, Thomashow MF. Natural variation in the C-repeat binding factor cold response pathway correlates with local adaptation of Arabidopsis ecotypes. Plant J. 2015;84(4):682–93.

    Article  PubMed  CAS  Google Scholar 

  69. Wu Y, Li X, Zhang JN, Zhao HQ, Tan SL, Xu WH, Pan JQ, Yang F, Pi EX. ERF subfamily transcription factors and their function in plant responses to abiotic stresses. Front Plant Sci. 2022;13:25.

    Article  Google Scholar 

  70. Harig L, Beinecke FA, Oltmanns J, Muth J, Müller O, Rüping B, Twyman RM, Fischer R, Prüfer D, Noll GA. Proteins from the FLOWERING LOCUS T-like subclade of the PEBP family act antagonistically to regulate floral initiation in tobacco. Plant J. 2012;72(6):908–21.

    Article  PubMed  CAS  Google Scholar 

  71. Tian C-E, Muto H, Higuchi K, Matamura T, Tatematsu K, Koshiba T, Yamamoto KT. Disruption and overexpression of auxin response factor 8 gene of Arabidopsis affect hypocotyl elongation and root growth habit, indicating its possible involvement in auxin homeostasis in light condition. Plant J. 2004;40(3):333–43.

    Article  PubMed  CAS  Google Scholar 

  72. Heinekamp T, Strathmann A, Kuhlmann M, Froissard M, Muller A, Perrot-Rechenmann C, Droge-Laser W. The tobacco bZIP transcription factor BZI-1 binds the GH3 promoter in vivo and modulates auxin-induced transcription. Plant J. 2004;38(2):298–309.

    Article  PubMed  CAS  Google Scholar 

  73. Seo PJ, Park C-M. Auxin homeostasis during lateral root development under drought condition. Plant Signal Behav. 2009;4(10):1002–4.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  74. Achard P, Cheng H, De Grauwe L, Decat J, Schoutteten H, Moritz T, Van Der Straeten D, Peng J, Harberd NP. Integration of plant responses to environmentally activated phytohormonal signals. Science. 2006;311(5757):91–4.

    Article  PubMed  CAS  Google Scholar 

  75. Fu X, Harberd NP. Auxin promotes Arabidopsis root growth by modulating gibberellin response. Nature. 2003;421(6924):740–3.

    Article  PubMed  CAS  Google Scholar 

  76. Hu J, Su HL, Cao H, Wei HB, Fu XK, Jiang XM, Song Q, He XH, Xu CZ, Luo KM. AUXIN RESPONSE FACTOR7 integrates gibberellin and auxin signaling via interactions between DELLA and AUX/IAA proteins to regulate cambial activity in poplar. Plant Cell. 2022;34(7):2688–707.

    Article  PubMed  PubMed Central  Google Scholar 

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Funding

This work was supported by the Science and Technology Project of Qiannan Science and Technology Bureau (2022qnkh09), the Education Quality Improvement Project of Qiannan Normal University for Nationalities (2021xjg018, 2022xjg038), the High-level Talent Research Project of Qiannan Normal University for Nationalities (2021qnsyrc07), the Innovation and Entrepreneurship Training Program for College Students of Guizhou Province (S202210670020, S202210670028).

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  1. School of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun, Guizhou, 558000, China

    Xinge Wang, Chunyu Jia, Lishuang An, Jiangyan Zeng, Aixia Ren & Xin Han

  2. Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou, 550025, China

    Yiqing Wang & Shuang Wu

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  1. Xinge Wang
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Contributions

X.G. Wang: Conceptualization, Methodology. C.Y. Jia: Data curation, Writing– original draft. L.S. An: Visualization, Investigation. J.Y. Zeng: Supervision. A.X. Ren: Software. Xin Han: Formal analysis. Y.Q. Wang, S. Wu: Writing - review & editing. All authors have read and agreed to the published version of the manuscript.

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Supplementary Material 1:

Figure S1 (Validation of RNA in various tissue parts of tea plants), S2 (Verification of plasmid construction in E. coli DH5α colonies using colony PCR), S3 (Verification of plasmid construction in Yeast Y1H colonies using colony PCR (A, B)), and S4 (Self-activation detection of CsGH3.14 and CsGH3.15)

Supplementary Material 2:

Table S6. Binding Site Prediction Results

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Wang, X., Jia, C., An, L. et al. Genome-wide identification and expression characterization of the GH3 gene family of tea plant (Camellia sinensis). BMC Genomics 25, 120 (2024). https://doi.org/10.1186/s12864-024-10004-y

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BMC Genomics

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