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Article

Comprehensive Genome-Wide Investigation and Transcriptional Regulation of the DHHC Gene Family in Cotton Seed and Fiber Development

by
Saimire Silaiyiman
1,2,3,†,
Qinyue Zheng
1,†,
Yutao Wang
2,3,
Lejun Ouyang
1,2,
Zhishan Guo
1,
Jieli Yu
1,
Rong Chen
1,
Rui Peng
1 and
Chao Shen
1,*
1
College of Biological and Food Engineering, Guangdong University of Petrochemical Technology, Maoming 525000, China
2
College of Life and Geographic Sciences, Kashi University, Kashi 844000, China
3
Key Laboratory of Biological Resources and Ecology of Pamirs Plateau in Xinjiang Uygur Autonomous Region, Kashi 844000, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Agronomy 2024, 14(6), 1214; https://doi.org/10.3390/agronomy14061214
Submission received: 18 April 2024 / Revised: 23 May 2024 / Accepted: 3 June 2024 / Published: 4 June 2024
(This article belongs to the Special Issue Analysis of Complex Traits and Molecular Selection in Annual Crops—2nd Edition)
Browse Figures
Versions Notes

Abstract

:
Protein palmitoylation, the most common and the only reversible post-translational lipid modification following protein translation, plays a pivotal role in the biochemical and physiological processes of both animals and plants. DHHC proteins, enriched with DHHC (Asp-His-His-Cys) domains, serve as catalyst for protein palmitoylation. However, research on DHHC in cotton remains scarce. This study conducted a systematic characterization and bioinformatics analysis on G. arboreum, G. raimondii, G. hirsutum, and G. barbadense, detecting 38, 37, 74, and 74 DHHC genes, respectively. Phylogenetic analysis categorized the DHHC gene family into six subgroups, consistent with previous evolutionary studies in Arabidopsis and rice. A further examination of protein structure revealed a correlation between genetic relatedness, structural similarity, and functional identity. Cis-element analysis identified elements predominantly associated with light response, stress, growth and development, and plant hormones. The integration of cotton seed development transcriptome, tissue expression pattern analysis, and population transcriptome data collectively suggests that Ghir_A05G027650 and Ghir_D05G027670 are promising candidate genes influencing seed development in upland cotton. Conversely, Gbar_A04G010750 and Gbar_A12G020520 emerge as potential candidates affecting both seed and fiber development in sea island cotton. These findings lay down a theoretical foundation for delving into the functional diversity of DHHC genes in cotton, thereby paving the way for the development of new breeding strategies and the optimization of cotton seed and fiber production, ultimately contributing to improved crop yield and quality.

1. Introduction

Palmitoylation involves attaching palmitic acid to specific cysteine residues of target proteins, making it the most prevalent lipid modification post protein translation and the sole reversible post-translational lipid alteration [1]. DHHC proteins feature a rich DHHC (Asp-His-His-Cys) domain with highly conserved sequences. Most possess palmitoyl transferase (PAT) activity, facilitating the addition of palmitate to substrate proteins and thus catalyzing protein palmitoylation [2]. This process significantly impacts protein structure, transportation and function, thereby regulating diverse physiological processes including membrane receptors, enzymatic reactions, and cell adhesion, etc. [3]. Its relevance extends to various biochemical and physiological reactions in both animals and plants [2].
In recent years, DHHC genes have been identified across multiple species, including yeast [4], Arabidopsis [5], rice [6], apple [7], human [8], etc. While many studies have focused on the functions of palmitoylation in animals and humans, DHHC21, for instance, is known for its role in regulating the T cell receptor pathway and T cell-mediated immune regulation [9,10], as well as its involvement in endothelial response to inflammation [11]. Human DHHC proteins are implicated in various diseases such as X-linked intellectual disability and Huntington’s disease [2], with DHHC9 notably playing a significant role in gametogenesis [12]. The DHHC3-mediated protein palmitoylation process has been implicated in supporting breast tumor growth through the regulation of cellular oxidative stress and senescence [13]. Furthermore, knockout experiments in mice have confirmed the importance of DHHC3 in the normal accumulation of GABAARs in synapses and receptor-dependent presynaptic innervation [14]. These examples underscore the vital regulatory role of DHHC proteins in the physiological activities of animals.
Compared to animals and humans, research on DHHC proteins in plants remains relatively scarce. In Arabidopsis thaliana, twenty-four DHHC members have been identified [5], impacting various aspects such as salt tolerance [15], root development [15], immune responses [16,17], signal transduction [18] and reproductive processes [19]. Similarly, in rice, OsDHHC1 has been shown to regulate plant structure and grain yield [20], and its transfer into rapeseed influences branching and seed yield in transgenic plants [21]. OsDHHC30 enhances the interaction between OsCBL2 and OsCBL3 through S-acylation, thereby improving salt tolerance [22], providing insights into the functioning of the OsDHHC-OsCBL-OsCIPK signaling pathway in rice [23]. Furthermore, DHHC09 mediates the S-acylation of the kinase STRK1, a crucial process for regulating hydrogen peroxide (H2O2) homeostasis and enhancing salt tolerance [24]. Notably, LOC_Os01g70100 encodes a protein that contains a zinc finger DHHC domain, implicating its involvement in the management of salt stress responses during the critical seedling stage in rice [25]. These studies underscore the significance of DHHC zinc finger proteins in regulating various physiological processes in plants and their impact on plant life activities. However, research on DHHC genes in cotton is still limited.
Cotton stands out as the most economically significant fiber crop globally. However, the DHHC gene family has not been thoroughly investigated across diploid and tetraploid cotton genomes. With the completion of reference genome sequences for diploid G. arboreum [26], G. raimondii [27], as well as tetraploid G. hirsutum TM-1 and G. barbadense 3-79 [28], there is now an opportunity for systematic identification and comprehensive comparative analysis.
Here, we identified 223 DHHC genes in G. arboreum, G. raimondii, G. hirsutum, and G. barbadense and evaluated their physical and chemical properties, subcellular organelle localization, protein structure, phylogenetic relationships, chromosome location, the tissue expression patterns, and cis-acting elements. Upon integrating cotton seed development transcriptome, tissue expression pattern analysis, and population transcriptome data, it is suggested that Ghir_A05G027650, Ghir_D05G027670, Gbar_A04G010750, and Gbar_A12G020520 emerge as potential candidate genes affecting both seed and fiber development in sea island cotton. These findings lay a solid groundwork for further investigations into cotton DHHC proteins and offer valuable insights into the broader understanding of DHHC proteins in plants.

2. Materials and Methods

2.1. Identification and Characterization of Cotton DHHC Genes

In order to identify the DHHC genes in cotton, genomic data from G. arboreum, G. raimondii, G. hirsutum, and G. barbadense were acquired from CottonFGD (https://cottonfgd.net/, accessed on 6 March 2024) and compared with the amino acid sequence of the Arabidopsis DHHC (AtDHHC) protein obtained from the TAIR database (https://www.arabidopsis.org/, accessed on 6 March 2024) using the BLASTp (protein–protein basic local alignment search tool) search with an e-value of 1.0 × 10−10 [29,30]. The hidden Markov model (HMM) profile PF01529 was obtained from the Pfam database (http://pfam.xfam.org, accessed on 6 March 2024), and potential DHHC proteins were identified using HMMER (version 3.1) with the default parameter [31]. Candidate DHHC genes were then determined using SMART (Simple Modular Architecture Research Tool; version 8.0) [32] and CDD (Conserved Domain Database) [33]. The physical and chemical properties of DHHC proteins among four cotton species were predicted using ProtParam (https://web.expasy.org/protparam, accessed on 6 March 2024) of ExPASy.

2.2. Sequence Alignment and Phylogenetic Analysis

ClustalX (version 1.83) [34] was employed for multiple sequence alignment with the default settings. Subsequently, the neighbor joining method was used to construct phylogenetic trees using MEGA (version 11) [35] with the Bootstrap repeat test set to 1000. The resulting phylogenetic trees were enhanced for clarity and aesthetics using iTOL (https://itol.embl.de/, accessed on 6 March 2024).

2.3. Conservation and Structure of Cotton DHHC Genes

Gene structure and conserved motif map were analyzed and illustrated with TBtools (version 1.123) subroutines for Gene Structure View and Simple MEME [36] based on the genome annotation information. Secondary structure prediction was conducted using SOPMA (https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_sopma.html, accessed on 6 March 2024), while three-dimensional structures were obtained from SWISS-MODEL (https://swissmodel.expasy.org/interactive, accessed on 6 March 2024). Subcellular location was predicted using the Bologna Unified Asian Component Annotator (BUSCA, http://busca.biocomp.unibo.it, accessed on 6 March 2024).

2.4. Chromosomal Location, Collinearity, and Multiple Synteny Analysis

The physical positions of DHHC genes were retrieved form genome data, mapped onto chromosomes, and visualized using the TBtools subroutine “show gene on chromosome” (version 1.123) [36]. Homologous gene pairs were identified using the Basic Local Alignment Search Tool with the default parameter [29]. Syntenic relationships were analyzed and visualized using MCScanX [37] and the TBtools (version 1.123) subroutine for multiple synteny plots [36].

2.5. Expression Patterns and Cis-Regulatory Elements Analysis

To determine the expression pattern of the DHHC gene, the tissue expression profile data of G. hirsutum TM-1 and G. barbadense 3-79 genes were obtained from Wang et al. [28]. A natural population of 210 upland cotton (Gossypium hirsutum) accession transcriptome data were obtained from the NCBI under project number PRJNA433615 [38]. The seed development transcriptome data were downloaded from the NCBI under project number PRJNA667195 [39]. The raw sequencing data were processed with Trimmomatic (v.0.32) for data quality control [40]. The clean data were then compared to reference genomes using hisat2 software (v.2.1.0) with default settings [41], and Cufflinks was used to calculate the FPKM (fragments per kilobase of transcript per million mapped reads) value, the gene expression quantity, and the search for differentially expressed genes [42]. The FPKM value was visualized as heatmaps using the TBtools Heatmap Illustrator (version 1.123) [36]. Cis-regulatory elements were analyzed by obtaining the upstream 2000 bp regions of the DHHC genes using PlantCARE software with default settings [43]. A visual display of differentially expressed genes was performed using EVenn software [44].

3. Results

3.1. Identification and Biophysical Characteristics of DHHC Genes

Here, we identified 223 DHHC genes, including 38 in G. arboretum, 37 in G. raimondii, 74 in G. hirsutum, and 74 in G. barbadense. Notably, tetraploid species exhibited nearly twice as many DHHC genes as diploid species. Furthermore, we characterized the biophysical properties of DHHC genes in these four cotton species, including amino acid count, isoelectric point (pI), molecular weight (MW) and subcellular localization, etc. (Tables S1–S4). The amino acid number of all the DHHC genes ranged from 122 (Ga08G2480) to 730 (Gorai.001G093300, Ghir_D07G009100, Gbar_A07G008800, and Gbar_D07G009150), the protein molecular weight varied from 13,951.97 Da (Ga08G2480) to 79,086.89 Da (Gorai.001G093300), the isoelectric point varied from 5.13 (Ghir_D03G007980) to 10.04 (Ghir_D12G013150), the instability coefficient ranged from 24.11 (Ghir_D08G022980) to 64.55 (Ghir_A13G007860), and the hydrophilic average coefficient ranged from −0.3 (Gorai.009G186300 and Gorai.009G286000) to 0.832 (Gbar_A03G004940), respectively (Tables S1–S4). According to BUSCA analysis, 70.40% of the DHHC genes were found in the inner membrane system, 28.25% in the plasma membrane, and only 1.35% in the nucleus. Most genes were located in the intimal system based on subcellular localization. Intriguingly, the genes present in the nucleus were exclusive to G. hirsutum, specifically Ghir_A01G017180, Ghir_A05G001390, and Ghir_D05G001550.

3.2. Intraspecific and Interspecific Phylogenetic Relationships of DHHC Genes

To elucidate the evolutionary relationships of the DHHC gene family within and between cotton species, phylogenetic trees were constructed. These trees revealed that the genes clustered into six subgroups and were randomly distributed (Figure 1 and Figure S1). Subgroup II contained the highest number of genes, accounting for 30.64%, while Subgroup VI harbored the fewest genes, comprising only 2.69% (Figure 1). Notably, we observed that diploid G. arboreum and G. raimondii each contained one DHHC gene, whereas tetraploid G. hirsutum and G. barbadense contained two DHHC genes, one for the A subgenome and one for the D subgenome. These results suggest that the genome duplication occurred during cotton evolution.

3.3. Gene Structure and Conserved Motifs of DHHC Genes

An analysis of gene structure and conserved motifs was conducted to elucidate the structural evolution of the DHHC gene family in cotton. The results revealed a diverse range of intron numbers across the four cotton species. G. arboreum exhibited three to fifteen introns, G. raimondii three to twelve introns, G. hirsutum two to twelve introns, and G. barbadense three to twelve (Figure 2 and Figure S2). Notably, genes within similar subgroups exhibited comparable genetic structures, with instances such as Ga08G2480, Ga13G0284, and Ga13G1189 containing three introns, while Ga12G1899 harbored fifteen. Ghir_A05G031690 stood out with only two introns (Figure S2A). Additionally, most DHHC genes contained four introns, with 9 genes in G. arboreum, 6 genes in G. raimondii, 19 genes in G. hirsutum, and 19 genes in G. barbadense (Figure 2 and Figure S2). Overall, the comparative analysis revealed considerable variability in intron number among the different cotton species, with neither the position nor the length of introns remaining conserved.
We performed the conserved motif analysis and extracted ten motifs, which showed that similar distribution patterns of the DHHC protein conserved motifs appear to cluster closely together within the same evolutionary clade (Figure 2 and Figure S2). Most of the DHHC genes had seven conserved motifs in G. raimondii (Figure S2B); however, most of the DHHC genes in the other three cotton species had six conserved motifs. Motifs 4 and 9 are common to all DHHC proteins. Most DHHC members contained motif 2, which indicated that it played an important, possibly similar structural role in DHHC proteins. In addition, some motifs occurred only in certain branches of gene evolution, such as motif 10, which suggested that the unique motifs of different branches may represent the conserved and specific functions of the DHHC gene family. Moreover, we found that DHHC proteins were closely related, and their motifs and their arrangement were similar in the same class of proteins.

3.4. Prediction of Secondary and Tertiary Structure of DHHHC Genes

Secondary and tertiary structures of DHHC genes predominantly comprised α-helices, β-turns, extended chains, and random coils (Figures S3 and S4). Among them, α-helix (21~54%) and random coils (26~62%) constituted the major components, with extended strands (85~27%) and aβ-turns (2~10%) representing minor proportions (Figure S3). It can be seen from the figure that members within the same group are more similar in three-dimensional structure than members between different groups. Notably, members within the same evolutionary group exhibited greater structural similarity compared to those from different groups, underscoring the evolutionary conservation of structural features within the DHHC gene family (Figure 1 and Figure S4).

3.5. Chromosomal Location of Cotton DHHC Genes

Moreover, 223 DHHC genes were identified and distributed across different chromosomes in the four species of cotton, revealing no significant correlation between the number distribution of each gene and chromosome length (Figure 3 and Figure S5). Furthermore, 38 DHHC genes were unevenly localized on all 13 chromosomes in G. arboreum. Notably, chromosomes Chr01, Chr03, Chr04, Chr06, and Chr10 harbored the fewest genes, each containing only one gene, whereas Chr02 contained the highest number, with six genes (Figure S5A). Similarly, 37 DHHC genes were scattered on all 13 chromosomes in G. raimondii. Chromosomes Chr05, Chr10, and Chr11 housed the fewest genes, each containing only one, while Chr13 accommodated the highest number, with five genes (Figure S5B). There were 74 DHHC genes unevenly distributed on 26 chromosomes in G. hirsutum, including 37 genes in At and 37 genes in Dt (Figure 3A). In G. barbadense, 74 DHHC genes were distributed on 26 chromosomes, including 35 genes in At, 36 genes in Dt, and 3 genes in scaffolds (Figure 3B). Notably, the distribution pattern of DHHC genes on the chromosomes of G. hirsutum and G. barbadense exhibited high similarity (Figure 3).

3.6. Collinearity of DHHC Genes

Whole-genome duplication events or polyploidy play pivotal roles in species evolution. To elucidate the evolutionary relationships of DHHC genes, a relative collinearity map was generated (Figure 4). By analyzing homologous genes, it was found that there were 32 pairs of homologous genes between the G. arboretum and At-subgenome of G. hirsutum (GhAt), as well as the G. arboretum and At-subgenome of G. barbadense (GbAt) (Figure 4A). Similarly, 34 orthologous gene pairs were identified between the G. raimondii and Dt-subgenome of G. hirsutum (GhDt), as well as the G. raimondii and Dt-subgenome of G. barbadense (GbDt) (Figure 4B). Further elucidating the duplication events of DHHC genes, we identified 24, 29, 37, and 35 pairs of fragment duplications in G. arboreum, G. raimondii, G. hirsutum, and G. barbadense, respectively (Figure S6). Additionally, a tandem duplication event was discovered between Ga12G1710 and Ga12G1711 in G. arboretum (Figure S6A).

3.7. Analysis of Cis-Regulatory Elements of DHHC Gene Family

Here, we used the upstream 2 kb sequence of the DHHC gene to perform the analyze, and 32–42 cis-regulatory elements were identified and categorized into four groups, light response, abiotic stress, growth and development, and plant hormones, among the four cotton species (Figure 5 and Figure S7). We found that light-responsive elements were the most common among the four cotton species, encompassing A-box, an ATCT-motif, chs-CMA1a, a TCT-motif, MRE, and a TCCC-motif. Additionally, it was found that three responsive elements related to growth and development were common in these four cotton species, including CAAT-box, CAT-box, and TATA-box. A comparative analysis revealed that some elements related to growth and development were solely detected in tetraploids, such as palisade mesophyll cell differentiation elements (HD-Zip1) and cis-acting regulatory elements involved in circadian control. Stress response elements, including drought response elements (MBS), defense- and stress-related elements (TC-rich repeats), and low-temperature response (LTR), were detected across all four cotton species. Moreover, hormone-related elements such as auxin (AuxRR-core), gibberellin (GARE-motif), jasmonic acid (CGTCA-motif), and abscisic acid (ABRE) were also identified.

3.8. Differentially Expressed DHHC Genes in Different Seed Development Stages and Tissue Expression Patterns of DHHC Genes

Tissue-specific expression patterns of DHHC genes offer valuable insights into their potential functions within the cotton genome. We conducted an in-depth analysis of transcriptome data from various tissues of both G. hirsutum and G. barbadense, revealing a widespread expression of DHHC genes. In G. hirsutum, the comprehensive expression profiling of the DHHC gene family unveiled expression across all tissues. Ghir_A01G018690, Ghir_D01G020130, and Ghir_A02G012640 exhibited high expression, specifically in anthers, indicating strong tissue-specific expression (Figure S8A), and the evolutionary tree also showed that they were in the same branch. Additionally, Ghir_A13G009850 and Ghir_D03G006270 were specifically expressed on the fifth and twenty-fifth days of fiber development, respectively (Figure S8A). Similarly, Ghir_A09G004800 and Ghir_D09G004240 displayed heightened expression during ovule development and fiber development (Figure S8A). Moreover, Ghir_A12G020440 and Ghir_D12G020700 exhibited peak expression levels on the 10th day of fiber development (Figure S8A). In contrast, G. barbadense demonstrated distinct expression patterns, with the gene Gbar_A13G10430 exhibiting higher expression levels across all tissues. Notably, Gbar_A01G019140, Gbar_A02G012400, Gbar_D01G020240, and Gbar_D03G018440 were exclusively highly expressed in stigmas (Figure S8B). Furthermore, Gbar_A12G020520 showed elevated expression levels during fiber development (Figure S8B).
Upon comparing the transcriptome data of three developmental stages of cotton seeds (10, 20, and 30 DPA) from G. hirsutum and G. barbadense, it was evident that the total number of differentially expressed genes in upland cotton surpassed that of sea island cotton (Figure 6). Notably, the comparative periods of ‘20 DPA vs. 10 DPA’ and ‘30 DPA vs. 20 DPA’ exhibited the highest overlap in terms of differentially expressed genes across both species (Figure 6A,C). Moreover, among the differentially expressed genes in G. hirsutum during ‘20 DPA vs. 10 DPA’, 11 DHHC genes were identified, with 1 exhibiting up-regulation and 10 showing down-regulation, such as Ghir_D05G027670 (Figure 6B and Figure S5A). However, no DHHC genes were found among the differentially expressed genes in ‘30 DPA vs. 10 DPA’. In ‘30 DPA vs. 20 DPA’, 12 DHHC genes were identified, with 3 showing up-regulation and 8 showing down-regulation (Figure 6B). In G. barbadense, during ‘20 DPA vs. 10 DPA’, nine DHHC genes were differentially expressed, with three up-regulated and six down-regulated. Meanwhile, ‘30 DPA vs. 10 DPA’ exhibited two DHHC genes with down-regulated expression. Lastly, ‘30 DPA vs. 20 DPA’ showed 10 DHHC genes, with 4 up-regulated and 6 down-regulated (Figure 6D). Further comparative analysis revealed a differential up-regulation of DHHC genes Gbar_A11G008320 and Gbar_D11G036050 during the periods of ‘20 DPA vs. 10 DPA’ and ‘30 DPA vs. 10 DPA’, while Gbar_A04G010750 and Gbar_A12G020520 demonstrated significant down-regulation during both periods. Additionally, Gbar_A12G013040 and Gbar_D12G013030 were found to be down-regulated in the comparative periods of ‘30 DPA vs. 10 DPA’ and ‘30 DPA vs. 20 DPA’ (Figure 6D). These findings underscore the involvement of DHHC genes in various aspects of cotton growth and development, highlighting their diverse functional roles across different tissues and developmental stages.

3.9. Expression of DHHC Genes in G. hirsutum Population

Utilizing the 3 terabyte population transcriptome data from 210 upland cotton fibers across a 15-day development period, we conducted an analysis revealing distinct expression patterns among members of the DHHC gene family within the population (Figure 7). Some genes exhibited consistently high expression levels across all population materials. For example, Ghir_A01G018690 and Ghir_D13G009350 displayed peak expression on the 15th day of fiber development (Figure 7). Conversely, certain genes demonstrated varying expression levels across different materials within the population. For instance, Ghir_A05G027650 and Ghir_D05G027670 exhibited high expression in some materials while displaying lower expression in others, and they also differentially down-regulated expressed genes during the ‘20 DPA vs. 10 DPA’ period of upland cotton seed development (Figure 7). Intriguingly, several genes showed consistently low expression levels across all population materials. This includes Ghir_D03G006270, Ghir_D01G020130, Ghir_A13G009850, and Ghir_A02G012640 (Figure 7).

4. Discussion

There exists a substantial population of palmitoylated modified proteins within plants, crucial for regulating various protein functions governing responses to abiotic stresses, plant growth and development, physiological diseases, and gamete formation [3,45]. Despite its significance, research on protein palmitoylation in plants remains limited, presenting considerable knowledge gaps [46,47]. Considering the huge economic value of cotton, it is imperative to identify and analyze cotton DHHC genes concerning cotton growth, development, and response to various abiotic stresses. Here, we identified and characterized the DHHC gene family in cotton, uncovering several candidate genes and highlighting their potential roles in seed and fiber development.
To date, DHHC genes have been identified in diverse plant species, including Arabidopsis [5], rice [20], and apple [7], where they play roles in protein trafficking and signal transduction. Here, we identified a total of 223 DHHC genes, encompassing 38 in G. arboretum, 37 in G. raimondii, 74 in G. hirsutum, and 74 in G. barbadense, which showed that there were almost twice as many tetraploids as diploids and indicated that they had undergone expansion during cotton chromosome duplication and evolution. Compared with 24 DHHCs in Arabidopsis [5], 30 DHHCs in rice [20], and 33 DHHCs in apple [7], the number of DHHCs in diploid cotton G. arboreum and G. raimondii is comparable, whereas in tetraploid G. hirsutum and G. barbadense, it is double that of diploids. This quantitative disparity in the DHHC gene family among different species indicates differentiation and expansion during plant evolution [48].
Gene identification and functional classification are key to exploring the functions of gene families. To obtain a deeper understanding of the DHHCs in cotton, we systematically investigated the biophysical characteristics, intraspecific and interspecific phylogenetic relationships, chromosomal location, collinearity, cis-acting elements, tissue expression pattern, and population transcriptional expression of DHHCs. The physicochemical properties of the DHHC gene family show a wide range of variation. The DHHC gene family has approximately 2–12 introns, and some members even have 15 introns, showing great structural complexity, suggesting the diversity of their structural functions [49].
Evolutionary relationships show that the DHHC gene family is divided into six subgroups. It is found that closely related members have similar gene structures, suggesting that the closer the relationship, the more similar the functions [50]. An examination of gene duplication in the DHHC gene family, based on the gene number, evolutionary relationships, and collinearity analysis between diploid and tetraploid species, suggests functional differentiation among the different subgenomes of cotton, as observed in Arabidopsis [51] and rice [52]. Notably, the phylogenetic analysis reveals both conserved and unique DHHC genes in cotton compared to other species, suggesting evolutionary diversification.
The promoter region of DHHC gene family members harbors various cis-regulatory elements, including those responsive to light, circadian clock, growth and development, and stress-related elements, indicating their involvement in gene regulation. The presented analysis is based on bioinformatic predictions using PantCare [36], which has some level of false discoveries [53], which serves as a base for searching more complex cis-regulatory modules [54], so the functionality of the presented regulatory elements should be further verified experimentally.
Conserved motifs in the DHHC gene family ensure functional connectivity, while differences in gene sequence and structure lead to functional divergence [55]. The amalgamation of cotton seed development transcriptome analysis, tissue expression pattern examination, and population transcriptome data collectively indicates that Ghir_A05G027650 and Ghir_D05G027670 stand out as promising candidate genes with significant influence on seed development in upland cotton. In contrast, Gbar_A04G010750 and Gbar_A12G020520 emerge as potential candidates exerting an impact on both seed and fiber development in sea island cotton.
The identification of key DHHC candidate genes involved in seed and fiber development opens new avenues for developing new cotton varieties related to high yield and fiber quality. Through the targeted modification of these candidate genes using highly efficient genome editing technology, such as CRISPR/Cas9 [56], it is possible to improve cotton yield and quality. Additionally, understanding the regulatory networks involving DHHC genes can inform strategies to optimize fiber development. Overall, these genes significantly impact seed and fiber development and warrant further investigation as candidate genes.

5. Conclusions

We conducted a comprehensive genome-wide analysis across four cotton species, encompassing the prediction, identification, comparison, and analysis of the DHHC gene family. Our findings revealed that the DHHC gene family segregates into six distinct subgroups, mirroring previous evolutionary investigations in model plants like Arabidopsis and rice. Notably, we observed a correlation between genetic relatedness, structural similarity, and functional congruence within these subgroups. Tissue-specific expression analyses in tetraploid upland cotton and sea island cotton unveiled specific and differential expression patterns of DHHC genes across various tissues. This suggests their involvement in different stages of cotton growth and their regulatory roles in tissue-specific development. Furthermore, the integration of transcriptomic data from upland cotton populations pinpointed Ghir_A05G027650 and Ghir_D05G027670 as genes exhibiting specific expression during seed development, highlighting their crucial roles in this process. Gbar_A04G010750 and Gbar_A12G020520 emerge as potential candidates exerting an impact on both seed and fiber development in sea island cotton. Our findings lay a foundation for understanding the diverse functionalities of DHHC genes in cotton and pave the way for further investigations into their roles in fiber development.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/agronomy14061214/s1, Figure S1: Phylogenetic tree of the DHHC gene family among four cotton species. Figure S2: Gene structure and conserved motifs of the DHHC gene family. (A) G. arboreum. (B) G. raimondii. Figure S3: The secondary structure of the DHHC gene family. (A) G. arboreum. (B) G. raimondii. (C) G. hirsutum. (D) G. barbadense. Figure S4: The tertiary structure of the DHHC gene family. (A) G. arboreum. (B) G. raimondii. (C) G. hirsutum. (D) G. barbadense. Figure S5: The chromosomal location of the DHHC gene. (A) G. arboreum. (B) G. raimondii. Figure S6: Collinearity analysis of DHHC within each cotton species. Figure S7: Cis-regulatory elements in the promoter regions of DHHC gene family. (A) G. arboreum. (B) G. raimondii. Figure S8: Expression pattern of the DHHC genes between G. hirsutum (A) and G. barbadense (B). Table S1: Biophysical characteristics and subcellular localization of G. arboreum DHHC protein. Table S2: Biophysical characteristics and subcellular localization of G. raimondii DHHC protein. Table S3: Biophysical characteristics and subcellular localization of G. hirsutum DHHC protein. Table S4: Biophysical characteristics and subcellular localization of G. barbadense DHHC protein.

Author Contributions

Conceptualization, C.S.; methodology, C.S. and Y.W.; investigation, S.S., Q.Z. and L.O.; data curation, S.S. and Q.Z.; methodology and data curation Z.G., J.Y., R.C. and R.P.; writing—original draft preparation, S.S. and Q.Z.; writing—review and editing, L.O., Y.W. and C.S.; and funding acquisition, C.S. All authors have read and agreed to the published version of the manuscript.

Funding

This work was financially supported by the National Natural Science Foundation of China (32201873), the Guangdong Basic and Applied Basic Research Foundation (2019A1515110288), and the Projects of Talents Recruitment of the Guangdong University of Petrochemical Technology (2019rc112).

Data Availability Statement

The data presented in this study are available on request from the corresponding author.

Conflicts of Interest

The authors declare no conflicts of interest.

References

  1. Won, S.J.; Martin, B.R. Temporal profiling establishes a dynamic S-palmitoylation cycle. ACS Chem. Biol. 2018, 13, 1560–1568. [Google Scholar] [CrossRef] [PubMed]
  2. Gottlieb, C.D.; Linder, M.E. Structure and function of DHHC protein S-acyltransferases. Biochem. Soc. Trans. 2017, 45, 923–928. [Google Scholar] [CrossRef] [PubMed]
  3. Li, J.; Zhang, M.; Zhou, L. Protein S-acyltransferases and acyl protein thioesterases, regulation executors of protein S-acylation in plants. Front. Plant Sci. 2022, 13, 956231. [Google Scholar] [CrossRef] [PubMed]
  4. Abdulrahman, D.A.; Meng, X.; Veit, M. S-Acylation of proteins of coronavirus and influenza virus: Conservation of acylation sites in animal viruses and DHHC acyltransferases in their animal reservoirs. Pathogens 2021, 10, 669. [Google Scholar] [CrossRef] [PubMed]
  5. Batistic, O. Genomics and localization of the Arabidopsis DHHC-cysteine-rich domain S-acyltransferase protein family. Plant Physiol. 2012, 160, 1597–1612. [Google Scholar] [CrossRef] [PubMed]
  6. Yuan, X.; Zhang, S.; Sun, M.; Liu, S.; Qi, B.; Li, X. Putative DHHC-cysteine-rich domain S-acyltransferase in plants. PLoS ONE 2013, 8, e7598. [Google Scholar] [CrossRef] [PubMed]
  7. Sun, M.; Zhao, X.; Xu, N.; Luo, X.; Zhang, Y.; Xu, R. Genomics and expression analysis of DHHC-cysteine-rich domain S-acyl transferase protein family in apple. Genes Genom. 2016, 38, 671–684. [Google Scholar] [CrossRef]
  8. Korycka, J.; Łach, A.; Heger, E.; Bogusławska, D.M.; Wolny, M.; Toporkiewicz, M.; Augoff, K.; Korzeniewski, J.; Sikorski, A.F. Human DHHC proteins: A spotlight on the hidden player of palmitoylation. Eur. J. Cell Biol. 2012, 91, 107–117. [Google Scholar] [CrossRef] [PubMed]
  9. Fan, Y.; Shayahati, B.; Tewari, R.; Boehning, D.; Akimzhanov, A.M. Regulation of T cell receptor signaling by protein acyltransferase DHHC21. Mol. Biol. Rep. 2020, 47, 6471–6478. [Google Scholar] [CrossRef] [PubMed]
  10. Bieerkehazhi, S.; Fan, Y.; West, S.J.; Tewari, R.; Ko, J.; Mills, T.; Boehning, D.; Akimzhanov, A.M. Ca2+-dependent protein acyltransferase DHHC21 controls activation of CD4+ T cells. J. Cell Sci. 2022, 135, jcs258186. [Google Scholar] [CrossRef] [PubMed]
  11. Beard, R.S., Jr.; Yang, X.; Meegan, J.E.; Overstreet, J.W.; Yang, C.G.; Elliott, J.A.; Reynolds, J.J.; Cha, B.J.; Pivetti, C.D.; Mitchell, D.A.; et al. Palmitoyl acyltransferase DHHC21 mediates endothelial dysfunction in systemic inflammatory response syndrome. Nat. Commun. 2016, 7, 12823. [Google Scholar] [CrossRef] [PubMed]
  12. Tay, C.L.; Jones, M.L.; Hodson, N.; Theron, M.; Choudhary, J.S.; Rayner, J.C. Study of Plasmodium falciparum DHHC palmitoyl transferases identifies a role for PfDHHC9 in gametocytogenesis. Cell. Microbiol. 2016, 18, 1596–1610. [Google Scholar] [CrossRef] [PubMed]
  13. Sharma, C.; Wang, H.X.; Li, Q.; Knoblich, K.; Reisenbichler, E.S.; Richardson, A.L.; Hemler, M.E. Protein acyltransferase DHHC3 regulates breast tumor growth, oxidative stress, and senescence. Cancer Res. 2017, 77, 6880–6890. [Google Scholar] [CrossRef] [PubMed]
  14. Kilpatrick, C.L.; Murakami, S.; Feng, M.; Wu, X.; Lal, R.; Chen, G.; Du, K.; Luscher, B. Dissociation of Golgi-associated DHHC-type zinc finger protein (GODZ)- and sertoli cell gene with a zinc finger domain-β (SERZ-β)-mediated palmitoylation by loss of function analyses in knock-out mice. J. Biol. Chem. 2016, 291, 27371–27386. [Google Scholar] [CrossRef] [PubMed]
  15. Zhou, L.Z.; Li, S.; Feng, Q.N.; Zhang, Y.L.; Zhao, X.; Zeng, Y.L.; Wang, H.; Jiang, L.; Zhang, Y. Protein S-ACYL transferase10 is critical for development and salt tolerance in Arabidopsis. Plant Cell 2013, 25, 1093–1107. [Google Scholar] [CrossRef] [PubMed]
  16. Chen, D.; Hao, F.; Mu, H.; Ahsan, N.; Thelen, J.J.; Stacey, G. S-acylation of P2K1 mediates extracellular ATP-induced immune signaling in Arabidopsis. Nat. Commun. 2021, 12, 2750. [Google Scholar] [CrossRef] [PubMed]
  17. Gao, J.; Huang, G.; Chen, X.; Zhu, Y. PROTEIN S-ACYL TRANSFERASE 13/16 modulate disease resistance by S-acylation of the nucleotide binding, leucine-rich repeat protein R5L1 in Arabidopsis. J. Integr. Plant Biol. 2022, 64, 1789–1802. [Google Scholar] [CrossRef] [PubMed]
  18. Liu, F.; Qu, P.Y.; Li, J.P.; Yang, L.N.; Geng, Y.J.; Lu, J.Y.; Zhang, Y.; Li, S. Arabidopsis protein S-acyl transferases positively mediate BR signaling through S-acylation of BSK1. Proc. Natl. Acad. Sci. USA 2024, 121, e2322375121. [Google Scholar] [CrossRef] [PubMed]
  19. Li, Y.; Li, H.J.; Morgan, C.; Bomblies, K.; Yang, W.; Qi, B. Both male and female gametogenesis require a fully functional protein S-acyl transferase 21 in Arabidopsis thaliana. Plant J. 2019, 100, 754–767. [Google Scholar] [CrossRef] [PubMed]
  20. Zhou, B.; Lin, J.Z.; Peng, D.; Yang, Y.Z.; Guo, M.; Tang, D.Y.; Tan, X.; Liu, X.M. Plant architecture and grain yield are regulated by the novel DHHC-type zinc finger protein genes in rice (Oryza sativa L.). Plant Sci. 2017, 254, 12–21. [Google Scholar] [CrossRef] [PubMed]
  21. Peng, D.; Tan, X.; Zhang, L.; Yuan, D.; Lin, J.; Liu, X.; Jiang, Y.; Zhou, B. Increasing branch and seed yield through heterologous expression of the novel rice S-acyl transferase gene OsPAT15 in Brassica napus L. Breed. Sci. 2018, 68, 326–335. [Google Scholar] [CrossRef] [PubMed]
  22. Yang, Y.; Zhang, C.; Tang, R.J.; Xu, H.X.; Lan, W.Z.; Zhao, F.; Luan, S. Calcineurin B-Like Proteins CBL4 and CBL10 mediate two independent salt tolerance pathways in Arabidopsis. Int. J. Mol. Sci. 2019, 20, 2421. [Google Scholar] [CrossRef] [PubMed]
  23. Mitchell, D.A.; Vasudevan, A.; Linder, M.E.; Deschenes, R.J. Protein palmitoylation by a family of DHHC protein S-acyltransferases. J. Lipid Res. 2006, 47, 1118–1127. [Google Scholar] [CrossRef] [PubMed]
  24. Tian, Y.; Zeng, H.; Wu, J.C.; Dai, G.X.; Zheng, H.P.; Liu, C.; Wang, Y.; Zhou, Z.K.; Tang, D.Y.; Deng, G.F.; et al. The zinc finger protein DHHC09 S-acylates the kinase STRK1 to regulate H2O2 homeostasis and promote salt tolerance in rice. Plant Cell 2024, 36, 919–940. [Google Scholar] [CrossRef] [PubMed]
  25. Leawtrakun, J.; Aesomnuk, W.; Khanthong, S.; Dumhai, R.; Songtoasesakul, D.; Phosuwan, S.; Nuanpirom, J.; Charoensawan, V.; Siangliw, J.L.; Ruanjaichon, V.; et al. Identification of Candidate Genes for Salt Tolerance at Seedling Stage in Rice Using QTL-Seq and Chromosome Segment Substitution Line-Derived Population. Agronomy 2024, 14, 929. [Google Scholar] [CrossRef]
  26. Du, X.; Huang, G.; He, S.; Yang, Z.; Sun, G.; Ma, X.; Li, N.; Zhang, X.; Sun, J.; Liu, M.; et al. Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits. Nat. Genet. 2018, 50, 796–802. [Google Scholar] [CrossRef]
  27. Paterson, A.H.; Wendel, J.F.; Gundlach, H.; Guo, H.; Jenkins, J.; Jin, D.; Llewellyn, D.; Showmaker, K.C.; Shu, S.; Udall, J.; et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 2012, 492, 423–427. [Google Scholar] [CrossRef]
  28. Wang, M.; Tu, L.; Yuan, D.; Zhu, D.; Shen, C.; Li, J.; Liu, F.; Pei, L.; Wang, P.; Zhao, G.; et al. Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nat. Genet. 2019, 51, 224–229. [Google Scholar] [CrossRef]
  29. Nowicki, M.; Bzhalava, D.; BaŁa, P. Massively parallel implementation of sequence alignment with basic local alignment search tool osing parallel computing in java library. J. Comput. Biol. 2018, 25, 871–881. [Google Scholar] [CrossRef]
  30. Matsuda, F.; Tsugawa, H.; Fukusaki, E. Method for assessing the statistical significance of mass spectral similarities using basic local alignment search tool statistics. Anal. Chem. 2013, 85, 8291–8297. [Google Scholar] [CrossRef]
  31. Finn, R.D.; Clements, J.; Eddy, S.R. HMMER web server: Interactive sequence similarity searching. Nucleic Acids Res. 2011, 39, W29–W37. [Google Scholar] [CrossRef] [PubMed]
  32. Letunic, I.; Doerks, T.; Bork, P. SMART: Recent updates, new developments and status in 2015. Nucleic Acids Res. 2015, 43, D257–D260. [Google Scholar] [CrossRef] [PubMed]
  33. Marchler-Bauer, A.; Derbyshire, M.K.; Gonzales, N.R.; Lu, S.; Chitsaz, F.; Geer, L.Y.; Geer, R.C.; He, J.; Gwadz, M.; Hurwitz, D.I.; et al. CDD: NCBI’s conserved domain database. Nucleic Acids Res. 2015, 43, D222–D226. [Google Scholar] [CrossRef] [PubMed]
  34. Thompson, J.D.; Gibson, T.J.; Higgins, D.G. Multiple sequence alignment using ClustalW and ClustalX. Curr. Protoc. Bioinform. 2002, 2, 2–3. [Google Scholar] [CrossRef] [PubMed]
  35. Kumar, S.; Stecher, G.; Li, M.; Knyaz, C.; Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 2018, 35, 1547–1549. [Google Scholar] [CrossRef] [PubMed]
  36. Chen, C.; Chen, H.; Zhang, Y.; Thomas, H.R.; Frank, M.H.; He, Y.; Xia, R. TBtools: An integrative toolkit developed for interactive analyses of big biological data. Mol. Plant 2020, 13, 1194–1202. [Google Scholar] [CrossRef] [PubMed]
  37. Wang, Y.; Tang, H.; Debarry, J.D.; Tan, X.; Li, J.; Wang, X.; Lee, T.H.; Jin, H.; Marler, B.; Guo, H.; et al. MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012, 40, e49. [Google Scholar] [CrossRef] [PubMed]
  38. Li, Z.; Wang, P.; You, C.; Yu, J.; Zhang, X.; Yan, F.; Ye, Z.; Shen, C.; Li, B.; Guo, K.; et al. Combined GWAS and eQTL analysis uncovers a genetic regulatory network orchestrating the initiation of secondary cell wall development in cotton. New Phytol. 2020, 226, 1738–1752. [Google Scholar] [CrossRef]
  39. Zhu, D.; Le, Y.; Zhang, R.; Li, X.; Lin, Z. A global survey of the gene network and key genes for oil accumulation in cultivated tetraploid cottons. Plant Biotechnol. J. 2021, 19, 1170–1182. [Google Scholar] [CrossRef] [PubMed]
  40. Bolger, A.M.; Lohse, M.; Usadel, B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 2014, 30, 2114–2120. [Google Scholar] [CrossRef]
  41. Kim, D.; Langmead, B.; Salzberg, S.L. HISAT: A fast spliced aligner with low memory requirements. Nat. Methods 2015, 12, 357–360. [Google Scholar] [CrossRef] [PubMed]
  42. Ghosh, S.; Chan, C.K. Analysis of RNA-Seq Data Using TopHat and Cufflinks. Methods Mol. Biol. 2016, 1374, 339–361. [Google Scholar] [PubMed]
  43. Lescot, M.; Déhais, P.; Thijs, G.; Marchal, K.; Moreau, Y.; Van de Peer, Y.; Rouzé, P.; Rombauts, S. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 2002, 30, 325–327. [Google Scholar] [CrossRef] [PubMed]
  44. Yang, M.; Chen, T.; Liu, Y.; Huang, L. Visualizing Set Relationships: EVenn’s Comprehensive Approach to Venn Diagrams. iMeta 2024, e184. [Google Scholar] [CrossRef]
  45. Lai, J.; Yu, B.; Cao, Z.; Chen, Y.; Wu, Q.; Huang, J.; Yang, C. Two homologous protein S-acyltransferases, PAT13 and PAT14, cooperatively regulate leaf senescence in Arabidopsis. J. Exp. Bot. 2015, 66, 6345–6353. [Google Scholar] [CrossRef] [PubMed]
  46. Zheng, L.; Liu, P.; Liu, Q.; Wang, T.; Dong, J. Dynamic protein S-acylation in plants. Int. J. Mol. Sci. 2019, 20, 560. [Google Scholar] [CrossRef] [PubMed]
  47. Lan, T.; Delalande, C.; Dickinson, B.C. Inhibitors of DHHC family proteins. Curr. Opin. Chem. Biol. 2021, 65, 118–125. [Google Scholar] [CrossRef] [PubMed]
  48. Tian, Y.; Zeng, H.; Wu, J.; Huang, J.; Gao, Q.; Tang, D.; Cai, L.; Liao, Z.; Wang, Y.; Liu, X.; et al. Screening DHHCs of S-acylated proteins using an OsDHHC cDNA library and bimolecular fluorescence complementation in rice. Plant J. 2022, 110, 1763–1780. [Google Scholar] [CrossRef] [PubMed]
  49. De, I.; Sadhukhan, S. Emerging roles of DHHC-mediated protein S-palmitoylation in physiological and pathophysiological context. Eur. J. Cell Biol. 2018, 97, 319–338. [Google Scholar] [CrossRef] [PubMed]
  50. Imran, M.; Shafiq, S.; Naeem, M.K.; Widemann, E.; Munir, M.Z.; Jensen, K.B.; Wang, R.R. Histone deacetylase (HDAC) gene family in allotetraploid cotton and Its diploid progenitors: In silico identification, molecular characterization, and gene expression analysis under multiple abiotic stresses, DNA damage and phytohormone treatments. Int. J. Mol. Sci. 2020, 21, 321. [Google Scholar] [CrossRef] [PubMed]
  51. Wan, Z.Y.; Chai, S.; Ge, F.R.; Feng, Q.N.; Zhang, Y.; Li, S. Rabidopsis PROTEIN S-ACYL TRANSFERASE4. Plant J. 2017, 90, 249–260. [Google Scholar] [CrossRef] [PubMed]
  52. Qin, A.; Xu, L. Advances in study of protein palmitoylation. Chem. Life 2012, 32, 332–336. [Google Scholar]
  53. Deyneko, I.V. Guidelines on the performance evaluation of motif recognition methods in bioinformatics. Front. Genet. 2023, 14, 1135320. [Google Scholar] [CrossRef] [PubMed]
  54. Deyneko, I.V. BestCRM: An Exhaustive Search for Optimal Cis-Regulatory Modules in Promoters Accelerated by the Multidimensional Hash Function. Int. J. Mol. Sci. 2024, 25, 1903. [Google Scholar] [CrossRef] [PubMed]
  55. Zhou, J.M.; Zhang, Y. Plant Immunity: Danger perception and signaling. Cell 2020, 181, 978–989. [Google Scholar] [CrossRef] [PubMed]
  56. Li, B.; Fu, C.; Zhou, J.; Hui, F.; Wang, Q.; Wang, F.; Wang, G.; Xu, Z.; Che, L.; Yuan, D.; et al. Highly Efficient Genome Editing Using Geminivirus-Based CRISPR/Cas9 System in Cotton Plant. Cells 2022, 11, 2902. [Google Scholar] [CrossRef] [PubMed]
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Figure 1. Phylogenetic tree of the DHHC gene family in four cotton species.
Figure 1. Phylogenetic tree of the DHHC gene family in four cotton species.
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Figure 2. Gene structure and conserved motifs of the DHHC gene family. (A) G. hirsutum. (B) G. barbadense.
Figure 2. Gene structure and conserved motifs of the DHHC gene family. (A) G. hirsutum. (B) G. barbadense.
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Figure 3. The chromosomal location of the DHHC gene. (A) G. hirsutum. (B) G. barbadense.
Figure 3. The chromosomal location of the DHHC gene. (A) G. hirsutum. (B) G. barbadense.
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Figure 4. Multiple synteny analysis of DHHC genes. (A) The genome-scale collinear link between At-subgenome of G. barbadense (GbAt), G. arboretum (A2), and At-subgenome of G. hirsutum (GhAt). (B) The genome-scale collinear link between Dt-subgenome of G. barbadense (GbDt), G. raimondii (D5), and Dt-subgenome of G. hirsutum (GhDt).
Figure 4. Multiple synteny analysis of DHHC genes. (A) The genome-scale collinear link between At-subgenome of G. barbadense (GbAt), G. arboretum (A2), and At-subgenome of G. hirsutum (GhAt). (B) The genome-scale collinear link between Dt-subgenome of G. barbadense (GbDt), G. raimondii (D5), and Dt-subgenome of G. hirsutum (GhDt).
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Figure 5. Cis-regulatory elements in the promoter regions of DHHC gene family. (A) G. hirsutum. (B) G. barbadense.
Figure 5. Cis-regulatory elements in the promoter regions of DHHC gene family. (A) G. hirsutum. (B) G. barbadense.
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Figure 6. Differentially expressed genes and DHHC genes at different seed development stages. (A) UpSet diagram of differentially expressed genes in different seed development stages of G. hirsutum. (B) Differentially expressed DHHC genes in two stages of G. hirsutum seed development. (C) UpSet diagram of differentially expressed genes in different seed development stages of G. barbadense. (D) Differentially expressed DHHC genes in two stages of G. barbadense seed development. The X-axis represents the number of genes.
Figure 6. Differentially expressed genes and DHHC genes at different seed development stages. (A) UpSet diagram of differentially expressed genes in different seed development stages of G. hirsutum. (B) Differentially expressed DHHC genes in two stages of G. hirsutum seed development. (C) UpSet diagram of differentially expressed genes in different seed development stages of G. barbadense. (D) Differentially expressed DHHC genes in two stages of G. barbadense seed development. The X-axis represents the number of genes.
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Figure 7. Expression patterns of DHHC genes during 15 days of fiber development in upland cotton populations. Star-shaped markers indicate differentially expressed genes in the ‘20 DPA vs. 10 DPA’ seed development stage.
Figure 7. Expression patterns of DHHC genes during 15 days of fiber development in upland cotton populations. Star-shaped markers indicate differentially expressed genes in the ‘20 DPA vs. 10 DPA’ seed development stage.
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Silaiyiman, S.; Zheng, Q.; Wang, Y.; Ouyang, L.; Guo, Z.; Yu, J.; Chen, R.; Peng, R.; Shen, C. Comprehensive Genome-Wide Investigation and Transcriptional Regulation of the DHHC Gene Family in Cotton Seed and Fiber Development. Agronomy 2024, 14, 1214. https://doi.org/10.3390/agronomy14061214

AMA Style

Silaiyiman S, Zheng Q, Wang Y, Ouyang L, Guo Z, Yu J, Chen R, Peng R, Shen C. Comprehensive Genome-Wide Investigation and Transcriptional Regulation of the DHHC Gene Family in Cotton Seed and Fiber Development. Agronomy. 2024; 14(6):1214. https://doi.org/10.3390/agronomy14061214

Chicago/Turabian Style

Silaiyiman, Saimire, Qinyue Zheng, Yutao Wang, Lejun Ouyang, Zhishan Guo, Jieli Yu, Rong Chen, Rui Peng, and Chao Shen. 2024. "Comprehensive Genome-Wide Investigation and Transcriptional Regulation of the DHHC Gene Family in Cotton Seed and Fiber Development" Agronomy 14, no. 6: 1214. https://doi.org/10.3390/agronomy14061214

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