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Genome-wide identification analysis of the ATP-binding cassette transporter family and expression analysis under methyl jasmonate treatment in Panax ginseng

BMC Plant Biology volume 25, Article number: 565 (2025) Cite this article

Abstract

The ATP-binding cassette (ABC) transporter family is one of the largest and oldest protein families and encodes a class of transmembrane transporter proteins that transport substances in living organisms. Panax ginseng is a traditional Chinese herbal medicine, and its main active ingredient is ginsenoside, a secondary metabolite. Transportation and accumulation of secondary metabolites require the participation of ABC transporter proteins. In this study, we performed a genome-wide identification and expression analysis of the ginseng ABC transporter family using bioinformatics tools. Analysis of 106 PgABC genes showed that they were classified into seven subfamilies, among which ABCG was the most abundant subfamily. Chromosomal localization and covariance analyses showed that PgABC genes were unevenly distributed on chromosomes and that tandem repeat sequences existed. Tissue expression analyses revealed that PgABC expression was tissue-specific in ginseng. Cis-acting element analyses showed that PgABC genes responded to induction by hormones such as methyl jasmonate (MeJA). Subsequent qRT-PCR analysis of MeJA-treated ginseng adventitious roots revealed dynamic expression changes in nine PgABC genes, with PgABC14, PgABC18, and PgABC24-01 showing significant upregulation. The identification and analysis of the ABC transporter family in ginseng lays a theoretical foundation for the subsequent study of the function of the ABC gene family in ginseng and provides a theoretical basis for the study of ABC transporter proteins in other medicinal plant species.

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Introduction

ATP-binding cassette (ABC) transporter proteins are one of the largest subfamilies of membrane proteins and are a class of transmembrane transport proteins prevalent in prokaryotes and eukaryotes. They contain the binding cassette of adenosine triphosphate (ATP), which can be utilized to use the energy generated by ATP hydrolysis to carry out transmembrane transport of the substrate to which it is bound and to take on the role of substrate transport in living organisms [1]. ABC transporter proteins were first discovered in bacteria, and subsequent studies have shown that they are found in a wide range of organisms, including microorganisms, higher plants, and humans [2]. ABC transporter proteins were first identified in bacteria. Varying numbers of ABC transporters and genes have been found in Escherichia coli, Arabidopsis thaliana, and humans, and the number of ABC transporter genes in land plants is two to four times higher than that in other organisms [3]. In higher plants, ABC transporter proteins represent a large family that can be phylogenetically divided into eight subfamilies, ABCA to ABCI, of which ABCH is not found in plants [4]. ABC transporter proteins are mainly involved in metabolite and hormone transport, organ formation, and substance synthesis in plants, and also play important roles in heavy metals, adverse stress, and the secretion of secondary metabolites [5,6,7,8]. Among them, the ABCG family is the most abundant and plays a major role in the export of biotic stress-inducing hormones, such as jasmonic acid and salicylic acid, which affect the important process of plant adaptation [9]. The ABCC family is involved in the control of transpiration through stomata in plants [10], and The ABCD family is responsible for transporting or influencing the synthesis of hormone precursors [11].

ABC transporters are composed of two hydrophilic nucleotide-binding domains (NBDs) located on the cytoplasmic surface of the membrane and two transmembrane structural domains (TMDs) that form a translocation pathway [12, 13]. Hydrophilic NBDs contain three conserved motifs: Walker A, Walker B, and the ABC tag sequence (also known as Walker C), which bind and hydrolyze ATP to generate energy. Hydrophobic TMDs also bind to and hydrolyze ATP to provide energy [14]. and hydrophobic TMDs are responsible for substrate recognition and transport, respectively [15]. Hydrophobic TMDs are responsible for substrate recognition and translocation processes. These two structural domains coordinate with each other to facilitate substance transport. Two NBDs and two TMDs form holomolecular transporter proteins that can function independently of each other. A semi-molecular transporter protein with one NBD and one TMD must form a homodimer or heterodimer to function as a transporter [16]. NBDs and TMDs form whole-molecule transport proteins that function independently of each other.

Ginseng is an ancient and valuable medicinal plant in China, mainly distributed in the northeast region of Jilin Province. Ginseng belongs to the genus Panax in the family Araliaceae and has high medicinal value, with a wealth of efficacy, and is widely used in human health care. It is a plant with high medicinal value and efficacy and is widely used in human health care. Ginsenoside is a secondary metabolite of ginseng with a complex structure that enhances immunity and exhibits anticancer and antioxidant properties [17]. Anti-cancer [18] Ginsenoside is a metabolite of ginseng that has a complex structure and enhances immunity, anti-cancer activity, and cardiovascular protection [19]. ABC transporter proteins are a class of transmembrane proteins involved in the transport and accumulation of secondary metabolites in organisms [20]. ABC transporter proteins are involved in the transport and accumulation of secondary metabolites in various organisms, including plants. However, there are few reports on ABC transporter proteins in ginseng. Therefore, the present study aimed to identify and analyze the ginseng ABC transporter based on the ginseng transcriptome database established by the laboratory in the early stages, to understand the composition of ABC transporter family in ginseng, protein structural characteristics, and evolutionary relationships, and to provide basic information for further in-depth investigation of ginseng transporter proteins, as well as for further investigation of ginseng transporter proteins in ginseng. The identification and analysis of the ginseng ABC transporter family provides a basis for further investigation of the function of PgABC genes in ginsenoside transport and accumulation in the future.

Materials and methods

Identification of the ATP-binding cassette transporter family members from P. ginseng

The identification of ginseng ABC transporter protein family members was based on the ginseng transcriptome database constructed in the laboratory during the preliminary stage. To ensure the integrity of the ABC transcription factor family in Jilin ginseng, we used different approaches in our methodology [21]. First, we downloaded the ABC transporter protein sequences of Arabidopsis thaliana, Triticum aestivum, Zea mays, Oryza sativa, Salvia miltiorrhiza, Ananas comosus, Solanum lycopersicum, Fagopyrum esculentum, Artemisia annua, and Brassica napus from the NCBI database (https://www.ncbi.nlm.nih.gov/) and compared these protein sequences with the ginseng transcriptome database in local tBlastn to obtain the corresponding transcripts. Second, we downloaded the Hidden Markov Model (PF00005) of the ABC transporter protein from the Pfam protein database (http://pfam-legacy.xfam.org/) and compared it with the Jilin ginseng protein database using the homegrown HMMER (Version 3.0) software to obtain protein sequences containing the structural domains of ABC transporter proteins, which were compared with the Jilin ginseng transcriptome database using a local tBlastn comparison. Finally, the protein sequences of the ABC gene family were downloaded from the Chinese Ginseng Genome website (http://ginsengdb.snu.ac.kr/), and the corresponding nucleic acid sequences were obtained by sequence comparison with the Ginseng Transcriptome Database. Subsequently, the results obtained from the three comparisons were compared, and duplicates were removed. The candidate nucleic acid sequences obtained were then uploaded to the NCBI CD Search (https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi) and NCBI ORF Finder (https://www.ncbi.nlm.nih.gov/orffinder/) to identify their conserved structural domains and open reading frames. The structural domains of the ABC transporter proteins were further verified using the SMART Tool Online (http://smart.embl-heidelberg.de/). Finally, we obtained eligible genes, which were categorized and named PgABC + numbers (01 – 40).

Multi sequence alignment and conserved motif analysis of PgABC genes

The amino acid sequences of the PgABC transporter proteins obtained from screening were subjected to multiple sequence comparisons using MEGA X [22]. The conserved motifs were predicted using the online MEME website (http://meme.nbcr.net/meme), and the results were visualized using TBtools [23].

Phylogenetic analysis of ABC gene family in ginseng

The amino acid sequences of ABC transporter proteins from A. thaliana [24], S. lycopersicum [25], and O. sativa [26] were downloaded from the NCBI (https://www.ncbi.nlm.nih.gov/), and the amino acid sequences of ABC transporter proteins from ginseng were combined to construct a phylogenetic tree using the Neighbor-Joining (NJ) method of the MEGA X software to study the evolutionary relationship of this protein family in ginseng. We used iTOL (https://itol.embl.de/) to beautify the phylogenetic trees [27].

Chromosome localization and collinearity analysis of PgABC genes

The PgABC gene sequences were locally analyzed using BLASTN with the ginseng genome to obtain positional information on ginseng chromosomes. We screened genes length ≥ 400 bp, organized the data format to upload them to the MG2C online website (http://mg2c.iask.in/mg2c_v2.1/) to draw a bar graph, screened the genes with match ≥ 95% and length ≥ 700 bp, and used R software (Version 4.1.2) to draw covariate pictures to analyze the covariate relationship between the PgABC gene family on the ginseng chromosomes.

Analysis of cis-acting elements of PgABC genes

Blastn was used to compare PgABC genes with the ginseng genome database to determine the positional information of the genes on chromosomes. The first 2000 bp sequences of the genes' starting positions on each chromosome were obtained from the NCBI website, and all the sequences were organized into FASTA format and uploaded to PlantCare (http://bioinformatics.psb.ugent.be/) to analyze the cis-acting proxies. The obtained results were processed by data processing and visualized using TBtools II and R software.

GO functional annotation analysis of PgABC genes

Functional annotation analysis of the PgABC gene family was performed using Blast2GO Version 6.0 [28] to annotate the gene family members in three aspects: cellular component (CC), biological process (BP), and molecular function (MF). The data were processed, and the corresponding graphs were plotted using R.

Gene expression patterns and co-expression analysis of PgABC genes

Perl Version5.24.1 was used to extract the expression of PgABC genes in 14 tissues of the ginseng, 42 ginseng farm cultivars, and four ages of ginseng roots, and TBtools II was used to draw expression heatmaps indicating the spatiotemporal expression patterns of this gene family. Sequence correlation analysis of the PgABC gene family was used R language to extract the expression of PgABC genes in 42 ginseng farm cultivars, the Spearman correlation coefficient was calculated, Bio Layout Express 3D Version3.0 was used to draw the co-expression interaction network diagrams representing the interrelationships among PgABC genes, and the changes in the number of edges and nodes were counted at different p-values to validate the correlation among PgABC genes.

PgABC candidate genes response study under MeJA treatment in ginseng adventitious roots by qRT-PCR

Ginseng adventitious roots (0.2 g) were inoculated into a 250 mL triangular flask containing 150 mL of 1/2 Murashige and Skoog (MS) liquid medium and placed in a shaker for cultivation (22 °C, 110 rpm). Methyl jasmonate (MeJA) was added at the middle logarithmic phase (approximately day 23) for induction, with a control group and three repeated experimental groups. The amount of MeJA added was 200 μM, and the treatment durations were 6, 12, 24, 48, 72, and 96 h after treatment. The experimental materials were harvested at each time point, including three biological replicates and a blank control sample. The ginseng samples were quickly frozen in liquid nitrogen and stored at -80 °C. RNA was extracted from the experimental materials obtained above was performed using the TRIzol method (TransGen Biotech). Using the extracted RNA as a template, cDNA was synthesized through reverse transcription with the All-in-RT Premix for qPCR (YALEPIC) kit. Following the experimental protocol provided by the 2 × Universal Blue SYBR Green qPCR Master Mix one-step RT-qPCR Kit (SERVICEBIO), fluorescence quantitative PCR was conducted using an ABI 7500 Fast Real-Time PCR System. We randomized nine PgABC candidate genes containing MeJA elements in abundance for gene expression pattern analysis at different regulatory times, and the GAPDH gene (GenBank accession No. KF699323) was used as the internal reference gene. The 20 μL reaction system consisted of 10 μL of 2 × Universal Blue SYBR Green qPCR Master Mix, 0.4 μL of each forward and reverse primer, 1 μL of cDNA template obtained from reverse transcription, and 8.2 μL of ddH2O. After performing three biological replicates, the internal reference gene was standardized, and the expression of the target gene was calculated using the 2−ΔΔCt method. Finally, bar graphs were generated using GraphPad Prism Version 8.3.0, and significant differences between the treatment and control groups were calculated.

Results

Identification of the ABC gene family in ginseng

This experiment was based on the ginseng transcriptome database, screened and de-weighted using three different methods, and then analyzed using the NCBI-CD search and the SAMRT online website. A total of 40 PgABC genes were obtained from 106 PgABC transcripts containing conserved structural domains of ABC, and complete reading frames were obtained and named PgABC + number (from 01 to 40) (Table S1).

Phylogenetic analysis of the PgABC gene family

To elucidate the evolutionary relationship of the PgABC gene family, 106 PgABC proteins were combined with the protein sequences of A. thaliana, O. sativa, and S. lycopersicum for multiple sequence alignment, and the NJ method was used to construct a phylogenetic tree. As shown in Fig. 1, the PgABC gene family was divided into seven subfamilies, and the sequences of different subfamilies were distinguished by different background colors. Among them, the ABCG subfamily had the largest number of members, with 53 proteins, whereas the ABCI subfamily had the smallest number, with only two. Phylogenetic tree analysis (Fig. 1, Table 2S) showed that sequences of the same subfamily tended to be on the same branch. In addition, PgABC proteins that are in the same branch as the exogenous species might have similar functions, such as PgABC16 being in the same branch as OsABCG18, which was proven to control rice cytokinin translocation to the shoots and seed yield [29]. OsABCG18 has been shown to control rice cytokinin transport to shoots and grain yield.

Fig. 1
figure 1

Phylogenetic tree and evolutionary analysis of the ABC gene family in P. ginseng. Three exogenous species were used as the representative outgroup, A. thaliana (Mark with red circles), O. sativa (Mark with orange pentagram), and S. lycopersicum (Mark with blue triangles). The seven subfamilies of the PgABC gene family were indicated using I, II, III, IV, V, VI, and VII

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Cis-acting elements analysis of the PgABC gene family

Cis-acting elements are a family of non-coding DNA molecules that affect the transcription of neighboring genes to control gene expression at different developmental stages. The promoter regions of the PgABC gene family in ginseng were analyzed to identify cis-elements involved in cellular processes (Fig. 2). As shown in Fig. 2, these include the CGTCA motif, an element that responds to methyl jasmonate, the MYB-binding site (MBS) element that can bind to MYB transcription factors, and various elements that respond to phytohormones. These predictions suggest that the ABC gene family in ginseng is involved in responses to hormone signaling and environmental stress.

Fig. 2
figure 2

Cis-regulatory element analysis of PgABC gene family. The cis-acting elements were predicted in the promoter sequences of the PgABC genes. Rectangular boxes of distinct colored boxes represent the different types of cis-acting elements

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Structural domains and conserved motifs analysis of the PgABC gene family

The analysis results (Fig. 3) showed that the number of conserved motifs in the PgABC gene family ranged from 1 to 15, with Motifs 2, 13, 1, 8, and 10 having the highest frequencies of occurrence among all genes. The phylogenetic tree results indicated that genes in the same evolutionary branch had similar conserved motifs and gene structures. Phylogenetic analysis, conserved structural domains, and motif analysis provided further evidence for understanding the gene structure and evolutionary relationships among members of the PgABC gene family.

Fig. 3
figure 3

Phylogenetic analysis, genes structure, and conserved motifs analysis of the PgABC gene family. Each motif is represented with a specific color

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Chromosomal distribution and covariance analysis of the PgABC gene family

The sequences of PgABC genes were compared with the ginseng genome, and 77 genes were found to be localized to the ginseng chromosomes (Fig. 4). The PgABC genes were unevenly distributed on 16 chromosomes, mainly chr4, chr8, chr10, and chr12, with 15 genes distributed on chromosome chr12, which had the largest number of genes (Fig. 4A). According to the results of gene localization, some transcripts of the same gene were all located in the same place, although these transcripts were all products of the transcription of the same gene. These products have different structures that may originate from gene splicing after transcription, producing different transcripts. Different transcripts may encode different proteins that have biological significance. Covariance analysis of PgABCs (Fig. 4B) showed 40 pairs of PgABC gene family sequences connected by a red line, indicating that there were duplicate sequences of these genes on the chromosome, and they may have undergone biological events such as gene doubling, gene fragment duplication, transposition, transversion, and chromosome crossover interchange during evolution. The localization results of genes in closer positions on the same chromosome may have the same function. Genes on the same chromosome at closer positions may perform similar functions.

Fig. 4
figure 4

Chromosomal localization and collinearity analysis of the PgABC gene family in ginseng genome. A Chromosomal localization of the ABC gene family in ginseng. B Collinearity analysis of PgABC gene family members within the ginseng genome. The ends of the red arcs point to parallel pairs generated by gene duplication

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PgABC genes spatiotemporal expression patterns analysis

To further investigate the spatiotemporal expression patterns of PgABC genes, we mobilized 106 PgABC transcripts from 14 different tissues of 4-year-old ginseng, four different aged ginseng roots, and 42 farm cultivars of 4-year-old ginseng roots (Fig. 5, Table 3S). Heatmap analysis of the expression of the PgABC gene family in 14 tissues of 4-year-old ginseng showed that 16 of 106 transcripts were expressed in all 14 tissues, whereas 14 transcripts were not expressed in any tissue (13%) (Fig. 5A). This family was expressed in a higher number of genes in the pedicel and fruiting pedicel, where PgABC14, PgABC15, PgABC32, and PgABC36 were highly expressed in 14 tissues. In four different aged ginseng roots, 19 PgABC transcripts (18%) were expressed in all four different aged roots, whereas 57 transcripts were not expressed (37%), and the number of non-expressed transcripts accounted for a relatively high percentage of the transcripts, indicating that this gene family had low expression in ginseng roots. Among them, PgABC14, PgABC15, PgABC32, and PgABC36 had the highest expression levels (Fig. 5B). The results of the study indicated that among the 42 farm cultivars of 4-year-old ginseng roots, 82 PgABC transcripts were expressed in at least one variety (77.4%), and 24 transcripts were not expressed in any of the cultivars (23%) (Fig. 5C). A high expression trend was observed for PgABC14, PgABC15, PgABC32, PgABC36, and PgABC20.

Fig. 5
figure 5

Heatmaps analysis spatiotemporal expression patterns of PgABC genes. Blue indicates low expression, and orange indicates high expression. A PgABC genes expression in 14 different tissues of 4-year-old ginseng. B PgABC genes expression in 4 different aged of ginseng roots. C PgABC genes expression in 42 farm cultivars of 4-year-old ginseng roots

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Functional categorization and annotation enrichment analysis of the PgABC gene family

To further understand the functional relationships among the PgABC gene family members, we analyzed the PgABC genes using GO functional annotation (Fig. 6). As shown in Fig. 6A, among the 106 transcripts, 103 genes were annotated to at least one of the three major functions: 90 were annotated to biological process (BP), 81 to cellular component (CC), and 103 to molecular function (MF). Thirteen of these transcripts were annotated for only one function, 90 transcripts were annotated for two major functions, and 81 transcripts were annotated for three major functions. At Level 2 (Fig. 6B), four sub-levels were enriched in BP: stimulus response (GO:0050896), cellular process (GO:0009987), biological process (GO:0044419), and cellular localization (GO:0051179); one sub-level was enriched as a cellular anatomical entity (GO:0110165) in CC; and four sub-levels were enriched in MF sub-levels for catalytic activity (GO:0003824), transporter activity (GO:0005215), molecular binding (GO:0005488), and ATP-dependent activity (GO:0140657). GO functional classification and enrichment demonstrated that PgABC proteins have molecular binding functions and transporter roles and function as transmembrane transporters during growth, development, and secondary metabolism in ginseng.

Fig. 6
figure 6

Functional categorization and annotation enrichment analysis of the PgABC genes. A Venn network of the PgABC genes were among the biological process (BP), cellular component (CC), and molecular function (MF) functional categories. B The PgABC genes were classified into nine GO functional categories, including four BP functional categories (Red), one CC functional categories (Green), and four MF functional category (Blue)

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Correlation and co-expression analysis among PgABC gene family members in ginseng

To validate the genes with functions related to PgABC gene family members, we performed a co-expression network analysis of the expression of PgABC genes in 42 different farm cultivars. We selected 82 of these transcripts for co-expression network analysis (the remaining 24 transcripts were not expressed in any of the 42 farm cultivars). The results of co-expression network mapping showed that at p ≤ 0.05, the 82 gene family members formed a co-expression network of 255 edges containing 80 nodes (Fig. 7), and at increasingly stringent p-values (p ≤ 1.0E-08), the PgABC gene family members formed 15 nodes and nine edges. It can be hypothesized that there is a close relationship between the PgABC genes in ginseng.

Fig. 7
figure 7

Co-expression network analysis of the PgABC genes expressed in the 4-year-old roots of 42 farm cultivars. The co-expression network constructed from the 106 PgABC transcripts. The network was constructed at p ≤ 0.05

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Expression analysis of PgABC candidate genes under MeJA treatment in ginseng

MeJA is a phytohormone that effectively triggers ginsenoside biosynthesis in ginseng [30]. Ginseng adventitious roots were treated with MeJA, and qRT-PCR was performed to detect the expression of PgABC candidate genes at different time points (Fig. 8). Of the 106 genes, 57 PgABC genes responded to MeJA stress. Nine PgABC candidate genes were randomly selected from five subfamilies (ABCB, ABCC, ABCF, ABCG, and ABCI) of the ABC gene family in ginseng, and their gene expression levels were analyzed after MeJA treatment. The results (Fig. 8) showed that the gene expression levels of PgABC14, PgABC18, and PgABC34-03 continuously increased after MeJA treatment and reached their highest levels after 72 and 96 h of treatment. The expression of PgABC27-04 and PgABC21-01 tended to increase and then decrease, reaching the highest levels at 6 h and 12 h, respectively. PgABC39-06 and PgABC11-01 showed a decreasing and then increasing trend, reaching their highest levels at 96 h and 72 h, respectively. PgABC04 and PgABC27-01 showed a significant decrease in gene expression levels compared with the control group after MeJA treatment, and with increasing treatment time, the expression level increased, but it was still lower than that in the control group or slightly higher than that in the control group. In summary, three PgABC genes (PgABC14, PgABC18, and PgABC24-01) showed a more significant response to MeJA and could be used as candidate genes for subsequent studies on the molecular mechanism of action of the ABC gene family in ginseng under MeJA regulation.

Fig. 8
figure 8

Expression analysis of PgABC candidate genes under MeJA treatment in ginseng adventitious roots by qRT-PCR. Nine PgABC gene expressions were analyzed at different MeJA treatment times (0, 6, 12, 24, 48, 72, and 96 h), significant differences relative to the control group (0 h) are indicated as follows: “*” p ≤ 0.05, “**” p ≤ 0.01, and “***” p ≤ 0.001

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Discussion

Ginseng, an important medicinal plant, has medicinal value that is directly influenced by the accumulation and transport of its active components, such as ginsenosides, polysaccharides, and polyphenols. The ABC transporter family plays a critical role in the transmembrane transport of plant secondary metabolites, environmental adaptation, and defence responses. In recent years, ABC transporters in many plants have been extensively studied; however, the identification and research of the ABC transporter family members in ginseng have not yet been reported. ABC transporters are widely present in plants, animals, and microorganisms and have diverse substrates involved in various biological activities within organisms [2]. Notably, 129, 133, 133, 170, and 314 ABC gene family members have been identified in the genomes of Arabidopsis [31], rice [32], maize [33], tea plants [34], and rapeseed [35]. In this study, 106 ABC gene family members were identified in the ginseng genome. Phylogenetic analysis categorized PgABC into seven subfamilies, revealing differences in the number of transcripts among the subfamilies. Conserved motif and domain analysis indicated variations in the number of conserved domains and motifs across subfamilies, suggesting that genes within the same subfamily may have similar functions. Previous research has reported the functional diversity of ABC transporters in plants, with different subfamilies performing distinct functions and coordinating with one another to facilitate substance transport and regulate plant life activities.

Consensuses are the primary active components of ginseng; however, the transport mechanisms from their synthesis sites (endoplasmic reticulum and cytoplasm) to storage locations (vacuoles and extracellular space) remain unclear. ABC transporters may play a role in regulating the transmembrane transport of consensus. According to the results of Gene Ontology (GO) functional annotation, 103 transcripts were annotated for molecular function (MF), primarily encompassing transport activity, catalytic activity, binding, and ATP-dependent functions. However, the transport of substances within organisms typically requires ATP for energy and assistance from membrane or carrier proteins, indicating that PgABC proteins mainly participate in transport processes in ginseng.

Studies have shown that ABCB1 is involved in auxin transport in Arabidopsis [36]. In Salvia miltiorrhiza, SmABCG1 mediates the export of salvianolic acids from pericellular cells [37]. In strawberries, FvABCC8 promotes anthocyanin accumulation in fruits [38]. Additionally, 81 PgABC transcripts were annotated to cellular components (CC), further suggesting that PgABC performs corresponding functions within cells. Furthermore, 90 PgABC transcripts were annotated to biological processes (BP), implying that PgABC transcripts participate in the regulation of growth and development in ginseng. Research has reported that ABC transporters regulate the development of citrus fruits, ZmABC6 confers cold and salt stress tolerance in maize, and AtABCC4 influences the efflux of cytokinins, affecting root development [39,40,41]. Analysis of the expression patterns of PgABC in 42 farm cultivars, 14 different tissues, and 4 different aged ginseng roots revealed that although the expression patterns of PgABC transcripts are inconsistent, the majority are expressed in cultivars, tissues, and ages. This provides valuable references for subsequent developmental biology studies on ginseng. Additionally, we discovered that a small number of transcripts were specifically expressed, making these PgABC transcripts promising candidates for functional studies in ginseng. The plant growth and development process is an extremely complex biological process, and the functionalities of ABC transporters depend on the synergistic interactions among the various subfamilies [3]. Co-expression network analysis results lay the groundwork for future research on the interaction mechanisms of ABC transcription factors in ginseng.

The prediction analysis of cis-acting elements identified various cis-elements involved in cellular processes among PgABC gene family members, including elements responsive to methyl jasmonate and hormonal elements, indicating that ABC transporters actively participate in the transport of hormones such as ABA, MeJA, auxins, and gibberellins. Methyl jasmonate (MeJA) is an exogenous inducer that effectively triggers ginsenoside biosynthesis in ginseng [30]. Therefore, in this study, MeJA was used to treat ginseng adventitious roots, and qRT-PCR was employed to detect the expression levels of genes from nine different subfamilies after various treatment durations. The results showed varying responses to MeJA across different subfamilies, indicating that the PgABC gene family is influenced by MeJA in the biological processes involved in ginsenoside biosynthesis in P. ginseng. This provides a basis for further exploration of the molecular mechanisms of the PgABC gene family in ginsenoside biosynthesis using molecular biology techniques.

Conclusion

In this study, we conducted a genome-wide analysis of the ATP-binding cassette (ABC) transporter family in P. ginseng. We identified 106 PgABC genes, which were classified into seven subfamilies (with ABCG being the largest). Chromosomal mapping revealed an uneven distribution and tandem repeats, suggesting evolutionary diversification. Spatiotemporal expression patterns highlighted the functional specialization of the PgABC genes. Cis-acting element analysis linked PgABC promoters to hormonal responses, notably to MeJA response. Subsequent qRT-PCR analysis of MeJA-treated ginseng adventitious roots revealed dynamic expression changes in nine selected PgABC genes, with PgABC14, PgABC18, and PgABC24-01 being significantly upregulated. This study lays a theoretical foundation for the functional study of the ABC gene family in ginseng and provides a genetic resource for studying ginsenoside transport under abiotic stress.

Data availability

No datasets were generated or analysed during the current study.

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Funding

This work was supported by an award from the Scientific Research Project of Education Department of Jilin Province (JJKH20250562KJ), the Department of Science and Technology of Jilin Province (20240402046GH).

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Authors and Affiliations

  1. College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China

    Mengna Liu, Jianfeng He, Gaohui He, Yu Zhang, Meiping Zhang, Yi Wang, Kangyu Wang & Mingzhu Zhao

  2. Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China

    Mengna Liu, Jianfeng He, Gaohui He, Yu Zhang, Meiping Zhang, Yi Wang, Kangyu Wang & Mingzhu Zhao

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  1. Mengna Liu
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  2. Jianfeng He
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Contributions

K.W., M.Z. (Mingzhu Zhao), Y.W., and M.Z. (Meiping Zhang) designed the experiments. M.L., K.W., and M.Z. (Mingzhu Zhao) wrote and revised the main manuscript. M.L., J.H., G.H., and Y.Z. performed the experiments and contributed to the data analysis. All the authors have reviewed and approved the final manuscript.

Corresponding authors

Correspondence to Yi Wang, Kangyu Wang or Mingzhu Zhao.

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All ginseng samples and ginseng adventitious root materials were stored at Jilin Agricultural University and Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization. All ginseng plant materials were used in accordance with national and international standards and local laws and regulations. The use of all plant materials does not pose any risk to other species. No specific permission was required for the collection of samples described in this study.

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Liu, M., He, J., He, G. et al. Genome-wide identification analysis of the ATP-binding cassette transporter family and expression analysis under methyl jasmonate treatment in Panax ginseng. BMC Plant Biol 25, 565 (2025). https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s12870-025-06611-w

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Keywords

BMC Plant Biology

ISSN: 1471-2229

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