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Article

Genome-Wide Identification of MYB Gene Family in Peach and Identification of MYBs Involved in Carotenoid Biosynthesis

by
Fengyi Liu
1,†,
Jiarui Zheng
1,†,
Yuwei Yi
1,†,
Xiaoyan Yang
2,
Leiyu Jiang
1,
Jiabao Ye
1,
Weiwei Zhang
1 and
Feng Xu
1,*
1
College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, China
2
School of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Forests 2024, 15(7), 1119; https://doi.org/10.3390/f15071119
Submission received: 3 May 2024 / Revised: 19 June 2024 / Accepted: 25 June 2024 / Published: 27 June 2024
(This article belongs to the Special Issue Genome-Wide Identification and Expression Analysis for the Genetic Improvement of Forest Plants)
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Abstract

:
Carotenoids are naturally occurring tetraterpenoids that play a key role in fruit coloration, and yellow peaches are one of the best sources of carotenoid intake. MYB transcription factors are one of the largest families in plants and play an important role in the regulation of plant secondary metabolite biosynthesis. However, peach MYB family genes have not been fully analyzed, and in particular, MYBs that regulate carotenoid biosynthesis have not been fully characterized. In this study, 190 peach MYB genes, containing 68 1R-MYBs, 118 2R-MYBs, 3 3R-MYBs, and 1 4R-MYB, were identified at the genome level using bioinformatics methods. These 190 MYBs were classified into 27 subfamilies based on their phylogenetic relationships with Arabidopsis thaliana MYB family members, and they were unevenly distributed across eight chromosomes. MYB genes of the same subfamily exhibit similar but not identical gene structures and conserved motifs. The promoter regions contain cis-acting elements associated with stress response, hormone response, and plant growth and development. There were 54 collinear pairs of MYB genes in the peach genome, compared with 233 and 221 collinear pairs with Rosa chinensis and Arabidopsis, respectively. Thirteen differentially expressed genes in the carotenoid biosynthesis pathway in yellow peach were identified by transcriptome sequencing and contained MYB binding sites on their promoters. Based on a phylogenetic analysis, we identified 13 PpMYBs that may be involved in carotenoid biosynthesis, and a correlation analysis revealed that they regulate carotenoid accumulation by positively or negatively regulating the expression of carotenoid biosynthetic genes. Further degradome sequencing screened that mdm-miR858 was able to target PpMYB17 and PpMYB126 involved in the regulation of carotenoid biosynthesis. Our findings provide new insights into the potential role of MYB transcription factors in carotenoid biosynthesis and provide a theoretical basis for their molecular mechanisms.
Keywords:
peach; MYB; carotenoids; miRNAs

1. Introduction

Peach (Prunus persica (L.) Batsch) is a perennial deciduous fruit tree of the genus Plum of the family Rosaceae originating in China, and its fruits are tasty and rich in a variety of vitamins, fruit acids, and mineral elements such as calcium, phosphorus, iron, etc., which are of high nutritional value and are well received by consumers [1]. The germplasm resources of cultivated peaches are rich in phenotypic diversity and can generally be classified into three types, namely red-fleshed peaches, white-fleshed peaches and yellow-fleshed peaches, based on the differences in fruit color [2]. Yellow-fleshed peaches are increasingly favored by consumers for their yellow flesh and rich carotenoids. Studies have shown that yellow-fleshed peaches are high in carotenoids, including different types of β-carotene, β-cryptoxanthin, lutein, zeaxanthin, and phytoene [3,4,5]. In addition to being important bioactive components, β-carotene is also a precursor substance for vitamin A synthesis in the human body, which is extremely important for human health [6]. Therefore, the study of carotenoids in peach fruits has been emphasized by researchers and breeding experts.
Carotenoids are a class of lipophilic, naturally occurring isoprenoid pigments that are widely found in nature and provide distinctive yellow, orange, and red colors to fruits, vegetables, plant leaves, and flowers. Currently, more than 1100 carotenoids have been identified in nature and they can be categorized as C30, C40, C45, and C50 carotenoids based on the number of carbon atoms that make up their structure [7,8]. C40 carotenoids are the most abundant in nature and generally consist of isoprene units linked by eight C5 carbon backbones, and they consist of polyene chains and terminal groups, and they are synthesized mainly in eukaryotic, archaeal, and bacterial species [8,9]. Carotenoids can be coarsely categorized into carotenes and xanthophylls based on the presence or absence of oxygen in their chemical composition. Carotenoids are mainly hydrocarbons, including α-carotene, β-carotene, γ-carotene, lycopene, etc. There is significant structural diversity in xanthophylls, which includes β-cryptoxanthin, lutein, neoxanthin, zeaxanthin, astaxanthin, zeaxanthin, astaxanthin, etc. These are groups (hydroxyl, carbonyl, aldehyde, carboxyl, epoxy, furanyloxy, etc.) that contain an oxygen molecule, while some xanthophylls exist in the form of fatty acid esters, glycosides, sulfates, and protein complexes [9,10,11]. Carotenoids play vital physiological roles in plants, animals, and humans. In plants, carotenoids constitute the basic structural units of photosynthesis [12,13,14] and photoprotectors [15]. Carotenoid catabolites are also involved in plant defense mechanisms; e.g., β-ionone, can participate in plant–insect interactions [16]. Carotenoids are also the precursor substances for the synthesis of two important phytohormones, abscisic acid (ABA) and strigolactone [17,18]. In addition to this, carotenoids are important for both animals and humans. β-carotene is the main dietary source of vitamin A synthesized in animals and humans [19,20], and carotenoids are protective against cardiovascular disease, cancer, and aging-related diseases [6,21]. Therefore, understanding carotenoid biosynthesis and regulatory processes can better guide the production of carotenoid-rich fruits.
At present, the structural genes and key enzymes of the carotenoid biosynthetic pathway in higher plants have been largely clarified, and this biosynthetic process is synthesized de novo in almost all species of plastids [9,22,23]. Carotenoid biosynthesis begins with the synthesis of isopentenyl pyrophosphate and dimethylallyl pyrophosphate via the methylerythritol phosphate pathway [13,22], and IPP and DMAPP are condensed by GGPP synthase to produce geranylgeranyl diphosphate (GGPP). Subsequently, various carotenes and xanthophylls are produced by the action of enzymes including PSY (phytoene synthase), PDS (phytoene desaturase), Z-ISO (ζ-carotene isomerase), ZDS (ζ-carotene desaturase), CRTISO (carotenoid isomerase), LCYB (lycopene β-cyclase), LCYE (lycopene ε-cyclase), CYP97A (cytochrome P450-type monooxygenase 97A), CYP97C, BCH (β-carotene hydroxylase), ZEP (zeaxanthin epoxidase), VDE (violaxanthin de-epoxidase), and NXS (neoxanthin synthase) [13,22,24,25,26].
Carotenoid synthesis is transcriptionally regulated by other factors, such as transcription factors, in addition to a series of enzymatic reactions. Transcription factors are central to the regulation of carotenoid gene transcription, and they can directly transcriptionally activate or repress the expression of carotenoid structural genes [27,28,29]. Several families of transcription factors have been reported to be participating in carotenoid biosynthesis, including MYB, NAC, WRKY, MADS, ERF, RIN, PIF, HY5, bHLH, and others [22,30,31,32,33,34,35,36]. Recent studies have shown that red light-induced FcrNAC22 mediates carotenoid synthesis in kumquat fruits [31], and the citrus phosphate starvation response factor CsPHL3 ultimately negatively regulates carotenoid metabolism by binding to the LCYB1 promoter [33]. In papaya, CpbHLH1 and CpbHLH2 promote carotenoid accumulation by activating the expression of LCYB1 and PSY [35]. In Citrus reticulate, CrMYB68 inhibits carotenoid biosynthesis by reducing CrBCH2 and CrNCED5 expression [37]. In Mimulus lewisii, the R2R3-MYB transcription factor MlRCP1 (reduced carotenoid pigmentation 1) is a major regulator of carotenoid biosynthesis and accumulation in flowers [38]. Kiwifruit (Actinidia deliciosa) AdMYB7 regulates carotenoid distribution by activating AdLCYB [39]. Cattleya (Rhyncholaeliocattleya) RcPCP1 (promoted carotenoid pigmentation 1) promotes the accumulation of α-carotene and lutein [5].
In this study, the peach genome was used to systematically characterize members of the MYB transcription factor family. Subsequently, the molecular characterization, phylogenetic relationships, gene structure, motifs, promoters, chromosomal localization, and co-lineage relationships of peach MYB genes were analyzed. The expression patterns of these MYB members and their regulatory relationships with differentially expressed genes (DEGs) were analyzed using transcriptome data. A further degradome sequencing data analysis identified miRNAs targeting PpMYBs. This study will contribute to a better overall understanding of the structure and function of peach MYB family members, providing a research basis and candidate targets for MYB involvement in the regulation of carotenoid biosynthesis.

2. Materials and Methods

2.1. Identification and Protein Characterization of MYB Family Members in the Peach Genome

Peach MYB family members were retrieved from the peach genome data [40], and Arabidopsis MYB family protein sequences were downloaded from the TAIR database [41]. The HMM file (PF00249) of the conserved structural domains of the MYB transcription factor family in the Pfam database [42] was used to find all MYB family members from the peach genome with the support of HMMER 3.3.2. Meanwhile, Arabidopsis MYB protein sequences were used as seed sequences to retrieve MYB candidate genes from the peach genome using the Blast program (https://sequenceserver.com/blog/citing-ncbi-blast/, accessed on 12 March 2023), with the E-value set to 0.00001. Finally, the candidate genes obtained from the two searches were combined and we searched for candidate MYB conserved structural domains using the NCBI website’s Batch CD-search, SMART [43], and InterPro tools [44] to further confirm MYB family-specific structural domains, and to remove MYB-free structural domains and redundant sequences.
Physicochemical properties such as amino acid length, isoelectric point, stability, etc., were analyzed and counted for all members of the candidate PpMYB using the Prot Param tool in the online website ExPASy (https://web.expasy.org/protparam/protpar-ref.html, accessed on 12 March 2023). The subcellular localization of PpMYB was analyzed using Wolf Psort (https://psort.hgc.jp/, accessed on 12 March 2023) and the signal peptide of PpMYBs was predicted using SignaIP-5.0 [45] online websites. The default parameters are used.

2.2. Chromosomal Localization and Collinearity Analysis of MYB Family Members

The positional information of MYB family members on chromosomes was extracted and visualized from the GFF3 annotation file of the peach genome using TBtools v.2.069 software [46] and subsequently beautified using AI 2021 software. The collinearity relationships of peach MYB family members within the genome were analyzed based on the MYB family member genes in the genome annotation file and genome file using the Advanced Circos tool [46].
The genomes of the model plant A. thaliana and Rosa chinensis were selected for a collinearity analysis. The Arabidopsis and R. chinensis genomes and annotation files were downloaded from the TAIR database [41] and Ensembl Plants database [47], respectively. The collinearity analysis was performed using MCScanX v.2 software and visualized using TBtools software [46]. The images were visualized using the MCScanX tool in TBtools under default parameter conditions. The E-value is set to 10−10. The number of blasthits is set to 5.

2.3. Ka and Ks Calculations

Ka (nonsynonymous) and Ks (synonymous) values for syntenic gene pairs were calculated using the TBtools [46] downstream program Simple Ka/Ks Calculator (NG). The parameters use the default.

2.4. Gene Structure, Conserved Motifs, and Structural Domain Analysis of the PpMYB Family

The MEME [48] online site was used for a conserved motif analysis of PpMYB protein sequences, with the conserved motif number set to 10 and the rest of the parameters set to default. The results of the conserved motif analysis were visualized by TBtools.
Gene structures such as exons and introns of all PpMYB family members were visualized using TBools software. The Batch CD-Search [49] tool in NCBI and the Interpro website [44] were used to analyze the PpMYB protein’s conserved structural domains.

2.5. Phylogenetic Tree Analysis of MYB Family Genes in Peach

The model plant A. thaliana MYB family and peach MYB family were selected to construct a phylogenetic evolutionary tree to classify peach MYB family members. The Arabidopsis MYB family protein sequences were downloaded from the TAIR database [41] and utilized for the multiple-sequence comparison of Arabidopsis and peach MYB protein sequences through MEGA-X software.
The phylogenetic tree was firstly compared and trimmed using TBtools, and then exported to MEGA-X software [50] to construct a phylogenetic tree using the neighbor-joining (NJ) method, with the following parameters: Bootstrap = 1000, Substitution Model—p-distance, and Missing Data Treatment—pairwise deletion. The constructed phylogenetic tree was exported to the Evolview online website [51] for beautification.

2.6. Analysis of Cis-Acting Elements of PpMYB Family Genes

A sequence 2000 bp upstream of the transcription start site of the peach MYB family gene was extracted as a promoter sequence using the TBtools tool. The extracted promoter sequences were imported into the Plant CARE [52] online tool for a cis-acting element analysis. The results were compiled and imported into TBtools software for visualization.

2.7. Heat Mapping and Correlation Analysis

Heat maps in this study were generated through the Heatmap tool of TBtools software, and the data were processed as a logarithmic function with a base of 2. Correlation coefficients were calculated through Excel 2019. Transcriptome and degradome sequencing data were looked up from our previous studies [5].

3. Results

3.1. Identification of PpMYB Family Members and Analysis of Chromosomal Localization

The MYB family members were identified from the peach genome by HMMER and BLAST methods, and a total of 190 peach MYB genes were obtained after removing redundant and MYB structural domain-less sequences, and were sequentially named as PpMYB1-PpMYB190 according to their order on the chromosomes (Figure 1; Table S1). A chromosomal localization analysis showed that these 190 PpMYBs were unevenly distributed on the eight chromosomes of peach, with 36, 23, 32, 15, 25, 31, 18, and 10 MYBs on chromosomes 1–8, respectively. The highest number of MYBs was found on chromosome 1, with 36 MYBs, and the lowest number of MYBs was found on chromosome 8, with 10 MYBs. Overall, PpMYB showed more distribution at both ends than in the middle position.

3.2. Analysis of Physicochemical Properties of PpMYB Family Members

A physicochemical analysis revealed that the No. of amino acids, protein molecular mass, and theoretical pI (isoelectric point) of the encoded proteins varied greatly among the 190 members of the peach MYB family identified, with amino acid sequence lengths ranging from 74 aa (PpMYB80) to 1047 aa (PpMYB127), and the relative molecular masses of the proteins ranging from 8.530 (PpMYB80) to 119.156 kDa (PpMYB127), and the pI ranged between 4.31 (PpMYB124) and 10.08 (PpMYB26). In addition, all MYB proteins had negative Gravy values, indicating that they are hydrophilic proteins. Stability prediction using ExPasy showed that 5 PpMYB proteins (PpMYB107, PpMYB129, PpMYB65, PpMYB118, and PpMYB133) were stable proteins (instability coefficients < 40) and 185 proteins were unstable proteins (instability coefficients > 40). The prediction of the subcellular localization of peach MYB family members found that, except for PpMYB171 (chloroplast), PpMYB177 (chloroplast), PpMYB19 (chloroplast), PpMYB41 (chloroplast), PpMYB11 (chloroplast), PpMYB40 (cytoplasm), PpMYB183 (cytoplasm), and PpMYB139 (plastid) were localized in the nucleus (Table S1). Signal peptide prediction showed no signal peptide for all MYBs except PpMYB49.

3.3. Intraspecific and Interspecific Collinearity Analysis of PpMYB Family Genes

To elucidate the evolutionary relationships of the peach MYB family, we analyzed the collinearity of 190 PpMYBs, and identified 54 pairs of collinear genes (blue line in Figure 2), which were unequally distributed across eight chromosomes, with chromosome 1 containing the highest number of genes (19, 35%), followed by chromosome 3 (13, 24%), and ranging from 2 to 10 distributed across the remaining chromosomes (Figure 2). The Ka and Ks values of the MYB genes were calculated to analyze whether they have been subjected to selection pressure during evolution. The results showed that the Ka/Ks values of these PpMYB sequences were all less than 1 (Table S2), suggesting that these genes were subjected to purifying selection during evolution, while PpMYB15-PpMYB123, PpMYB22-PpMYB64, PpMYB41-Prupe.2G289800.1, PpMYB64-PpMYB172, PpMYB81-PpMYB95, PpMYB83-PpMYB96, PpMYB89-PpMYB118, and PpMYB96-PpMYB102 were the eight pairs of sequences that exhibited a High Sequence Divergence Value (pS ≥ 0.75).
The results of the collinearity analysis between peach and A. thaliana and R. chinensis showed that there were 221 collinear gene pairs between peach and A. thaliana containing 120 members of the PpMYB family members, and 233 collinear gene pairs of peach and R. chinensis containing 155 PpMYBs, and these results suggested a closer evolutionary relationship between peach and R. chinensis (Figure 3).

3.4. Phylogenetic Relationship between Peach and Arabidopsis MYB Proteins

A phylogenetic evolutionary tree was constructed for the 190-member protein sequences of the peach MYB family together with the 125 protein sequences of the Arabidopsis MYB family (Figure 4) to further explore the evolutionary relationships, and the members of the peach MYB family were divided into 37 subgroups according to the Arabidopsis MYB family grouping and denoted by S1–S34, S37–S38, S44, and S46. Among them, S29 and S34 were not clustered with Arabidopsis MYB.

3.5. Motif Analysis, Domain, and Gene Structure Analysis of PpMYB Family Genes

In order to gain an in-depth understanding of the structure of the 190 peach MYB gene family members, this study utilized the MEME online website to analyze the conserved motifs of the peach MYB proteins, and the 10 conserved motifs identified were named motif 1~motif 10 (Figure 5). Among them, the most MYBs contained motif 1, with 123 MYBs, suggesting that motif 1 is the most conserved motif in the family; motif 2 was the second largest, with 121 MYBs, and motif 10 was the smallest, with only 29 MYBs. The visualization results show that different subclasses of proteins with close affinity are more conserved and composed of more similar types of motifs.
An analysis of 190 PpMYB protein sequences by the CDD search tool in NCBI and Interpro revealed that the peach MYB protein sequences contain 17 domains such as Myb_DNA-bindng, SANT, and Myb_CC-LHEQLE, with different members containing different numbers and types of structural domains. Among them, SANT, Myb_DNA-binding, and Myb_DNA-bind_6 appeared most frequently. The gene structures of all peach MYB gene family members were examined, and the results showed that the number, distribution, and gene lengths of CDSs in peach MYB gene family members varied greatly, with unequal numbers and varying lengths.

3.6. Analysis of Cis-Acting Elements in the Promoters of MYB Family Genes

We extracted 2000 bp upstream of the transcription start site of 190 PpMYB genes as promoter sequences and analyzed their cis-acting elements (Figure 6) and their number (Table S3). A total of 4951 cis-elements were obtained from the promoter analysis of these genes, from which 24 important core elements were identified and could be categorized into light-responsive elements, phytohormone-responsive elements, adversity-responsive elements, plant growth and developmental elements, etc., according to their functions.

3.7. Identification of PpMYB Involved in Carotenoid Biosynthesis

To further identify MYB that may be participating in carotenoid biosynthesis in peach, a phylogenetic evolutionary tree was constructed by clustering the 190 PpMYBs together with the reported AdMYB7, MlRCP1, CrMYB68, MtWP1, AtPAP1, and AtMYB113 involved in carotenoid biosynthesis, and the results showed that these MYBs involved in carotenoid biosynthesis were clustered with peach PpMYB in subfamilies S6, S14, S20, and S21, respectively (Figure 7). Thus, 25 PpMYBs in these subfamilies may be involved in carotenoid biosynthesis. In addition, we analyzed the number and position of MYB repeat sequences in 190 PpMYB genes, which showed a total of 68 1R-MYBs (blue branch), 118 2R-MYBs (red branch), 3 3R-MYBs (green branch), and 1 4R-MYB (yellow branch).
We previously conducted a comprehensive analysis and characterization of carotenoid content and gene expression levels in the pericarp of yellow peach at different developmental periods by the metabolome and transcriptome [5]. A further analysis revealed that a total of 13 of these 25 PpMYBs potentially involved in carotenoid biosynthesis were expressed (Figure 8A) and 12 were not. A further correlation analysis of these 13 PpMYBs with carotenoid content revealed that PpMYB80 showed positive correlation with the content of carotenoids and xanthophylls with a correlation coefficient of more than 0.9; meanwhile, PpMYB126, PpMYB6, PpMYB17, PpMYB169, PpMYB164, PpMYB60, and PpMYB75 showed negative correlation and correlation coefficients less than −0.8 with the contents of carotenoids and xanthophylls (Figure 8B). PpMYB178, PpMYB29, PpMYB146, PpMYB76, PpMYB126, PpMYB6, PpMYB17, and PpMYB169 showed a positive correlation with carotenes’ content, and the correlation was higher than 0.8 or more (Figure 8B).

3.8. PpMYB Regulates the Expression of Key Genes for Carotenoid Biosynthesis

To further investigate the molecular mechanism of PpMYB in regulating carotenoid synthesis, a total of 13 DEGs were identified from the transcriptome of yellow peach pericarp at different developmental periods [5], and the correlation between PpMYB and the DEGs was analyzed. The results showed that PpMYB80 was positively correlated with ZDS2, ZEP1, crtISO1, VDE, PSY1, and LCYE, while it was negatively correlated with NCED3, PSY2, ZDS1, CHYB1, NCED2, NCED1, and LCYB (Figure 9A). PpMYB141, PpMYB146, PpMYB76, PpMYB178, and PpMYB29 were negatively correlated with ZDS2 and ZEP1 (r < −0.8), and positively correlated with NCED3, PSY2, ZDS1, CHYB1, and NCED2 (r > 0.6). PpMYB60 and PpMYB75 were negatively correlated with crtISO1, VDE, PSY1, and LCYE (r < −0.8) and positively (r > 0.8) with PSY2, ZDS1, NCED1, and LCYB. PpMYB164 and PpMYB169 were negatively correlated (r < −0.8) with ZDS2, ZEP1, crtISO1, VDE, PSY1, and LCYE and positively correlated (r > 0.8) with NCED3, PSY2, ZDS1, CHYB1, NCED2, NCED1, and LCYB. PpMYB17, PpMYB126, and PpMYB6 were negatively correlated with ZDS2, ZEP1, PSY1, and LCYE (r < −0.8), and positively correlated with NCED3, PSY2, ZDS1, CHYB1, and NCED2 (r > 0.8). Meanwhile, an analysis of the promoters of these 13 DEGs revealed that they all contained MYB binding sites, suggesting that these DEGs in the carotenoid biosynthesis pathway may be potential targets of PpMYB.

3.9. miRNA Targeting PpMYB Involved in Carotenoid Biosynthesis

From the previous degradome sequencing results, we looked for the presence of miRNAs capable of targeting these 13 candidate genes, and a total of four miRNA-PpMYB pairs were identified (Figure 10), namely ath-miR858a_L-1R+1-PpMYB60, PC-5p-103273_40-PpMYB80, mdm-miR858-PpMYB17, and mdm-miR858-PpMYB126, where the relative p-values of the mdm-miR858-PpMYB17 and mdm-miR858-PpMYB126 targets were less than 0.05.

4. Discussion

4.1. Bioinformatics Analysis of the Peach MYB Family

MYB transcription factors are important for secondary metabolite synthesis in plants. However, there have been no systematic studies on the identification of MYB family members in peach. A total of 190 MYB genes were identified from the peach genome, which is comparable to the number of MYB genes (182) in Casuarina equisetifolia [53] but higher than those in Arabidopsis thaliana (125), Populus tremula (152) [54], and the pear Chinese Pear (129 Pyrus bretschneideri Rehd.) [55], but less than the number of MYBs (229) in apple [56]. A phylogenetic analysis showed that the peach 190 PpMYB genes were classified into 37 subfamilies, of which 35 subgroups were able to cluster with Arabidopsis MYBs, which were relatively conserved during evolution. And two subfamilies clustered independently, indicating that they were acquired during evolution. Consistent with the distribution of MYBs on chromosomes in Casuarina equisetifolia, populus, and walnut [57], the 190 MYBs of peach were unevenly distributed on chromosomes, with 10–36 MYBs per chromosome, and most of them were distributed at the ends of chromosomes. In addition, the PpMYB genes showed a high level of similarity in terms of amino acid sequence, gene structure, and conserved motifs. These results suggest that PpMYB genes have both similarities and differences, highlighting their possible functional conservation and diversity. A total of 54 collinear gene pairs were identified on eight chromosomes containing 32 1R-MYB, 57 R2R3-MYB, and 1 3R-MYB. Based on the findings and speculations, the duplication of these segments may be important for the expansion of the R2R3-type MYB gene [58].

4.2. PpMYB Is Involved in Carotenoid Biosynthesis

MYB transcription factors are an essential class of regulators in plants, playing important regulatory roles in plant growth and development, adversity defense responses, and secondary metabolite synthesis. Multiple members of the MYB family have been reported to be involved in carotenoid biosynthesis, and the R2R3-MYB transcription factor of M. lewisii, MlRCP1, regulates carotenoid synthesis and accumulation in flowers [38]. AdMYB7 activates AdLCYB to regulate carotenoid distribution in Actinidia deliciosa [39]. Rhyncholaeliocattleya RcPCP1 promotes the accumulation of α-carotene and lutein [5]. CsMYB110 was able to cluster with MtWP1, AtPAP1, and AtMYB113 and was identified as a candidate key transcription factor for carotenoid biosynthesis, and its expression pattern and overexpression were analyzed to validate CsMYB110 as a key transcription factor for carotenoid biosynthesis [59,60].
In this study, we constructed a phylogenetic tree by comparing 190 PpMYB family members with reported MYBs involved in carotenoid biosynthesis in different species, and these MYBs involved in carotenoid biosynthesis were mainly clustered with members of peach MYB family S6, S14, S20, and S21, suggesting that PpMYB genes in these subfamilies may be involved in carotenoids in yellow peach biosynthesis. A further correlation analysis showed that these PpMYBs clustered in subfamilies S6, S14, S20, and S21 were strongly correlated with differentially expressed genes in the carotenoid biosynthesis pathway, further suggesting that these PpMYBs may be important regulators of carotenoid biosynthesis. CrMYB68 is able to inhibit the conversion of α- and β-branched carotenoids [37], and PpMYB178, PpMYB169, PpMYB141, PpMYB29, and PpMYB146, which are homologous to CrMYB68, were negatively correlated with ZDS2 and LCYE (r < −0.8), and the positive correlation coefficients with LCYB were all lower than 0.5, and thus may have a similar function to CrMYB68. In addition to this, carotenoid biosynthesis is also regulated by the MBW complex [60]. In tea, CsMYB110 regulates carotenoid biosynthesis through the MBW complex, and the overexpression of CsMYB110 alone was also able to increase the carotenoid content [59].

4.3. miRNA Targets PpMYB Involved in the Regulation of Carotenoid Biosynthesis

miRNAs typically regulate gene expression by cleaving target mrna or inhibiting the translation of target mRNA [61]. Studies have shown that a variety of miRNAs target transcription factors involved in plant developmental processes, such as miR156 targeting SBP transcription factors, miR164 targeting NAC transcription factors, and miR394 targeting F-box transcription factors [62]. miRNAs can directly target or indirectly affect the expression of structural genes and transcription factors involved in carotenoid biosynthesis [63,64]. The degradome is an important means to find miRNA target genes. In plants, miR858 targeting of MYBs involved in plant secondary metabolite biosynthesis is common. In apple, MdMYB9 and MdMYBPA1 are able to bind to MBS in the promoter to activate MdANS/UFGT expression, whereas mdm-miR858 is involved in apple anthocyanin accumulation by targeting the transcription factors MdMYB9 and MdMYBPA1 [65]. mdm-miR858 negatively regulates proanthocyanidin (PA) accumulation by targeting MdMYB9/11/12 in the pericarp [66]. The miR858 primary product encoding peptide priPEP858a regulates flavonoid biosynthesis and auxin signaling pathways in A. thaliana, which in turn affects plant growth and development [67]. MiR858 family members regulate proanthocyanidin and flavonol metabolism by targeting specific MYBs in kiwifruit and Arabidopsis. The genes for the R2R3-MYB transcription factors AtTT2 (AtMYB123) and AtMYB12 are involved in the regulation of proanthocyanidins and flavonols [67], and ath-MIR858L was able to significantly inhibit the transcriptional activities of AtMYB123 and AtMYB12; the kiwifruit R2R3-MYB genes AcMYB123 (Acc28234) and AcMYB164 (Acc31558), a homolog of AtTT2 (AtMYB123) and AcMYB164 and AtMYB12, were repressed by ache-mir858c [68]. Similarly, miR2105 in rice was able to mediate OsbZIP86 to affect ABA content by regulating the expression of NCED3 [69]. Understanding the regulatory mechanisms of carotenoids will help to breed yellow peach varieties with high carotenoid content by manipulating key regulatory elements through biotechnological methods.

5. Conclusions

In this study, a total of 190 MYB family members were identified from the peach genome by bioinformatics methods, and these MYB members were analyzed for physicochemical properties, phylogeny, and collinearity within the peach genome and with A. thaliana and Rosa chinensis. We found that mdm-miR858 was able to target PpMYB17 and PpMYB126 by degradome sequencing, while PpMYB17 and PpMYB126 were negatively correlated with ZDS2, ZEP1, PSY1, and LCYE and positively correlated with NCED3, PSY2, ZDS1, CHYB1, and NCED2. Thus, mdm-miR858 may be involved in the regulation of carotenoid biosynthesis by targeting PpMYB17 and PpMYB126. Based on these findings, the present study proposes a regulatory network in which miRNAs are involved in the regulation of carotenoid biosynthesis in yellow peaches through MYB (Figure 11). In summary, this study comprehensively identified miRNAs involved in carotenoid biosynthesis, deepened the understanding of carotenoid accumulation and its regulatory mechanisms in yellow peach pericarp, and expanded the gene regulatory network of carotenoid synthesis.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/f15071119/s1, Table S1. Information on 190 members of the Peach MYB family. Table S2. The Ka/Ks ratio of duplicated PpMYB genes. Table S3. Analysis of cis-acting elements in the promoter sequences of peach (Prunus persica) MYB family members. Figure S1. Heat map of MYB family member expression in yellow peach pericarp at different developmental periods.

Author Contributions

Conceptualization, F.X.; methodology, F.L., J.Z. and Y.Y.; data curation, Y.Y. and J.Y.; validation, W.Z.; writing—original draft, F.L., J.Z. and Y.Y.; writing—review and editing, F.X. and X.Y.; visualization, L.J.; project administration, F.X. All authors have read and agreed to the published version of the manuscript.

Funding

This research was supported by the National Natural Science Foundation of China (No. 32201603).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Data are contained within this article and Supplementary Materials.

Conflicts of Interest

The authors declare no conflicts of interest.

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Figure 1. The distribution of the MYB family on chromosomes in peach. The colors on the chromosomes represent gene density. The 190 MYB genes in peach were distributed on the 8 chromosomes.
Figure 1. The distribution of the MYB family on chromosomes in peach. The colors on the chromosomes represent gene density. The 190 MYB genes in peach were distributed on the 8 chromosomes.
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Figure 2. The collinearity analysis of MYB family members in the peach genome. The images were visualized using the MCScanX tool in TBtools under default parameter conditions. The E-value is set to 10−10. The number of blasthits is set to 5. Grey lines represent the collinear blocks within the P. persica genome, and the blue lines highlight the syntenic MYB gene pairs. The red lines represent gene density. Detailed information of the synteny relationship is shown in Table S2.
Figure 2. The collinearity analysis of MYB family members in the peach genome. The images were visualized using the MCScanX tool in TBtools under default parameter conditions. The E-value is set to 10−10. The number of blasthits is set to 5. Grey lines represent the collinear blocks within the P. persica genome, and the blue lines highlight the syntenic MYB gene pairs. The red lines represent gene density. Detailed information of the synteny relationship is shown in Table S2.
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Figure 3. Co-linearity of peach MYB family genes with MYB genes in the Arabidopsis and moon genomes, respectively. Grey lines represent the collinear blocks within different genomes, and the cyan lines highlight the syntenic MYB gene pairs. The images were visualized using the MCScanX tool in TBtools under default parameter conditions. The E-value is set to 10−10. The number of blasthits is set to 5.
Figure 3. Co-linearity of peach MYB family genes with MYB genes in the Arabidopsis and moon genomes, respectively. Grey lines represent the collinear blocks within different genomes, and the cyan lines highlight the syntenic MYB gene pairs. The images were visualized using the MCScanX tool in TBtools under default parameter conditions. The E-value is set to 10−10. The number of blasthits is set to 5.
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Figure 4. The phylogenetic relationship between peach and Arabidopsis MYB family genes. The peach MYB family was categorized according to the Arabidopsis family. Red circles represent peach MYB genes and blue circles represent Arabidopsis MYB genes.
Figure 4. The phylogenetic relationship between peach and Arabidopsis MYB family genes. The peach MYB family was categorized according to the Arabidopsis family. Red circles represent peach MYB genes and blue circles represent Arabidopsis MYB genes.
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Figure 5. The distribution of conserved motifs, domains, and gene structures of the 190 PpMYB genes.
Figure 5. The distribution of conserved motifs, domains, and gene structures of the 190 PpMYB genes.
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Figure 6. The analysis of cis-acting elements in the promoters of peach MYB family members.
Figure 6. The analysis of cis-acting elements in the promoters of peach MYB family members.
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Figure 7. Phylogenetic analysis of PpMYB involved in carotenoid biosynthesis.
Figure 7. Phylogenetic analysis of PpMYB involved in carotenoid biosynthesis.
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Figure 8. The correlation analysis of candidate PpMYBs involved in carotenoid biosynthesis with carotenoid content of yellow peach at different developmental periods. (A) Expression patterns of 13 candidate PpMYBs at different developmental periods of yellow peach. DAF: days after flower. (B) The correlation analysis of the expression of candidate PpMYB with carotenoid content. Numerical values indicate correlation coefficients, with larger absolute values indicating more positive or negative correlation. Correlation coefficients were calculated through Excel 2019. Red and blue colors indicate higher or lower correlation.
Figure 8. The correlation analysis of candidate PpMYBs involved in carotenoid biosynthesis with carotenoid content of yellow peach at different developmental periods. (A) Expression patterns of 13 candidate PpMYBs at different developmental periods of yellow peach. DAF: days after flower. (B) The correlation analysis of the expression of candidate PpMYB with carotenoid content. Numerical values indicate correlation coefficients, with larger absolute values indicating more positive or negative correlation. Correlation coefficients were calculated through Excel 2019. Red and blue colors indicate higher or lower correlation.
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Figure 9. The correlation analysis between PpMYB and differentially expressed genes (A) and analysis of MYB binding sites in the promoters (B).
Figure 9. The correlation analysis between PpMYB and differentially expressed genes (A) and analysis of MYB binding sites in the promoters (B).
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Figure 10. T-plots of target genes of miRNAs. Red dots in the T-plots indicate the cleavage sites of miRNAs on the target mRNA sequences.
Figure 10. T-plots of target genes of miRNAs. Red dots in the T-plots indicate the cleavage sites of miRNAs on the target mRNA sequences.
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Figure 11. A regulatory model for the MYB regulation of carotenoid biosynthesis in yellow peach. PpMYB126 and PpMYB17 are target genes of mdm-miR858.
Figure 11. A regulatory model for the MYB regulation of carotenoid biosynthesis in yellow peach. PpMYB126 and PpMYB17 are target genes of mdm-miR858.
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Liu, F.; Zheng, J.; Yi, Y.; Yang, X.; Jiang, L.; Ye, J.; Zhang, W.; Xu, F. Genome-Wide Identification of MYB Gene Family in Peach and Identification of MYBs Involved in Carotenoid Biosynthesis. Forests 2024, 15, 1119. https://doi.org/10.3390/f15071119

AMA Style

Liu F, Zheng J, Yi Y, Yang X, Jiang L, Ye J, Zhang W, Xu F. Genome-Wide Identification of MYB Gene Family in Peach and Identification of MYBs Involved in Carotenoid Biosynthesis. Forests. 2024; 15(7):1119. https://doi.org/10.3390/f15071119

Chicago/Turabian Style

Liu, Fengyi, Jiarui Zheng, Yuwei Yi, Xiaoyan Yang, Leiyu Jiang, Jiabao Ye, Weiwei Zhang, and Feng Xu. 2024. "Genome-Wide Identification of MYB Gene Family in Peach and Identification of MYBs Involved in Carotenoid Biosynthesis" Forests 15, no. 7: 1119. https://doi.org/10.3390/f15071119

APA Style

Liu, F., Zheng, J., Yi, Y., Yang, X., Jiang, L., Ye, J., Zhang, W., & Xu, F. (2024). Genome-Wide Identification of MYB Gene Family in Peach and Identification of MYBs Involved in Carotenoid Biosynthesis. Forests, 15(7), 1119. https://doi.org/10.3390/f15071119

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