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Article

Genome-Wide Identification of CaPLATZ Family Members in Pepper and Their Expression Profiles in Response to Drought Stress

by
Xingliang Wang
1,
Yue Huang
1,
Na Yang
2,
Xue Wang
1,
Yuanqian Wang
1,
Wenyao Ma
1 and
Hui Zhang
1,*
1
Horticultural Branch of Heilongjiang Academy of Agricultural Sciences, Harbin 150069, China
2
Harbin Academy of Agricultural Sciences, Harbin 150029, China
*
Author to whom correspondence should be addressed.
Genes 2025, 16(6), 632; https://doi.org/10.3390/genes16060632
Submission received: 6 May 2025 / Revised: 22 May 2025 / Accepted: 23 May 2025 / Published: 24 May 2025
(This article belongs to the Special Issue Abiotic Stress in Plants: Molecular Genetics and Genomics—2nd Edition)
Browse Figures
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Abstract

Background: The plant AT-rich sequence and zinc binding (PLATZ) transcription factors constitute a zinc-dependent protein family implicated in various developmental processes and responses to abiotic stress. Nevertheless, comprehensive investigations on PLATZ gene functions in pepper (Capsicum annuum) have not been extensively performed. Methods: In the present study, bioinformatics methods coupled with quantitative real-time PCR (qRT-PCR) were employed to characterize the phylogenetic relationships, chromosome distribution, structural composition, cis-regulatory elements, evolutionary dynamics, and expression responses of CaPLATZ genes under drought stress conditions. Results: Phylogenetic analyses categorized the CaPLATZ genes into four distinct subgroups, each exhibiting similar gene structures and conserved motif patterns within its subgroup. A total of 11 CaPLATZ genes were nonuniformly located across eight pepper chromosomes, and synteny analyses identified a duplication event involving a single gene pair. The assessment of cis-acting regulatory elements indicated potential involvement of CaPLATZ genes in responses to abiotic stresses and various phytohormones. Furthermore, qRT-PCR results revealed differential expression of most CaPLATZ genes under drought-induced stress. Conclusions: Collectively, these findings support the functional roles of CaPLATZ transcription factors in mediating developmental processes and enhancing drought tolerance in pepper.

1. Introduction

Regulation of gene expression by transcription factors is a fundamental mechanism by which plant development programs are modulated and plant responses to environmental stressors are achieved adaptively. Transcription factors act by binding specifically to given cis-acting elements upstream of target gene promoters to either activate or repress transcription [1]. Among plant transcription factor families, zinc finger proteins form a notably large group implicated in several biological activities such as morphogenesis and transcriptional regulation, as well as in stress responses, as seen in WRKY and ZAT proteins [2]. The plant-specific PLATZ subfamily, originally identified in pea (Pisum sativum) as PLATZ1, contains zinc-binding proteins, which are AT-rich sequences nonspecifically interacting and acting as transcriptional repressors in a primary capacity [3]. Computational structure analyses have identified two strongly conserved zinc finger domains in PLATZ proteins: an N-terminal motif (C-x2-H-x10-C-x2-C-x4–5-C-x2-C-x3–7-H-x2-H) and a central region motif (C-x2-C-x10–11-C-x3-C). Both motifs require zinc ions for performing their activities in binding to DNA [4].
Research on the PLATZ gene family has increased significantly in recent years, where a number of members of the PLATZ gene family have been identified in various plant species, such as Solanum lycopersicum [5], Triticum aestivum [6], Malus [7], Ginkgo biloba [8], and Glycine max [9]. A number of studies have addressed functions of PLATZ transcription factors in regulating plant growth and development. In Arabidopsis thaliana, AtPLATZ3 has a function of controlling leaf growth and senescence-like responses [10]. Furthermore, AtPLATZ7 plays a key role in regulating the development of the Arabidopsis RAM by mediating root meristem growth factor 1 (RGF1) signaling [11]. VviPLATZ1 plays a critical role in controlling female flower morphology in grapes, with loss-of-function mutants exhibiting reflex stamens [12]. In rice, the PLATZ transcription factor GL6 promotes increased grain length through facilitating cell proliferation within the developing caryopses and panicles [13]. The soybean GmPLATZ protein presumably functions by directly interacting with cyclin and GmGA20OX gene promoters, thereby stimulating gene expression and subsequent cell proliferation [14].
Drought is a major abiotic stress factor that severely impacts global agricultural production, driving significant research efforts to develop drought-tolerant crops. Emerging evidence highlights the critical roles of PLATZ transcription factors in regulating plant responses to drought stress conditions. For example, in A. thaliana, AtPLATZ1 increases dehydration tolerance in vegetative tissues [15]. AtPLATZ4 targets the promoter of the plasma membrane aquaporin PIP2;8, inhibiting its expression and enhancing drought resistance [16]. Overexpression of PhePLATZ1 enhances drought stress resistance in transgenic plants by modulating osmotic balance, improving water retention, and reducing membrane and oxidative damage [17]. Ectopic expression of cotton-derived GhPLATZ1 in transgenic Arabidopsis plants confers enhanced tolerance to osmotic stress induced by salt and mannitol treatments, thereby accelerating seed germination and seedling establishment [18].
Pepper (C. annuum L.) is a significant vegetable crop, valued for its nutritional and economic importance. Pepper cultivation in China accounts for about 8–10% of the total vegetable planting area, contributing an output value of approximately 250 billion yuan. This makes pepper the leading vegetable in terms of both planting area and economic value. Throughout its growth period, pepper is often exposed to a variety of abiotic and biotic stresses, including drought, cold temperatures, insufficient illumination, pests, and pathogens [19]. Members of the PLATZ gene family play critical roles in orchestrating plant developmental pathways and adaptive responses to environmental stresses. However, research on PLATZ transcription factors has primarily concentrated on model plant systems, and comprehensive studies in pepper have not yet been reported. This study systematically identified and characterized the pepper PLATZ family, including analyses of their evolutionary history, chromosomal distribution patterns, gene structures, cis-regulatory elements, phylogenetic relationships, and drought-responsive expression profiles. The results provide valuable theoretical insights into CaPLATZ gene functions and present a molecular basis for breeding drought-tolerant pepper cultivars.

2. Materials and Methods

2.1. Genomic Identification of CaPLATZ Genes in Pepper

The complete genomic sequence of pepper cultivar Zunla-1 (C. annuum L.) was selected as a reference, with genomic data sourced from the Sol Genomics Network database [20]. Initially, Arabidopsis PLATZ proteins served as queries to conduct a homology search against the pepper protein dataset using the BlastP (NCBI-BLAST v2.10.1+) algorithm. Subsequently, the Hidden Markov Model (HMM) profile of PLATZ domains (PF04640.17) was retrieved from the Pfam database (https://pfam.xfam.org/) and utilized in hmmsearch analyses (HMMER v3.0), applying an E-value cutoff below 1 × 10−5. Candidate CaPLATZ proteins were ultimately identified through combined domain analyses using SMART (http://smart.embl.de/) and the Conserved Domain Database (CDD, https://www.ncbi.nlm.nih.gov/cdd/?term=, accessed on 22 May 2025), retaining only sequences harboring confirmed PLATZ structural domains. Eleven CaPLATZ genes were identified in pepper. These genes were systematically renamed as CaPLATZ1–CaPLATZ11 according to their chromosomal location. Online tools were employed to predict the physicochemical properties of the CaPLATZ proteins. Subcellular localization predictions for these proteins were performed using the WoLF PSORT server (https://wolfpsort.hgc.jp/).

2.2. Phylogenic Analysis

Based on the work of Kumar et al. [21], the ClustalW (ClustalW v2.0.11) method within the MEGA-X ((MEGA v10.2)) software was used to run multiple sequence alignments of pepper and Arabidopsis CaPLATZ amino acid (AA) sequences. After that, we used the maximum likelihood (ML) technique to build a phylogenetic tree, and we tested the reliability of each node using bootstrap analysis with 1000 replications. All the sequences used in the phylogenetic analysis are provided in Table S1.

2.3. Analysis of Synteny and Homologous Gene Pairs

Syntenic comparisons among the A. thaliana, S. lycopersicum, and Oryza sativa genomes were carried out using TBtools software (TBtools v2.225) [22]. Genomic sequences for these comparative species were obtained from the Ensembl Plants database (https://plants.ensembl.org/).

2.4. Analysis of CaPLATZ Gene Structures and Phylogenetics

By leaving all other parameters at their default values, MEME Suite was able to identify conserved motifs in the pepper PLATZ gene family, with a target of 10 unique motifs. Genome annotation files in the GFF3 format were used to extract the exon–intron architecture of CaPLATZ genes. With 1000 bootstrap repeats for support, phylogenetic reconstruction was carried out using the ML technique in MEGA-X, and ClustalW was used to build multiple sequence alignments.

2.5. Identification of Cis-Regulatory Elements in CaPLATZ Genes

We used the PlantCARE database (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/) to systematically identify cis-acting regulatory elements (CAREs), and we recovered promoter sequences (2000 bp upstream) for all eleven CaPLATZ genes from the genomic dataset [23]. In order to facilitate complete biological data analysis, the discovered CAREs were then visually represented using TBtools software [22].

2.6. Plant Materials and Stress Treatment Protocols

A growing substrate that consisted of vermiculite, peat, and perlite in a proportion of 1:3:1 (v/v/v) was used to nurture pepper seedlings in plastic containers with dimensions of 10 cm × 10 cm × 10 cm, with each container housing one seedling. The seedlings were cultivated in a glasshouse under carefully regulated conditions, with temperatures maintained at 28 °C during the day and 22 °C during the night, along with a relative humidity of 75%. To conduct osmotic stress treatments, we exposed seedlings to a 400 mM D-mannitol solution in a liquid medium when they were uniformly four leaves old. At 0, 6, 12, and 24 h after treatment, data were obtained from both the control and treated groups. The freshly picked leaves were promptly placed in liquid nitrogen for flash freezing and kept at a temperature of −80 °C. For each condition in the experiment, six seedlings were used.

2.7. Expression Analysis for CaPLATZ Genes

The transcriptional patterns of PLATZ family members were examined utilizing public transcriptomic datasets GSE45037 (https://www.ncbi.nlm.nih.gov/) and PepperHub (http://lifenglab.hzau.edu.cn/) [20,24]. Visualization of gene expression differences was accomplished by generating heatmaps with TBtools software. To validate gene expression under drought stress conditions, total RNA was extracted from pepper tissues exposed to drought stress using a RNAprep Pure Plant Kit (TianGen, Beijing, China). Reverse transcription into complementary DNA was subsequently performed with a KOD One™ PCR Master Mix reverse transcription kit (TOYOBO, Shanghai, China). Quantitative real-time PCR (qRT-PCR) was conducted using an ABI QuantStudio 3 system (Applied Biosystems, Waltham, MA, USA) and 96-well reaction plates under the following parameters: initial denaturation at 95 °C for 3 min, 40 cycles of denaturation at 95 °C for 10 s, and annealing/extension at 68 °C for 15 s. Relative expression of target genes was calculated according to the 2−ΔΔCT method, and primer details are listed in Supplementary Table S2.

3. Results

3.1. Identification of CaPLATZ Members in Pepper

Through iterative homology searches using the PLATZ domain (Pfam: PF04640) as a query combined with BlastP analysis, eleven CaPLATZ genes were identified in the pepper genome. Subsequent analyses characterized these CaPLATZ proteins based on chromosomal distribution, AA length, molecular weight (MW), and theoretical isoelectric points (pI) (Table 1). Uneven distribution of the CaPLATZ genes was observed across chromosomes 1, 2, 4, 5, 6, 7, 9, and 10. The length of CaPLATZ proteins ranged from 174 AAs (CaPLATZ6) to 247 AAs (CaPLATZ10). Additionally, the MWs ranged between 20,057.15 Da (CaPLATZ6) and 28,113.13 Da (CaPLATZ10), and their theoretical pI varied from 6.16 (CaPLATZ4) to 9.73 (CaPLATZ3). A phylogenetic tree constructed from CaPLATZ and AtPLATZ sequences classified these proteins into four distinct groups (Figure 1).

3.2. Duplication Modes and Collinearity Analysis of the CaPLATZ Gene Family in Pepper

Gene families typically arise via tandem duplications or large-scale segmental duplications during evolution. Segmental duplication analysis showed significant similarity between CaPLATZ1 and CaPLATZ3, suggesting intra-chromosomal or segmental duplication events (Figure 2A). To further explore the evolutionary dynamics of PLATZ genes, synteny analyses among pepper, A. thaliana, S. lycopersicum, and O. sativa were conducted. The analysis identified eight pairs of homologous PLATZ genes between pepper and A. thaliana, nine pairs between pepper and S. lycopersicum, and only two pairs between pepper and O. sativa (Figure 2B–D).

3.3. Gene Structure Analysis of the CaPLATZ Genes in Pepper

Based on phylogenetic relationships, the 11 PLATZ proteins were categorized into four distinct groups, aligning with the earlier classification results (Figure 3A). The MEME suite analysis identified ten distinct conserved motifs (motifs 1–10) within the pepper CaPLATZ protein family (Table 2). These motifs, comprising 11–41 AAs, showed varying degrees of conservation among the groups. Specifically, motifs 1, 4, and 8 were conserved across all the CaPLATZ proteins. Moreover, the motif distribution was highly similar among the CaPLATZ proteins belonging to the same phylogenetic group, reflecting group-specific motif conservation (Figure 3B). Exon–intron structure analysis revealed substantial variation among the CaPLATZ genes; notably, CaPLATZ8 contained only two exons, while the majority included three or four exons (Figure 3C). Such structural diversity likely contributes to the functional specialization of members within the PLATZ gene family.

3.4. Analysis of Cis-Acting Elements in CaPLATZ Promoter Regions in Pepper

To investigate potential regulatory roles of CaPLATZ genes, a total of 154 CAREs were detected within the 2000 bp promoter sequences upstream of the identified genes. These CAREs were grouped into three functional classes associated with plant growth/development, hormonal signaling pathways, and abiotic stress responsiveness. Of particular significance was the abundance of elements responsive to stress stimuli and hormonal regulation. Notably, ethylene-responsive elements (EREs) were particularly enriched in CaPLATZ gene promoters, indicating their possible involvement in ethylene-mediated signaling cascades (Figure 4). These observations suggest complex regulatory networks involving multiple cis-elements that govern CaPLATZ expression in developmental processes and adaptive stress responses.

3.5. Expression Analysis of the CaPLATZ Genes in Pepper

To elucidate the comprehensive expression patterns of the CaPLATZ genes across different tissues and under various environmental stresses, RNA-seq datasets from public resources and the Pepper Hub were examined, and the resulting profiles were visualized using heatmap analysis (Figure 5). Most CaPLATZ genes were expressed widely but displayed considerable variation across different tissues and developmental stages. Specifically, CaPLATZ8 exhibited root-specific expression, whereas CaPLATZ4, CaPLATZ9, and CaPLATZ10 showed extremely low or undetectable expression in all the tested tissues. Further analysis was conducted to investigate the response of the CaPLATZ genes to various abiotic stresses. Under different stress treatments in root tissues, significant upregulation of CaPLATZ1, CaPLATZ3, and CaPLATZ7 was observed, with CaPLATZ1 notably responding to D-mannitol and NaCl stresses. Additionally, CaPLATZ5 exhibited marked induction in both leaves and roots under high-temperature conditions, suggesting involvement in abiotic stress responses.

3.6. Expression Patterns of CaPLATZ Genes Under Drought Stress

We performed qRT-PCR analyses to confirm RNA-seq-derived expression patterns of CaPLATZ genes during drought stress. The transcription levels of CaPLATZ1, CaPLATZ3, and CaPLATZ7 significantly increased following drought treatment. The rapid induction of CaPLATZ1 and CaPLATZ3 (peaking at 6 h) likely reflects their role in early drought signaling. Their subsequent decline at 12 h may indicate feedback inhibition or prioritization of other stress-adaptive mechanisms. In contrast, the sustained upregulation of CaPLATZ7 suggests its involvement in long-term drought adaptation. Moreover, CaPLATZ4 and CaPLATZ6 showed decreased expression at 3 h, which subsequently increased after 6 h of treatment (Figure 6). These findings indicate that different CaPLATZ members may participate in diverse regulatory pathways responding to drought stress.

4. Discussion

PLATZ family genes are zinc-dependent DNA binding proteins that have been proven to be involved in orchestrating plant developmental pathways and adaptive responses to environmental stresses [3]. Research on the PLATZ gene family has increased significantly in recent years, and a number of members of the PLATZ gene family have been identified in various plant species. In this study, we discovered 11 CaPLATZ genes based on the pepper genome sequence. The number of PLATZ gene family members in pepper was comparable to that in Citrullus lanatus (12) and Hordeum vulgare (11), but lower than in Medicago sativa (55) and Linum usitatissimum (28) [25,26,27,28]. Notably, the pepper genome (3.48 Gb) is 3.7 times larger than that of M. sativa (810 Mb) [29] and 10.04 times the size of that of L. usitatissimum (302 Mb) [30], suggesting no direct correlation between genome size and the number of PLATZ gene family members. Phylogenetic analysis delineated four distinct groups of CaPLATZ, aligning with findings in soybean [9]. Inter-chromosomal segment duplication and tandem duplication represent significant driving forces in the evolution of plant genomes and genetic systems [31]. Through chromosomal mapping and synteny analysis, a pair of segmentally duplicated genes was identified, indicating that segmental duplication mechanisms were primarily responsible for the expansion of the PLATZ gene family. Furthermore, the collinearity analysis revealed intimate evolutionary relationships among the PLATZ family genes in tomato and pepper, aligning with findings in S. lycopersicum [32], thus indicating similar functions of these gene families within the Solanaceae family. Analyzing gene structures and conserved motifs is essential in studying gene family evolution [33]. The analysis results revealed that the gene structures and motif distribution were notably consistent among CaPLATZ proteins within the same phylogenetic group, while variations were observed among different groups. These results indicated that structural and motif differences in the CaPLATZ gene family may confer functional diversity in the regulation of plant growth.
CAREs are important transcriptional regulators that adjust a wide range of biological phenomena, including developmental regulation, as well as responses to environmental stressors [34]. From the analysis of promoter sequences, several CaPLATZ genes were identified as having a number of hormone-signaling, as well as stress response, elements in this analysis. Ten CaPLATZ genes contained the element ERE, suggestive of a potential role in modulating mechanisms of adaptation to ethylene-mediated stress mechanisms [35]. Antioxidant-responsive elements (AREs) were also identified in ten CaPLATZ genes, strongly correlating with plant stress responses [36]. The existence of such regulatory elements as ERE constitutes structural evidence of CaPLATZ gene involvement in stress-related signaling mechanisms, providing insight into potential mechanisms of stress tolerance in pepper.
In this study, the majority of CaPLATZ genes exhibited significant expression in pepper roots, suggesting their potential involvement in root growth and development. Similarly, tomato SlPLATZ17 showed elevated expression levels in root and floral tissues [5]. Among the Malus MdPLATZ genes (MdPLATZ1, MdPLATZ2, MdPLATZ4, MdPLATZ6, MdPLATZ7, MdPLATZ11, and MdPLATZ19), higher expression levels were observed in roots, consistent with tissue-specific expression analyses performed here [7]. These findings collectively indicate that PLATZ genes are highly expressed in roots across diverse plant species, implying a conserved functional role in root development.
Drought stress is a major factor affecting plant growth and development, which limits agricultural production [37]. To investigate the functional role of CaPLATZ genes in pepper’s response to drought stress, we analyzed their expression patterns under drought conditions. The transcription levels of CaPLATZ1, CaPLATZ3, and CaPLATZ7 increased significantly following drought treatment. Specifically, CaPLATZ1 and CaPLATZ3 expression peaked at 6 h post-treatment but declined sharply by 12 h. In contrast, CaPLATZ7 expression exhibited a sustained increase under prolonged drought stress. For example, overexpression of AtPLATZ1 enhanced drought tolerance in transgenic Arabidopsis [18]. In tomato, the expression of SlPLATZ17 was significantly upregulated during the initial phase of three independent stress treatments, reaching a peak at 1.5 h post-induction, followed by a gradual decline, though remaining consistently higher than pretreatment levels throughout the experimental period. Furthermore, SlPLATZ17 silencing markedly reduced plant resistance to both salinity and drought stresses. Notably, this expression pattern aligns with those observed for CaPLATZ1 and CaPLATZ3 in related species, strongly suggesting conserved functional roles in abiotic stress adaptation among these PLATZ family members [5]. Similarly, overexpression of GmPLATZ17 in soybean increased drought sensitivity and suppressed stress-related gene transcription, whereas silencing GmPLATZ17 improved drought tolerance in transgenic soybean hairy roots [9]. Collectively, these findings suggest that CaPLATZ genes may contribute to pepper’s drought stress response, meriting further investigation.

5. Conclusions

In this study, 11 CaPLATZ genes were non-uniformly located across eight pepper chromosomes, and synteny analyses identified a duplication event involving a single gene pair. Phylogenetic analyses categorized the CaPLATZ genes into four distinct subgroups, each exhibiting similar gene structures and conserved motif patterns within its subgroup. The assessment of cis-acting regulatory elements indicated potential involvement of CaPLATZ genes in responses to abiotic stresses and various phytohormones. The qRT-PCR results showed that the transcription levels of CaPLATZ1, CaPLATZ3, and CaPLATZ7 significantly increased following drought treatment. These results indicated that these genes are particularly critical in drought response. Overall, these findings provide insight into CaPLATZ gene evolution and form a worthwhile foundation for future breeding programs focusing on increased stress resistance in pepper.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/genes16060632/s1. Table S1 The identified amino acid sequences of PLATZ in Arabidopsis, pepper. Table S2 The primer sequences used in this study.

Author Contributions

Conceptualization, X.W. (Xingliang Wang); data curation, X.W. (Xingliang Wang), Y.H., N.Y., X.W. (Xue Wang), Y.W., and W.M.; formal analysis, Y.H.; funding acquisition, X.W. (Xingliang Wang) and H.Z.; investigation, X.W. (Xingliang Wang), Y.H., N.Y., and Y.W.; project administration, H.Z.; software, N.Y. and X.W. (Xue Wang); supervision, X.W. (Xue Wang); validation, Y.H.; visualization, W.M.; writing—original draft preparation, X.W. (Xingliang Wang); writing—review and editing, X.W. (Xingliang Wang), N.Y., and H.Z. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by the Foundation for Key Research and Development Program of Heilongjiang Province (grant number SC2022ZX02C0202) and the Foundation for Key Research and Development Program of Shandong Province (grant number 2024LZGCQY009).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Data are contained within the article and Supplementary Materials.

Conflicts of Interest

The authors declare no conflicts of interest.

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Figure 1. Phylogenetic trees depicting PLATZ family members in A. thaliana and pepper. The PLATZ proteins were classified into 4 groups distinguished by different colors.
Figure 1. Phylogenetic trees depicting PLATZ family members in A. thaliana and pepper. The PLATZ proteins were classified into 4 groups distinguished by different colors.
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Figure 2. Chromosome-level analyses of the CaPLATZ gene family in the pepper genome assembly. (A) Chromosomal positions and synteny relationships among CaPLATZ genes. Red lines indicate syntenic gene pairs. (B–D) Synteny analyses comparing pepper PLATZ genes with those of A. thaliana, S. lycopersicum, and O. sativa, respectively.
Figure 2. Chromosome-level analyses of the CaPLATZ gene family in the pepper genome assembly. (A) Chromosomal positions and synteny relationships among CaPLATZ genes. Red lines indicate syntenic gene pairs. (B–D) Synteny analyses comparing pepper PLATZ genes with those of A. thaliana, S. lycopersicum, and O. sativa, respectively.
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Figure 3. Conserved motifs and gene structures of the CaPLATZ gene family in pepper. (A) Phylogenetic relationships among the CaPLATZ proteins. (B) Motif composition patterns in the CaPLATZ proteins. (C) Exon–intron structural variations of the CaPLATZ genes.
Figure 3. Conserved motifs and gene structures of the CaPLATZ gene family in pepper. (A) Phylogenetic relationships among the CaPLATZ proteins. (B) Motif composition patterns in the CaPLATZ proteins. (C) Exon–intron structural variations of the CaPLATZ genes.
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Figure 4. Distribution of CAREs in CaPLATZ gene promoters in pepper.
Figure 4. Distribution of CAREs in CaPLATZ gene promoters in pepper.
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Figure 5. Expression patterns of the CaPLATZ gene family across different tissues and abiotic stresses. (A) Heatmap illustrating CaPLATZ expression in pepper tissues, including root, stem, leaf, bud, flower, and fruit developmental stages. The 1–9 stages of fruit development are presented in the five early stages of color breaking (0–1, 1–3, 3–4, and 4–5 cm long fruits and mature-green fruits), the color breaking stage (fruit beginning to turn red), and three late stages of color breaking (3, 5, and 7 days after color breaking), respectively. (B–E) Expression profiles under abiotic stresses: (B) cold stress, (C) heat stress, (D) drought stress, and (E) salt stress. Abbreviations: R, roots; L, leaves; Dev., developmental stages.
Figure 5. Expression patterns of the CaPLATZ gene family across different tissues and abiotic stresses. (A) Heatmap illustrating CaPLATZ expression in pepper tissues, including root, stem, leaf, bud, flower, and fruit developmental stages. The 1–9 stages of fruit development are presented in the five early stages of color breaking (0–1, 1–3, 3–4, and 4–5 cm long fruits and mature-green fruits), the color breaking stage (fruit beginning to turn red), and three late stages of color breaking (3, 5, and 7 days after color breaking), respectively. (B–E) Expression profiles under abiotic stresses: (B) cold stress, (C) heat stress, (D) drought stress, and (E) salt stress. Abbreviations: R, roots; L, leaves; Dev., developmental stages.
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Figure 6. Validation of CaPLATZ gene expression under drought stress conditions using qPCR. Statistical significance levels: * p ≤ 0.05; ** p ≤ 0.01; *** p ≤ 0.001; **** p ≤ 0.0001 (t-test).
Figure 6. Validation of CaPLATZ gene expression under drought stress conditions using qPCR. Statistical significance levels: * p ≤ 0.05; ** p ≤ 0.01; *** p ≤ 0.001; **** p ≤ 0.0001 (t-test).
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Table 1. Description of pepper PLATZ genes.
Table 1. Description of pepper PLATZ genes.
NumberGene IDGene NameChrStartStopStrandSize (aa)MWs (Da)pILoc
1CaPLATZ1Capana01g001082129,898,51029,900,326−23125,991.489.30nucl
2CaPLATZ2Capana01g0035771229,778,174229,780,086−24127,134.368.93nucl
3CaPLATZ3Capana01g0043381296,584,241296,586,323−18220,484.669.73nucl
4CaPLATZ4Capana02g0011472111,660,814111,663,906−24027,282.986.16nucl
5CaPLATZ5Capana04g0000214366,427367,644−24227,830.568.25nucl
6CaPLATZ6Capana05g000900534,861,70534,865,244+17420,057.158.84nucl
7CaPLATZ7Capana06g001532636,555,37736,556,697−24527,769.759.30nucl
8CaPLATZ8Capana07g000312715,338,56615,340,312−20423,382.87.05chlo
9CaPLATZ9Capana07g0012627168,116,678168,126,780+18921,752.298.75cyto
10CaPLATZ10Capana09g00010994,956,3824,957,541−24728,113.138.30nucl
11CaPLATZ11Capana10g00153210163,187,426163,189,479+20422,819.098.97nucl
Note: Loc, subcellular location.
Table 2. Characteristics of conserved motifs identified in pepper PLATZ proteins.
Table 2. Characteristics of conserved motifs identified in pepper PLATZ proteins.
MotifLength (aa)Best Possible Match
141HKDHRLJQIRRYVYHDVVRLNEIZKYJDCSSVQTYIINSAK
235KPPWLKPLLKEKFFVACKIHEDAKKNEKNMYCLDC
329KGVTNTCEICERSLLDSFRFCSLGCKVVG
417NYKTMKRRKGIPHRAPL
511VVFLNERPQPR
641FLRRCTTLQLGPDFFIPNDMGDDDMANETAHSTIVDSDEPW
714NKIQSFSPSTPPPT
811NLALCPHCLSS
921VMSFPCTEFVRKKRSGLHVCG
1017TSKNFVKKPKQSPEKKR
141HKDHRLJQIRRYVYHDVVRLNEIZKYJDCSSVQTYIINSAK
235KPPWLKPLLKEKFFVACKIHEDAKKNEKNMYCLDC
329KGVTNTCEICERSLLDSFRFCSLGCKVVG
417NYKTMKRRKGIPHRAPL
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Wang, X.; Huang, Y.; Yang, N.; Wang, X.; Wang, Y.; Ma, W.; Zhang, H. Genome-Wide Identification of CaPLATZ Family Members in Pepper and Their Expression Profiles in Response to Drought Stress. Genes 2025, 16, 632. https://doi.org/10.3390/genes16060632

AMA Style

Wang X, Huang Y, Yang N, Wang X, Wang Y, Ma W, Zhang H. Genome-Wide Identification of CaPLATZ Family Members in Pepper and Their Expression Profiles in Response to Drought Stress. Genes. 2025; 16(6):632. https://doi.org/10.3390/genes16060632

Chicago/Turabian Style

Wang, Xingliang, Yue Huang, Na Yang, Xue Wang, Yuanqian Wang, Wenyao Ma, and Hui Zhang. 2025. "Genome-Wide Identification of CaPLATZ Family Members in Pepper and Their Expression Profiles in Response to Drought Stress" Genes 16, no. 6: 632. https://doi.org/10.3390/genes16060632

APA Style

Wang, X., Huang, Y., Yang, N., Wang, X., Wang, Y., Ma, W., & Zhang, H. (2025). Genome-Wide Identification of CaPLATZ Family Members in Pepper and Their Expression Profiles in Response to Drought Stress. Genes, 16(6), 632. https://doi.org/10.3390/genes16060632

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