Genome-wide identification and expression analysis of JmjC domain-containing family in Vitis vinifera L.

Abstract

Background

In eukaryotes, histone methylation is essential for controlling chromatin structure, gene transcription, and related chromatin processes. Jumonji C (JmjC) domain-containing demethylases (JMJs) regulate histone methylation levels. The JMJ gene family has been discovered in various plants, including Arabidopsis thaliana, Oryza sativa, Malus domestica, and Zea mays.

Results

In this study, a total of 23 Vitis vinifera VvJMJ gene family members related to histone methylation were identified utilizing genomic and transcript databases. We analyzed the chromosomal location distribution, protein properties, phylogenetic relationships, gene structures, motifs, evolutionary patterns, promoter sequences, and expression profiles of the VvJMJ gene family. The VvJMJ genes were classified into five subfamilies: KDM3, KDM4, KDM5, JMJD6, and JMJC. Co-linearity analysis showed that VvJMJs are highly conserved with AtJMJs and OsJMJs genes. Analysis of the promoter sequences revealed that VvJMJ gene promoter regions are enriched with elements associated with stress response, growth and development, hormone response, and light reactions. Transcriptional profiling and qRT-PCR analysis showed that VvJMJs may play various roles in the multiple biological processes of V. vinifera. For example, VvJMJ2, VvJMJ16, VvJMJ18 may participate in the ripening process of V. vinifera fruits; VvJMJ1, VvJMJ4, VvJMJ6, VvJMJ13, VvJMJ17, VvJMJ20, VvJMJ21, VvJMJ23 may participate in various hormone responses; VvJMJ1, VvJMJ4, VvJMJ10, VvJMJ11 may participate in the stress response of V. vinifera.

Conclusions

This study initially identified the characteristics of V. vinifera JmjC domain-containing genes. The results established a basis for functional analyses of VvJMJ genes in V. vinifera, facilitating the exploration of the mechanisms of underlying the growth, development, and fruit maturation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-025-11995-y.

Introduction

Recent advancements in histone modification detection technologies and related research have revealed that histones undergo post-translational modifications not only at the N-terminus amino acid residues but also at the middle and C-terminal regions [1]. These modifications influence gene expression and regulate various growth and developmental processes in organisms [2]. Histone modifications encompass methylation, acetylation, phosphorylation, ubiquitination, among other types [3]. Histone methylation is a reversible and dynamic regulatory process, including methylation and demethylation. The occurrence, removal, and functional roles of these modifications are primarily regulated by histone modification enzymes and their cofactors, known as Writers, Erasers, and Reader/Effectors [4]. The steady-state equilibrium of histone methylation is dynamically regulated by two counteracting enzyme families: histone methyltransferases (HMTs) and histone demethylases (HDMs). These enzymes achieve this regulation through post-translational modifications, either depositing or removing methyl groups from specific histone residues, thereby controlling transcription factor accessibility to genomic DNA [5]. Histone demethylases, characterized by the JmjC domain, are crucial for maintaining histone methylation homeostasis and are significantly linked to plant growth and development. Research has identified proteins encoding JMJ-C genes in Arabidopsis thaliana [6], Zea mays [7], Citrus sinensis [8], Oryza sativa [9] Gossypium hirsutum [10], Solanum lycopersicum [11], Malus domestica [12], and Jatropha curcas [13].

In Arabidopsis, 21 JmjC proteins are categorized into five subfamilies based on sequence similarity: KDM4/JHDM3, KDM5/JARID1, JMJD6, KDM3/JHDM2, and JMJ-C only domain [6]. They are crucial in controlling leaf development, floral transition, flowering timing, and response to abiotic stress [14]. AtJMJ16, AtJMJ14, AtJMJ15, AtJMJ18, AtJMJ12, and AtJMJ13 regulate plant development by modulating histone methylation. AtJMJ16 reduces H3K4me3 levels to inhibit leaf maturation and regulate senescence [15]. AtJMJ14 decreases H3K4me to suppress FT expression, promoting floral transition [16]. AtJMJ15 and AtJMJ18 lower H3K4 levels to reduce FLC expression, stimulating flowering [17]. AtJMJ12 and AtJMJ13 adjust FLC histone methylation in response to temperature and light, influencing flowering time in Arabidopsis [18]. In O. sativa, 20 proteins containing the JmjC domain have been identified [6, 19]. OsJMJ706 functions as an H3K4me 1/2/3 demethylase and plays a role in regulating the development of floral organs in O. sativa [20]. OsJMJ703, an H3K4 demethylase, is essential for O. sativa transposon silencing, stem elongation, and drought stress defense [21–23]. In Medicago truncatula, MtJMJC5 experiences cold-induced alternative splicing and potentially plays a role in freezing tolerance response [24]. Moreover, in many higher plants, including Solanum lycopersicum and Musa nana, fruit development is also closely related to histone methylation. Solanum lycopersicum SlJMJ6 demethylates fruit maturation-related genes and H3K27me3, activating ACS4 and ACO1 to enhance mature inhibitor expression [11]. Meanwhile, S. lycopersicum SIJMJ7 demethylates H3K4me1, H3K4me2, and H3K4me3, directly suppressing DMS2 expression to regulate fruit maturation [25]. Musa nana MaJMJ15 facilitates fruit maturation by demethylating H3K27me3 on chromatin, thereby activating key RRGs expression [26].

Vitis viniferas, a woody vine from the Vitis vinifera family, are globally prevalent and valued for their economic, nutritional, and medicinal benefits [27]. Research on V. vinifera histone demethylase gene identification and function are currently limited. This study employed bioinformatics to systematically identify and characterize the V. vinifera VvJMJ gene family. Comprehensive analyses were subsequently performed to investigate their physicochemical properties, chromosomal distribution, phylogenetic relationships, gene evolution, motifs, conserved domains, and cis-elements. Additionally, we analyzed the types of gene duplication within the VvJMJ gene family and confirmed that its expansion primarily relies on transposed duplication. Utilizing transcriptome data, we systematically investigated the performance of VvJMJ family members across varietal differences, fruit development, and responses to biotic and abiotic stresses. This multidimensional analysis enhanced the depth and breadth of existing research. This detailed study of VvJMJ genes establishes a basis for future research into their roles in V. vinifera growth, development, stress response, and hormone signaling. These results will provide valuable genomic insights and directions for further research on the VvJMJ genes.

Materials and methods

Identification and classification of V. vinifera JMJ genes

The V. vinifera genome and gff annotation files were obtained from the Ensemble plant online website (https://plants.ensembl.org/). The Arabidopsis JMJ gene family amino acid (aa) sequences were obtained from the TAIR (https://www.arabidopsis.org/). The gene identifier (ID) is available in Table S1.

Candidate JMJs genes in V. vinifera were identified using two BLAST methods implemented in TBtools [28]. BLAST analysis was conducted using the protein sequences of Arabidopsis JMJs as queries. Additionally, relevant hidden Markov models (PF02373) were obtained from the Pfam database (http://pfam.xfam.org/), and employed to search the V. vinifera protein sequence data using the HMMER 3.0 software with a stringent threshold of E ≤ 10^–20. A preliminary set of candidate sequences was determined after eliminating redundancy and duplicates. The gene family candidate members were identified by integrating the results from the aforementioned methods. The Web CD-Search tool on the National Center for Biotechnology Information (NCBI) website (https://www.ncbi.nlm.nih.gov/Structure/bwrb/bwrpsb.cgi/) was utilized to analyze the conserved protein domains of the target gene family in V. vinifera [29]. This study investigated the presence of the conserved domain associated with the target gene family protein in each candidate sequence. Candidate sequences with complete domains were selected for further analysis. Sequences with varying or incomplete domains were first evaluated for integrity using the SoftBerry website (http://linux1.softberry.com/), followed by analysis with the Batch Web CD-Search tool to compare their domain similarity with Arabidopsis JMJs sequences.

The physicochemical properties of gene family proteins were assessed using ExPASy ProtParam tool (https://web.expasy.org/protparam/), which includes parameters like aa count, molecular weight, isoelectric point (pI), instability index, aliphatic index, and grand average of hydropathicity (GRAVY). The chromosomal locations of confirmed histone methylation modification genes were extracted from the V. vinifera genome's GFF3 file and visualized on V. vinifera chromosomes using TBtools. The subcellular localization of V. vinifera JMJ genes was predicted using the Wolf Psort online tool (https://wolfpsort.hgc.jp/), with the most likely prediction chosen as the result.

Phylogenetic analysis of histone methylation modification proteins in V. vinifera and A. thaliana

Amino acid sequences of JMJs in Arabidopsis and V. vinifera were sourced from the TAIR and Ensemble plant databases, respectively. The sequences were aligned with MUSCLE in MEGA 11. The optimal model was selected using MEGA 11 software, and a phylogenetic tree was constructed via the maximum likelihood (ML) method [30]. The evolutionary history of the analyzed taxa is represented by the bootstrap consensus tree derived from 1000 replicates [31]. TBtools was used to visualize and optimize the phylogenetic tree.

Chromosomal distribution and synteny analysis

The Amazing Gene Location tool in TBtools was utilized to map JMJs to chromosomes using data from GTF/GFF files. The Dual Synteny Plotter tool in TBtools was used to visualize synteny blocks within the V. vinifera genome and between the genomes of V. vinifera, Arabidopsis, and O. sativa. The One Step MCScanX Super Fast method was used to generate these synteny blocks. The O. sativa genome data were obtained from the Ensembl Plants database (https://plants.ensembl.org/index.html).

Identification of duplicated gene types

We employed the DupGen_finder tool (https://github.com/qiao-xin/DupGen_finder) to classify the types of duplicated genes. DupGen_finder_unique categorizes plant genome duplicated genes into five categories based on a specific algorithm: whole-genome duplication (WGD), proximal duplication (PD), transposed duplication (TRD), dispersed duplication (DSD), and tandem duplication (TD) [32]. Using Arabidopsis as an outgroup for V. vinifera, we followed the recommended workflowof DupGen_finder for our analysis and parameter configuration.

Sequence analysis

The conserved features of JMJs sequences were analyzed and visualized based on motifs using the Multiple Em for Motif Elicitation (MEME) suite 5.4.1 (https://meme-suite.org/meme/tools/meme) [33] and TBtools. The gene structure of JMJ genes were assessed using Gene Structure Shower in TBtools, utilizing information from the V. vinifera genome GFF3 file. To identify the cis-elements in the promoters of JMJ genes, PlantCare (https://bioinformatics.psb.ugent.be/webtools/plantcare/html/) was employed [34].

Expression profiling of JMJ genes in V. vinifera

JMJ gene expression patterns under abiotic, hormone, and biotic stress treatments were retrieved from the SRA database on the NCBI website. The study IDs included V. vinifera fruit development (GSE62745, GSE62744), NAA and ABA response (GSE150343), MeJA and SA response (PRJNA845078), light stress (GSE129916), and Colletotrichum viniferum stress (PRJNA952825). The expression of genes was quantified using Kallisto, an RNA-seq analysis tool [35]. This study estimated gene expression using the FPKM (fragments per kilobase of exon per million mapped reads) method.

Plant materials and hormone treatment

The experimental material used was six year old V. vinifera cv.'Muscat Hamburg'. One week before the fruit color change period, a solution of 500 mg/L ethylene (ETH) containing 0.05% Tween 20 was sprayed on the fruit. The control treatment (CK) involved spraying the fruit with distilled water containing 0.05% Tween 20. The experiment was repeated three times, with each treatment consisting of three plants. Sampling was conducted at 0 d, 5 d, 10 d, and 15 d after treatment. For each replicate, 10 bunches of fruit were randomly sampled, deseeded, frozen in liquid nitrogen, and stored at −80 °C.

RNA extraction, library construction, sequencing, and data analysis

Total RNA was extracted from berry skins using the RNAprep Pure Plant Kit (TianGen, Beijing, China) in accordance with the manufacturer's instructions. The integrity of the extracted RNA was confirmed through gel electrophoresis, while the concentration and quality were assessed using a NanoDrop One Spectrophotometer (Thermo Scientific, MA, USA). A total of 3 μg of RNA was utilized to construct an RNA-Seq library with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA). Subsequently, all library preparations were sequenced on an Illumina HiSeq platform (HiSeq 4000, 150PE) by Novogene Bioinformatics Technology Co. Ltd (Beijing, China).

Raw data in FASTQ format were initially processed using in-house Perl scripts by Novogene (China). Clean reads were obtained by removing adaptors and low-quality read pairs. The Vitis vinifera gene sequence and annotation for ‘Pinot noir’ (12X) were downloaded from http://www.genoscope.cns.fr/externe/GenomeBrowser/Vitis/. Bowtie v2.2.3 was employed to index the reference genome [36], and HISAT 2.0 was utilized to map clean reads to the grapevine reference genome [37]. HTSeq v0.6.1 was used to calculate the number of reads mapped to each gene [38]. Fragments Per Kilobase Million (FPKM) for each gene were calculated based on gene length and the number of reads mapped to that gene [39]. Differential expression analysis for each group (two biological replicates per group) was performed using the DESeq R package (1.18.0) [39]. Genes with |log2(Fold change)| greater than 1 and FDR ≤ 0.05 were defined as differentially expressed genes (DEGs).

Quantitative reverse transcription polymerase chain reaction

Total RNA was extracted from V. vinifera fruits using the hot borate method as outlined in prior research [40]. First-strand cDNA was synthesized from 1 µg of total RNA using Reverse Transcriptase M-MLV (RNase H-) (Takara Biomedical Technology Co., Ltd., Shiga, Japan) for reverse transcription-PCR. qRT-PCR was performed using Takara SYBR Premix Ex Taq II (Takara Biomedical Technology Co., Ltd.) on a Light Cycler 480 instrument (Roche, Basel, Switzerland). The amplification parameters were 95 ℃ for 3 min followed by 40 cycles at 95 ℃ for 15 s, 60℃ for 30 s, 72 ℃ for 30 s for plate reading. Ubiquitin1 served as an internal control [41]. The primers utilized are detailed in Supplementary Table S2.

Results

Identification of JMJs in V. vinifera

The V. vinifera JMJ gene family was identified by using Arabidopsis protein sequences and the JMJ gene family structural domain (PF02373) as search queries, resulting in 23 identified members, as detailed in Table 1.

Table 1.

JMJ genes identified in V. vinifera

Gene Name	Gene ID	Chromosome	Length (aa)	MW (kDa)	pI	II	AI	GRAVY	Subcellular localization prediction
VvJMJ1	Vitvi02g00329	chr2	1852	210383.12	6.27	47.75	91.33	−0.25	Chloroplast
VvJMJ2	Vitvi02g00759	chr2	876	99182.32	6.54	56.49	70.25	−0.50	Nuclea
VvJMJ3	Vitvi02g04368	chr2	70	7937.22	7.77	14.49	71.14	−0.15	Cytoplasmic
VvJMJ4	Vitvi02g01290	chr2	371	41541.88	5.53	58.85	77.84	−0.30	Nuclea
VvJMJ5	Vitvi04g01989	chr4	509	57077.70	5.83	55.48	68.92	−0.81	Nuclea
VvJMJ6	Vitvi06g00167	chr6	411	45958.13	5.05	53.51	85.91	−0.20	Nuclea
VvJMJ7	Vitvi07g00075	chr7	544	61130.22	5.25	50.55	89.10	−0.29	Nuclea
VvJMJ8	Vitvi07g00618	chr7	899	102075.98	5.78	55.16	67.60	−0.58	Nuclea
VvJMJ9	Vitvi07g04214	chr7	252	27661.12	5.97	51.47	71.23	−0.34	Nuclea
VvJMJ10	Vitvi08g00216	chr8	507	57836.18	7.97	49.30	83.20	−0.30	Nuclea
VvJMJ11	Vitvi10g00053	chr10	881	100648.82	6.74	59.31	71.77	−0.64	Nuclea
VvJMJ12	Vitvi10g00339	chr10	1021	117007.49	8.63	58.72	82.02	−0.53	Nuclea
VvJMJ13	Vitvi10g01120	chr10	1086	122284.90	5.31	53.43	72.14	−0.47	Nuclea
VvJMJ14	Vitvi10g01394	chr10	1256	139897.99	7.00	52.98	60.60	−0.98	Nuclea
VvJMJ15	Vitvi13g04179	chr13	1533	169920.49	6.01	49.18	72.82	−0.58	Nuclea
VvJMJ16	Vitvi14g00196	chr14	946	107326.79	5.66	46.86	72.94	−0.72	Nuclea
VvJMJ17	Vitvi14g00627	chr14	1271	142180.89	6.08	49.19	76.86	−0.47	Nuclea
VvJMJ18	Vitvi15g00950	chr15	1011	114583.91	7.88	47.31	65.58	−0.83	Nuclea
VvJMJ19	Vitvi16g00120	chr16	659	74924.90	9.04	45.42	67.75	−0.55	Nuclea
VvJMJ20	Vitvi16g01410	chr16	2319	254657.19	5.73	43.61	66.25	−0.74	Nuclea
VvJMJ21	Vitvi17g00875	chr17	493	57514.20	5.26	39.53	79.11	−0.41	Chloroplast
VvJMJ22	Vitvi17g01001	chr17	1329	148429.94	8.64	49.22	68.10	−0.58	Nuclea
VvJMJ23	Vitvi18g00437	chr18	970	110481.76	5.38	44.11	83.33	−0.34	Cytoplasmic

Within the identified family members, VvJMJ3 was unique with a predicted aa sequence length of 70 aa, whereas the remaining VvJMJ family members exhibited aa lengths between 252 aa (VvJMJ9) and 2319 aa (VvJMJ20). The predicted molecular weight of VvJMJ3 was 7937.22 Da, while the other members ranged from 27661.12 Da (VvJMJ9) to 254657.19 Da (VvJMJ20). The predicted pI varies from 5.05 (VvJMJ6) to 9.04 (VvJMJ19), with 17 genes encoding proteins that are alkaline (PI ≤ 7) and six genes encoding proteins that were acidic. The instability index (II) ranged from 14.49 (VvJMJ3) to 59.31 (VvJMJ11). Two genes, VvJMJ3 and VvJMJ21, encodes stable proteins with instability coefficients below 40 in vitro. In contrast, proteins encoded by the remaining 21 genes had instability coefficients exceeding 40, indicating in vitro instability. The aliphatic index (AI) of V. vinifera JMJ family proteins varies from 60.60 (VvJMJ14) to 91.33 (VvJMJ1), while the grand average of hydropathicity (GRAVY) ranges from −0.98 (VvJMJ14) to −0.15 (VvJMJ3), indicating their hydrophilic nature as all GRAVY values are negative. Predicted subcellular localization suggested that while VvJMJ1 and VvJMJ21 are in the chloroplast and VvJMJ3 and VvJMJ23 are in the cytoplasm, the remaining VvJMJ proteins are nuclear, indicating a primary nuclear function for this gene family.

Analysis of chromosomal distribution and evolutionary relationships of VvJMJ genes

Figure 1A illustrated the chromosomal distribution of JMJ genes in V. vinifera. The analysis revealed that the V. vinifera genome comprises 18 chromosomes, with VvJMJ genes distributed unevenly across 12 of these chromosomes (not present on chromosomes 01, 03, 05, 09, 11, and 12). These genes were named VvJMJ1 to VvJMJ23 based on their arrangement along the chromosomes. The distribution pattern of VvJMJ genes on the 12 chromosomes was not uniform, with most genes located in the central region of the chromosomes. Only VvJMJ4 and VvJMJ20 were found at the distal ends of chromosomes 2 and 16, respectively. Furthermore, chromosomes 2 and 10 each contain four genes, the highest number; chromosome 7 had three genes, the second highest; chromosomes 14, 16, and 17 had two genes each; and chromosomes 4, 6, 8, 13, 15, and 18 had only one gene each, the lowest number. The scattered distribution of V. vinifera JMJ gene family members across the 12 chromosomes suggested the possibility of genetic variation during the natural growth and development of V. vinifera [25]. The results of the chromosomal positioning did not show any gene tandem duplication phenomena. Figure 1B illustrated that gene co-linearity analysis reveals a pair of genes, VvJMJ18 and VvJMJ20, demonstrating strong co-linearity. This suggested they have experienced segmental duplication and are paralogous. Chromosomal positioning analysis revealed no tandem duplication genes within the V. vinifera JMJ gene family. The presence of one pair of genes undergoing segmental duplication and the absence of tandem duplication pairs in the V. vinifera JMJ gene family suggested that segmental duplication events contribute to its expansion.

Fig. 1.

Chromosomal distribution and collinearity analysis of JMJ genes in V. vinifera. A Chromosomal distribution and duplication analysis of JMJs in V. vinifera. B Collinearity analysis of JMJ genes family in V. vinifera

The analysis of gene collinearity and gene duplication events using the MCScanX software revealed the evolutionary relationship of the V. vinifera JMJ gene family. Figure 1B illustrated that collinearity analysis identifies a gene pair, VvJMJ18 and VvJMJ20, with strong collinearity, suggesting they are paralogous genes resulting from segmental duplication. However, the chromosomal location analysis did not identify any tandem duplication genes in the V. vinifera JMJ gene family. In the V. vinifera JMJ gene family, a single gene pair had experienced segmental duplication, indicating that such events contribute to the family's expansion, with no evidence of tandem duplication.

To analyze the distribution of subfamily members in the V. vinifera JMJ gene family and their phylogenetic relationships with Arabidopsis and O. sativa, aa sequences from 21 AtJMJs and 16 OsJMJs genes were extracted from the genomes of these model plants. Clustal was used for multiple sequence alignment, followed by phylogenetic tree construction using the ML method in MEGA11, with a bootstrap value of 1000. iTOL (https://itol.embl.de/) was utilized to visualize and enhance the phylogenetic tree, illustrating the evolutionary relationships within the V. vinifera JMJ gene family (Fig. 2). In order to analyze the distribution of the subfamily members of the V. vinifera JMJ gene family and their phylogenetic relationships with Arabidopsis and O. sativa, the aa sequences of 21 AtJMJs and 16 OsJMJs genes were extracted from the genomes of these model plants to construct phylogenetic trees, and the evolutionary relationship of the VvJMJ gene family was elucidated (Fig. 2). Phylogenetic analysis classified 23 V. vinifera JMJ genes into five major subfamilies: JARID1/KDM5, JHDM3/KDM4, JHDM2/KDM3, JMJD6, and JmjC domain-only (JmjC), alongside corresponding members from Arabidopsis and O. sativa. Among the five subfamilies: KDM3 had the most members, with seven VvJMJs genes, accounting for 30.4% of the total members; both JMJC and KDM4 subfamilies contained five VvJMJs genes, accounting for 21.7%; KDM5 subfamily had four VvJMJs genes, accounting for 17.39%; and JMJD6 had only two VvJMJs genes, accounting for 8.69%. Most VvJMJ genes clustered with Arabidopsis genes, suggesting a closer genetic relationship between V. vinifera and Arabidopsis JMJ genes compared to O. sativa. Exceptions included VvJMJ18 and VvJMJ20, VvJMJ5 and OsJMJ719 in the KDM3 subfamily, VvJMJ7 and VvJMJ9 in the JMJC subfamily, VvJMJ2 and VvJMJ19 in the KDM4 subfamily, and VvJMJ13 and OsJMJ704 in the KDM5 subfamily, which formed separate clusters.

Fig. 2.

Phylogenetic relationship of JMJ proteins from V. vinifera, O. sativa, and Arabidopsis. The bootstrap consensus of tree was inferred from 1000 replicates, and the phylogenetic tree was constructed using the ML method. In the figure, squares represent Arabidopsis proteins, circles represent V. vinifera proteins, and stars represent O. sativa proteins

We performed a comparative syntenic analysis of V. vinifera, Arabidopsis, and O. sativa genomes to better understand the origin, evolution, and function of JMJ genes (Fig. 3). As shown in Fig. 3, there were a total of 11 syntenic gene pairs between V. vinifera and Arabidopsis, which included VvJMJ1-AtJMJ17, VvJMJ2-AtJMJ13, VvJMJ6-AtJMJD5, VvJMJ10-AtJMJ22, VvJMJ11-AtJMJ29, VvJMJ11-AtJMJ26, VvJMJ15-AtEFL6, VvJMJ16-AtJMJ24, VvJMJ21-AtJMJ20, VvJMJ22-AtJMJ12, and VvJMJ23-AtJMJ21. There were five syntenic gene pairs between V. vinifera and O. sativa, namely VvJMJ6-OsJMJ712, VvJMJ12-OsJMJ25, VvJMJ19-OsJMJ707, VvJMJ19-OsJMJ706, and VvJMJ21-OsJMJ709. The syntenic gene count suggested that the V. vinifera JMJ genome is more conserved with Arabidopsis compared to its more distant relationship with O. sativa. The specific information for the collinear genes between species is shown in Table S3.

Fig. 3.

Synteny analysis of JMJs of V. vinifera, Arabidopsis, and O. sativa

Sequence and structure analysis of JMJs

The gene structure analysis showed that within the KDM4 subfamily (VvJMJ2 ~ VvJMJ22), except for VvJMJ3 which had one exon, the remaining members had 7 to 10 exons; within the KDM5 subfamily (VvJMJ1 ~ VvJMJ17), VvJMJ1 had 33 exons, VvJMJ13 and VvJMJ17 had 11 exons, while VvJMJ8 had eight exons; within the JMJD6 subfamily (VvJMJ10, VvJMJ23), VvJMJ10 had two exons, and VvJMJ23 had 16 exons; within the KDM3 subfamily (VvJMJ16 ~ VvJMJ20), except for VvJMJ5 with six exons and VvJMJ11 and VvJMJ18 with 12 exons, VvJMJ16, VvJMJ12, VvJMJ14, and VvJMJ20 all had 13 exons; within the JMJC subfamily (VvJMJ4 ~ VvJMJ7), the number of exons varies among the genes, with VvJMJ4 having four exons, VvJMJ6 having six exons, VvJMJ21 having nine exons, VvJMJ9 having two exons, and VvJMJ7 having 15 exons (Fig. 4A).

Fig. 4.

Phylogenetic analysis, motif composition, conserved domains of VvJMJ proteins and exon–intron structures of VvJMJ genes. The phylogenetic tree and gene structures of the VvJMJ genes (A), motif composition (B) and the distribution of conserved domains (C) of VvJMJs. Green rectangles represent untranslated regions (UTRs); yellow rectangles represent coding sequence (CDS) or exons; grey lines represent introns

Based on the annotation information of the V. vinifera JMJ genes, a motif structure diagram was constructed (Fig. 4B). The analysis showed that within the KDM4 subfamily (VvJMJ2 ~ VvJMJ22), except for VvJMJ3 which contained only one Motif 2, the remaining members all contained multiple motif sequences; within the KDM5 subfamily (VvJMJ1 ~ VvJMJ17), each member contained eight to ten motif sequences; within the JMJD6 subfamily (VvJMJ10, VvJMJ23), VvJMJ10 contained one Motif 1, and VvJMJ23 contained one Motif 1 and one Motif 3; within the KDM3 subfamily (VvJMJ16 ~ VvJMJ20), except for VvJMJ16 and VvJMJ12 lacking Motif 15, and VvJMJ5 having only 6 motifs, the remaining genes all contain 15 motifs, and the motif types and arrangements were completely consistent. In the JMJC subfamily (VvJMJ4 to VvJMJ7), all genes except VvJMJ21, which included Motif 1 and Motif 6, contain only Motif 1. This suggested that Motif 1 is the conserved motif within this subfamily.

Conserved domain analysis corroborated the motif analysis, reinforcing the similarity in domain structures within gene subfamilies (Fig. 4C). Conserved domain analysis of the KDM4 subfamily (VvJMJ2 to VvJMJ22) revealed that all genes, except VvJMJ3 which hasd a single cupin_RmlC-like superfamily domain, possess two conserved domains: JmjC and JmjN. In the KDM5 subfamily (VvJMJ1 to VvJMJ17), all genes feature three conserved domains: JmjC, JmjN, and the zinc finger structure zf-C5HC2. Additionally, VvJMJ13 and VvJMJ17 had two FYRC and FYRN domains, while VvJMJ1 included three domains: ARID, two copies of PHD, and two copies of the PLU-1 superfamily. The JMJD6 subfamily (VvJMJ10, VvJMJ23) contained two conserved domains: Cupin 8 superfamily and F-box-like. In the KDM3 subfamily (VvJMJ16 to VvJMJ20), all genes except VvJMJ5, which had only a cupin_RmlC-like superfamily domain, contain two domains: cupin_RmlC-like superfamily and zf-4CXXC_Rl superfamily. Within the JMJC subfamily (VvJMJ4 to VvJMJ7), all genes except VvJMJ21, which hasd a Cupin 8 superfamily domain, contain a single Cupin 8 domain. Detailed amino acid sequences of VvJMJ motifs and MEME site analysis were provided in Supplementary Table S4.

Cis-elements in the promoter of VvJMJs

Researchers had identified 22 cis-elements in the promoter sequences of V. vinifera JMJ family genes to explore their regulatory mechanisms and stress responses. These elements included those responsive to abscisic acid, light, anaerobic conditions, salicylic acid, low temperatures, MeJA, wounds, and gibberellin, as well as MYB binding sites related to light and drought, defense and stress response, zein metabolism, meristem and endosperm expression, cell cycle regulation, circadian control, seed-specific regulation, and a gapA element associated with light responsiveness. According to their functional roles, these elements are divided into four major categories: non-biological and biological stress responses, plant growth and development, plant hormone responses, and light responses (Fig. 5B and C). All VvJMJs gene promoters contained these four types of cis-elements.

Fig. 5.

The cis-elements analysis of VvJMJ promoters. The distribution (A) and number (B and C) of cis-elements in the promoter of VvJMJ genes

The non-biological and biological stress response category included 10 cis-elements, with 266 elements in total in VvJMJs genes, including: 70 MYC elements, the highest percentage being 26.3%, with the exception of VvJMJ19 which did not contain this element; 38 STRE elements, with six genes (VvJMJ10, VvJMJ8, VvJMJ14, VvJMJ18, VvJMJ6, and VvJMJ9) not containing this element; 67 ARE elements for anaerobic induction, the second highest percentage being 25.2%, with the exception of VvJMJ4 and VvJMJ21 which did not contain this element; 21 MBS elements for drought stress, with VvJMJ5 containing the most, three elements; three DRE core elements, the lowest percentage being 1.1, with only VvJMJ2 and VvJMJ3 containing two and one elements, respectively.

The plant growth and development category comprised eight cis-acting elements, totaling 79 in VvJMJs genes. Among these, 42 were AAGAA-motif elements, constituting 53.2%, except in VvJMJ1, VvJMJ17, VvJMJ5, VvJMJ18, and VvJMJ7, which lacked this element. Other elements included nine CAT-box elements for fungal tissue expression, five each of GCN4_motif, A-box, CCGTCC motif, and CCGTCC-box elements, and seven O2-site elements. The MSA-like element was the least common, present only in VvJMJ3.

The plant hormone response category included nine cis-elements, with 184 elements in total in VvJMJs genes, including: 57 ABRE elements for abscisic acid responsiveness, the highest percentage being 30.5%, with VvJMJ15 and VvJMJ2 containing nine and eight ABRE elements, respectively; 44 ERE elements for ethylene responsiveness, the second highest percentage being 23%; four VvJMJs genes (VvJMJ10, VvJMJ13, and VvJMJ20) containing the most ERE elements, four each; The CGTCA-motif and TGACG-motif elements, accounting for 10.2%, were associated with MeJA responsiveness. 17 P-box and six GARE-motif elements for gibberellin responsiveness; 15 TCA-element elements for salicylic acid responsiveness; six TGA-element and one AuxRE-core element for auxin responsiveness, with only VvJMJ18 containing one AuxRE-core element.

The light response category included 11 cis-elements, with 220 elements in total in VvJMJs genes, including: 76 Box four elements for a part of the conserved DNA light response, the highest percentage being 34.5%, with VvJMJ1, VvJMJ10, VvJMJ6, and VvJMJ18 containing 11, seven, six, and six elements, respectively; 41 G-box elements for light-responsive cis-regulatory elements, the second highest percentage being 18.6%, with VvJMJ15, VvJMJ19, and VvJMJ2 containing eight, five, and five elements, respectively; four LAMP-element elements, the lowest percentage being 1.8%, with VvJMJ4, VvJMJ21, and VvJMJ18 containing two, one, and one element, respectively; three ACE elements, the lowest percentage being 1.4%, with VvJMJ19, VvJMJ3, and VvJMJ8 each containing one element.

In the V. vinifera JMJ gene family, VvJMJs genes contained a significant number of MYC elements, AAGAA-motif elements, abscisic acid response elements ABRE, and conservative DNA light response elements Box 4. These results suggested that they are important response elements for inducing VvJMJs gene expression.

Expression profile of VvJMJ in the development process of fruits

This study analyzed VvJMJs expression profiles during V. vinifera fruit development across various varieties using publicly available transcriptome data (Fig. 6). The findings indicated that VvJMJ3, VvJMJ9, VvJMJ14, and VvJMJ19 had reduced expression levels across both the five white and five red fruit varieties. VvJMJ14 exhibited marginally elevated expression levels during the Pea and Harv developmental stages in the five red fruit varieties compared to the other stages. VvJMJ16 and VvJMJ20 exhibited elevated expression levels during the Pea and Touch developmental stages across ten V. vinifera varieties, compared to the Soft and Harv stages. Notably, VvJMJ20 expression gradually declined as the fruit matured, indicating a potential role for these genes in V. vinifera fruit development. The expression profile of VvJMJ23 varied among different varieties, exhibiting elevated levels during the Touch developmental stage in the white fruit varieties'Moscatobianco'and'Passerina'. VvJMJ23 exhibited elevated expression levels during various developmental stages in the fruits of four red fruit varieties:'Sangiovese'(Pea and Touch),'Negroamaro'(Touch),'Refosco'(Touch), and'Primitivo'(Pea and Touch). The expression trend of VvJMJ2 is notable, as its overall expression levels decrease during the middle and late stages of fruit development across all varieties, except for'Refosco'. VvJMJ4 exhibited elevated expression levels during the Harv developmental stage in the five white fruit varieties, whereas in the red fruit varieties, expression was typically lower, with the exception of the'Sangiovese'and'Primitivo'varieties. The results suggested that certain VvJMJ genes may be involved in V. vinifera fruit development and exhibit varietal differences.

Fig. 6.

Expression profiles of V. vinifera VvJMJ genes in different varieties and different developmental stages of fruits. Different shades of red and blue denote the extent of the expression values according to the color bar provided [log₂(FPKM + 1)]

V. vinifera fruit samples (V. vinifera L. cv. Shine Muscat) were collected from the same location and under the same cultivation conditions at four different developmental stages of the fruit in the same year. The four stages were 20 days after flowering (Pea), before the fruit color change (Touch), at the end of the fruit color change (Soft), and at the time of full maturity and harvest (Harv). Samples from each stage were collected in triplicate and promptly preserved in liquid nitrogen for total RNA extraction.

To confirm the expression trends of VvJMJ genes during V. vinifera fruit development, four VvJMJ genes were analyzed using qRT-PCR (Fig. 7). The analysis indicated that VvJMJ18 expression progressively declined during fruit maturation, reaching a minimum at the Soft stage. VvJMJ11 expression decreased slowly across the initial three developmental stages, followed by a sharp increase at the Harv stage, suggesting its role in the final maturation phase. VvJMJ16 expression consistently decreased as the V. vinifera fruit developed, while VvJMJ20 expression peaked at the Touch stage before declining. The above results were basically consistent with the transcriptome analysis results.

Fig. 7.

The qRT-PCR analysis of some VvJMJ genes during the development of V. vinifera fruits. The mean values ± SEM are shown for three biological replicates. Different letters above the bars indicate significant differences according to Duncan-test (p < 0.05)

Tissue-specific expression patterns of VvJMJ genes in V. vinifera

To gain more insights in potential roles of VvJMJ genes during grapevine development, the organic specific expression patterns of all the VvTCP genes were analyzed using an expression atlas of V. vinifera cv. ‘Corvina’ from the GEO DataSets (GSE36128), which contained 42 various organs/tissues at different developmental stages obtained by microarray analysis. As shown in Fig. 8, some VvJMJ genes exhibited similar expression patterns across different tissues, while others displayed significant tissue specificity, suggesting functional differentiation of VvJMJ genes during the development of various V. vinifera organs or tissues. For instance, VvJMJ18 showd relatively high expression levels in all tested tissues, whereas VvJMJ6, VvJMJ7, and VvJMJ8 demonstrated low expression across tissues. Notably, VvJMJ2 and VvJMJ19 exhibited minimal expression in most tissues but show significantly elevated expression in pollen, indicating their potential involvement in V. vinifera pollen formation. Similarly, VvJMJ11 and VvJMJ13 both display marked tissue-specific high expression in pollen, suggesting their association with pollen development and fertility. VvJMJ5 showed elevated expression during fruit skin development and bud swelling phases, potentially regulating fruit skin maturation and playing critical roles in bud expansion. VvJMJ10 maintained sustained high expression during postharvest fruit ripening, likely influencing post-storage fruit quality. These findings provided important clues for further investigation into the transcriptional regulatory mechanisms of VvJMJ genes during V. vinifera fruit development and ripening processes.

Fig. 8.

Expression profiles of grapevine VvJMJ genes in various tissues and developmental stages. Different shades of red and blue denote the extent of the expression values according to the color bar provided [log2(FPKM + 1)]. Bud-AB, bud after burst; Bud B, Bud burst; Bud-W, winter bud; Bud-L, latent bud; Bud-S, bud swell; Flower-F, flowering; Flower-FB, flowering begins; FS, fruit set; Inflorescence-Y, young inflorescence with single flowers separated; Inflorescence-WD, well-developed inflorescence; Leaf-FS, mature leaf; Leaf-S, senescing leaf; Leaf-Y, young leaf; MR, mid-ripening; R, ripening; PFS, post fruit set; Stem-G, green stem; Stem-W, woody stem; V, véraison

Expression profiles of the Vitis vinifera VvJMJs in response to hormone treatment

Plant hormones are essential for plant growth and development [42]. We examined VvJMJs gene expression profiles in response to hormone treatments with NAA, ABA, MeJA, and SA using publicly accessible transcriptome data (Fig. 9). The findings indicated that VvJMJ3, VvJMJ9, and VvJMJ19 had minimal or no expression across all four hormone treatments, while VvJMJ14 demonstrated reduced expression specifically under ABA and NAA treatments. In V. vinifera fruits treated with NAA, VvJMJ1 expression significantly increased at stages EL34, EL35, EL36, and EL38 compared to the control, whereas VvJMJ13 expression slightly decreased. ABA treatment in V. vinifera fruits resulted in a significant increase in the expression levels of VvJMJ20 compared to the control. In V. vinifera leaves treated with MeJA, the expression levels of VvJMJ4, VvJMJ12, and VvJMJ21 consistently increased over time, whereas VvJMJ2, VvJMJ10, VvJMJ20, and VvJMJ22 initially increased and then decreased. Under SA treatment, the expression levels of VvJMJ4, VvJMJ6, and VvJMJ17 progressively rose with prolonged treatment, whereas VvJMJ21 exhibited a slight decline. In summary, we speculated that the above genes may participate in the process of V. vinifera response to different hormone treatments and play an important role.

Fig. 9.

Expression profiles of VvJMJ genes in fruits and leaves under corresponding hormone treatments in V. vinifera. Different shades of red and blue denote the extent of the expression values according to the color bar provided [log2(FPKM + 1)]

We selected some VvJMJ genes for qRT-PCR analysis after MeJA and SA treatments. One-year-old grapevines (V. vinifera L. cv. Shine Muscat) grapes were grown in a light incubator set to 25 °C with 65% relative humidity, following a 16 h light and 8 h dark cycle. Plants with similar growth conditions were selected as experimental materials. MeJA (Sigma Aldrich Chemicals GmbH, Schnelldorf, Germany) was prepared at a final concentration of 100 μM by dissolving it in 10% ethanol with 0.2% Tween-20, using 0.2% Tween-20 as the control. Before spraying, the leaves were washed with distilled water and then dried before being evenly sprayed onto the surface of the grapevine leaves using a spray bottle. Leaves were collected at 12, 24, and 48 h post-spraying for total RNA extraction, with three leaves sampled at each interval and preserved in liquid nitrogen. SA (Sigma Aldrich Chemicals GmbH, Schnelldorf, Germany) was prepared at a concentration of 100 μM in 10% ethanol, with distilled water serving as the control. The spraying method and sampling method were the same as those for the MeJA treatment.

The study found that MeJA treatment significantly upregulated the expression of VvJMJ4, VvJMJ12, and VvJMJ13. VvJMJ15 and VvJMJ18 showed increased expression at 12 h post-treatment before declining, while VvJMJ20 exhibited a pattern of initial decrease, followed by an increase, and then a subsequent decrease (Fig. 10A). Following SA treatment, VvJMJ4, VvJMJ16, and VvJMJ17 showed significant upregulation, while VvJMJ21 peaked at 12 h and VvJMJ15 at 24 h post-treatment, both subsequently declining (Fig. 10B). The above results were basically consistent with the transcriptome analysis results.

Fig. 10.

The qRT-PCR analysis of some VvJMJ genes under MeJA, SA, NAA and ABA treatments. The leaves of annual V. vinifera were sprayed with MeJA and SA, with 0.2% Tween-20 and distilled water serving as controls, and samples were collected 12 h, 24 h, and 48 h post-spraying, with three biological replicates. Using six-year-old V. vinifera cv.'Muscat Hamburg'as experimental material, the fruits were sprayed with ABA and NAA solutions, while a control group was treated with distilled water containing 0.05% Tween-20. Sampling was conducted at 0, 5, 10, and 15 d post-treatment. Each treatment included three biological replicates to ensure statistical reliability. The mean values ± SEM are shown for three biological replicates. Different letters above the bars indicate significant differences according to Duncan-test (p < 0.05)

To further clarify the role of the VvJMJ gene family in the response of V. vinifera fruits to ethylene (ETH), we conducted RNA-seq analysis on fruits treated with ETH. The analysis results were shown in Fig. 11, where VvJMJ3, VvJMJ9, VvJMJ14, and VvJMJ19 were found to be in a state of very low or no expression. The expression level of VvJMJ15 on the 5 d and 10 d after ETH treatment was significantly higher than that of the control group. Notably, the expression levels of VvJMJ23 at all three time points (5d, 10 d, and 15 d) after ETH treatment were higher than those of the corresponding control group. Furthermore, we performed qRT-PCR analysis on selected VvJMJ genes. The results revealed that the relative expression levels of VvJMJ13 and VvJMJ15 were significantly higher in ETH-treated fruits compared to the control group at 5 and 10 d post-treatment. In contrast, the relative expression of VvJMJ20 increased progressively with treatment duration, showing significant elevation at 5, 10, and 15 d compared to the control. Notably, VvJMJ23 exhibited a decline in expression at 10 d but a marked increase at 15d. These findings suggested that these genes may play roles in mediating V. vinifera fruit responses to ethylene signaling.

Fig. 11.

Expression profiles of VvJMJ genes in V. vinifera fruits under ETH treatment and qRT-PCR analysis of selected VvJMJ genes. Different shades of red and blue denote the extent of the expression values according to the color bar provided [log2(FPKM + 1)]. The mean values ± SEM are shown for three biological replicates. Different letters above the bars indicate significant differences according to Duncan-test (p < 0.05)

Expression profiles of VvJMJs in grapevine under biotic and abiotic stresses

Light conditions are known to significantly impact V. vinifera berry ripening and phenolic compound accumulation [43]. We examined VvJMJs expression in V. vinifera berries at different developmental stages in response to light using publicly available transcriptome data (Fig. 12A). The findings indicated that VvJMJ2 and VvJMJ19 were either minimally expressed or not expressed in both the experimental and control groups. Following cluster bagging treatment, VvJMJ1 and VvJMJ10 exhibited elevated expression levels compared to the control group across the EL31, EL35, EL36, EL37, and EL38 stages. Their expression progressively increased with V. vinifera berry maturation, indicating a potential role in the berries'response to light.

Fig. 12.

Transcriptional profiles of VvJMJs genes in V. vinifera under photostress and biotic stress responses. Different shades of red and blue denote the extent of the expression values according to the color bar provided [log2(FPKM + 1)]

C. viniferum, responsible for V. vinifera ripe rot and leaf spot, poses a significant threat to V. vinifera production and quality [44]. We examined the expression levels of VvJMJ genes in V. vinifera leaves subjected to C. viniferum infection stress using publicly available transcriptome data (Fig. 12B). The study found that the expression levels of VvJMJ1, VvJMJ11, VvJMJ17, and VvJMJ23 progressively rose following infection onset, whereas VvJMJ2 and VvJMJ13 initially decreased before increasing. Following infection onset, the expression levels of VvJMJ4, VvJMJ12, VvJMJ20, and VvJMJ22 decreased, while VvJMJ6 initially increased before declining.

Discussion

Chromosomal localization analysis revealed that the 23 VvJMJ genes are unevenly distributed among the V. vinifera 12 chromosomes (Fig. 1A). To better understand the systematics of the V. vinifera VvJMJ gene family, we constructed a phylogenetic tree with A. thaliana and O. sativa (Fig. 2). The V. vinifera VvJMJ family aligns with the classification of the AtJMJ family in A. thaliana and the OsJMJ family in O. sativa, encompassing KDM5/JARID1, KDM4/JHDM3, KDM3/JHDM2, JMJD6, and the JmjC domain. In the VvJMJ subfamily, there were seven gene members in the KDM 3 subfamily, which was the largest proportion, consistent with the research in species such as G. hirsutum [10] and Betula platyphylla [45]; in the JMJD6 subfamily, there were two gene members, which was the smallest proportion, consistent with the research in species such as A. thaliana, O. sativa, S. lycopersicum, M.. nana, and Cucumis melo [46]. The similar proportion of gene members across subfamilies in various species suggested conservation of these genes among different species.

Gene family expansion primarily results from tandem gene, segmental, and whole-genome duplications [47]. This study identified only one pair of duplicated genes in V. vinifera. In other words, the VvJMJ genes were more conserved during the evolutionary process of V. vinifera. Furthermore, using A. thaliana as an outgroup, we identified the types of gene duplication within the VvJMJ gene family using DupGen_finder. The results revealed that within the VvJMJ family: two gene pairs (VvJMJ23-VvJMJ21 and VvJMJ10-VvJMJ21) were classified as DSD (Dispersed Duplication); eight gene pairs (VvJMJ3-VvJMJ22, VvJMJ5-VvJMJ11, VvJMJ7-VvJMJ6, VvJMJ8-VvJMJ1, VvJMJ9-VvJMJ6, VvJMJ12-VvJMJ18, VvJMJ14-VvJMJ11, and VvJMJ19-VvJMJ2) belonged to TRD (Tandem Replicated Duplication); one gene pair (VvJMJ18-VvJMJ20) was categorized as WGD (Whole Genome Duplication) (Table S5). These findings indicated that the primary mode of expansion in the VvJMJ gene family is transposed duplication.

Research indicates that proteins in the KDM5/JARID subfamily demethylate H3K4me1/2/3 [48], while those in the KDM4/JHDM3 subfamily target H3K9me2/3 and H3K36me2/3 [49]. The KDM3/JHDM2 subfamily is responsible for demethylating H3K9me1 and H3K9me2 [50]. Additionally, JMJD6 subfamily proteins act on H3K27me2/3 [51], and proteins with the JmjC domain remove methylation from H3K27me3 [52]. The AtJMJ16 gene in A. thaliana, part of the KDM5 subfamily, suppresses leaf senescence by reducing H3K4me3 levels and inhibiting WRKY53 and SAG201 gene expression [15]. This suggests that the Vitis vinifera VvJMJ17 gene, closely related to AtJMJ16, might play a crucial role in V. vinifera leaf senescence regulation. Additionally, the AtJMJ27 gene in Arabidopsis, homologous to V. vinifera VvJMJ18 and VvJMJ20 genes, can delay flowering by downregulating CONSTANS (CO) and upregulating FLOWSYS LOCUS C (FLC) [53]. AtJMJ27 also binds to drought stress regulators GOLS2 and RD20, contributing to drought response [54]. The AtJMJ25 gene in A. thaliana, closely related to the VvJMJ14 gene within the KDM3 subfamily, is involved in early embryonic development and embryo sac formation in A. thaliana [55], suggesting that VvJMJ14 may perform similar functions. The A. thaliana genes AtJMJ30 and AtJMJ32, closely related to VvJMJ6 and VvJMJ4 in the JMJC subfamily, can demethylate H3K27me2/3 from FLC to inhibit early flowering under appropriate temperatures [56]. They also activate SnRK2.8 expression by removing H3K27me3, thereby participating in the ABA response during seedling root development [57].

Gene structure analysis revealed variability in exon numbers across different subfamilies and within members of the same subfamily. However, most genes within the same subfamily, excluding the JMJC subfamily, exhibited similar exon structures (Fig. 4A). Motif structures can reflect the evolutionary situation of JMJ genes, and in this study, there were conserved motifs of different numbers and types in each subfamily (Fig. 4B). Protein domains are the basic structure and functional units of the tertiary structure of proteins [58]. The analysis showed that the types and numbers of structural domains between subfamilies of V. vinifera JMJ genes were not similar, but each subfamily had the same conserved structural domains (Fig. 4C). VvJMJ proteins contain conserved structural domains like FYRN, FYRC, Zf-C5HC2, ARID, PLU-1, and zf-4CXXC_R1, which facilitate DNA-binding and contribute to the specific functions of JmjC proteins [59]. In addition, the conserved structural domains JmjC and JmjN in the KDM4 subfamily, which are shorter in amino acid sequence length than JmjC, have been shown to disrupt the stability and activity of JmjC if removed [60]. The PHD domain of the KDM5 subfamily can identify both unmodified and methylated histone tails [61], while the PLU-1 domain is potentially involved in DNA binding and transcription [62]. The F-box domain in the JMJD6 subfamily can recognize multiple substrates and regulate important biological processes in plants by degrading cellular proteins [63].

Transcriptional regulatory elements in gene promoter regions are essential for transcription and gene expression regulation [64]. This study examined the promoter region of V. vinifera VvJMJ genes, identifying numerous cis-acting elements associated with plant hormones, abiotic stress, growth and development, and light response (Fig. 5). Key cis-acting elements identified include MYC, AAGAA-motif, ABRE, and Box 4. Collinear gene pairs VvJMJ18 and VvJMJ20 share similar cis-acting elements, including ARE, ABRE, G-box, and Box 4, indicating potential co-induction under non-abiotic stress, hormone, and light conditions.

Usually, the interaction between hormones affects the development and maturation of fruits [64], and abscisic acid is closely related to fruit ripening [65–67]. Studies have shown that exogenous ABA treatment promotes the softening of Fragaria ananassa [68] and mangoes [69], thereby affecting fruit ripening. The study identified numerous plant hormone response elements, notably the prevalent ABA response element ABRE, alongside other elements such as the ethylene response element ERE, MeJA response elements CGTCA-motif and TGACG-motif, GA3 response elements P-box and GARE-motif, SA response element TCA-element, and IAA response elements TGA-element and AuxRE-core. Transcriptional profiling revealed that VvJMJ20 was highly expressed across all 10 V. vinifera varieties prior to full ripening and showed increased expression in V. vinifera fruits treated with ABA compared to the control. The promoter region of VvJMJ20 contains three ABA response elements (ABRE), indicating its role in regulating the ABA response during V. vinifera fruit ripening. MeJA, a plant hormone and signaling molecule associated with damage, is commonly found in plants. Its exogenous application can induce the expression of defense-related genes [70]. Both transcriptional profiling and qRT-PCR analysis revealed that VvJMJ4 and VvJMJ12 gene expression significantly increased during exogenous MeJA treatment. Conversely, their expression levels significantly decreased following infection in the transcriptional profiling analysis of biotic stress. This suggests that VvJMJ4 and VvJMJ12 may be involved in the biotic stress response mediated by MeJA signaling.

This study examined VvJMJ gene expression patterns throughout V. vinifera fruit development and their reactions to biotic and abiotic stresses, as well as hormone treatments. Analysis of VvJMJ gene expression profiles suggests their significant involvement in diverse biological processes in V. vinifera (Fig. 13). These results will provide directions for further research on the VvJMJ genes. Due to the data for gene expression calculations being sourced from online databases, we performed qRT-PCR analysis on a select few gene family members related to fruit development, MeJA, and SA treatments. We recommend conducting experimental verification to elucidate the precise functions of VvJMJ genes of interest to researchers.

Fig. 13.

The role the VvJMJ genes in V. vinifera

Conclusions

This study identified 23 VvJMJ genes in V. vinifera through bioinformatics analysis, which are distributed on 12 chromosomes of different densities and have been analyzed for their protein physicochemical properties. They were categorized into five subfamilies according to their phylogenetic relationship with Arabidopsis and O. sativa. The JMJ gene family was highly conserved between Arabidopsis and V. vinifera. Promoter analysis indicated that VvJMJs are potentially crucial in V. vinifera fruit growth and development, as well as in responses to light, hormones, and stress. Analysis of VvJMJs transcription levels across different V. vinifera varieties and developmental stages suggested diverse roles in fruit development, with distinct variety-specific and stage-specific traits. VvJMJ18 and VvJMJ16 demonstrated a decreasing trend during fruit ripening, while VvJMJ23 was highly expressed in the Touch stage across six varieties. VvJMJ4, VvJMJ12, VvJMJ13, VvJMJ21 may participated in the hormone response process to exogenous MeJA in V. vinifera; VvJMJ4, VvJMJ6, VvJMJ15, VvJMJ17, and VvJMJ21 participated in the response to exogenous SA in V. vinifera. VvJMJ1 and VvJMJ13 may participate in the response to exogenous NAA in V. vinifera; VvJMJ20 may participate in the response to exogenous ABA in V. vinifera. VvJMJ13, VvJMJ15, VvJMJ20, and VvJMJ23 may participate in the response to ethylene. VvJMJ1 and VvJMJ10 could be associated with the V. vinifera photo stress response. VvJMJ1, VvJMJ4, VvJMJ11, VvJMJ12, VvJMJ17, VvJMJ20, VvJMJ22, VvJMJ23 may participate in regulating the process of V. vinifera response to biotic stress. In summary, our results have laid a foundation for further studying the functions of VvJMJ genes and exploring the mechanisms of V. vinifera growth and development and fruit maturation.

Abbreviations

JmjC

Jumonji C

JMJs

Jumonji C domain

qRT-PCR

Quantitative real-time PCR

ABA

Abscisic Acid

MeJA

Methyl Jasmonate

NAA

1-Naphthlcetic Acid

SA

Salicylic acid

ETH

Ethylene

Authors’ contributions

SX conceived and designed this study. WM analyzed the data and wrote the manuscript. WJ performed experiments and analyzed the data. ZW performed the data analysis. All authors read and approved the manuscript.

Funding

This research was funded by Natural Science Research Project of Anhui Educational Committee (2024AH051983), Anhui Province High-End Talent Introduction and Cultivation Action Project. Anhui Province Forestry Research and Innovation Project, (Document No. 4 [2024]).

Data availability

The expression pattern of *VvJMJ* genes were obtained from SRA database in NCBI website. The study IDs were as follows: GSE62745, GSE62744, GSE150343, PRJNA845078, GSE129916 and PRJNA952825.

Declarations

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.