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Distribution of OsMYBs on rice chromosomes. The rod represents the 12 chromosomes of rice, and the scale on the left indicates its length. Different colors represent the different MYB type: 1R_MYB (Black); 2R_MYB (Red); 3R_MYB (purple); 4R_MYB (blue). The repeat gene pairs were linked using red curves.
Source publication
The myeloblastosis (MYB) family comprises a large group of transcription factors (TFs) that has a variety of functions. Among them, the R2R3-MYB type of proteins are the largest group in plants, which are involved in controlling various biological processes such as plant growth and development, physiological metabolism, defense, and responses to ab...
Contexts in source publication
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... on the number of adjacent repeats, they were named as Os1R_MYB1~Os1R_MYB87, Os2R_MYB1~Os2R_MYB99, Os3R_MYB1~Os3R_MYB3, and Os4R_MYB1. The results of chromosome visualization (Figure 1) showed that 190 OsMYB genes are located on 12 chromosomes. There were more OsMYB genes on chromosomes 1, 2, and 6 (35, 23, and 22, respectively) and fewer OsMYB genes on chromosomes 9, 10, and 11 (9, 7, and 5, respectively). ...
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... phylogenetic trees of MYB proteins in Oryza sativa L. and Arabidopsis thaliana were constructed (Figure 2) to further study the evolutionary relationships between 2R-MYB proteins. Multiple sequence alignment of rice 2R-MYB proteins (Supplementary Figure S1) showed the "-W-(X18/X19)-W-(X18/X19)-W-. . . -W/F/I/L-W(X18/X19)-W-" structure, thus forming the helix-turn-helix (HTH) fold. ...
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... TF family is one of the most abundant families in plants, with complex and diverse functions. This study identified 190 MYB family members in the rice genome unevenly distributed on all 12 chromosomes (Figure 1), of which 99 were R2R3-MYB (52.1%). R2R3-MYB group is one of the largest group of proteins in plants. ...
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... structure in the Nterminal of MYB domain is the key sequence of its complex functions. We aligned the sequences of the 2R-MYB protein of rice ( Figure S1), and the results showed that almost all 99 2R-MYB proteins contained the structure. The first W of the R3 domain was usually replaced by aromatic or hydrophobic amino acids such as leucine (L), isoleucine (I), or phenylalanine (F), which together form a hydrophobic core [2,27], conferring their complex functions. ...
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... Materials: The following supporting information can be downloaded at: https: //www.mdpi.com/article/10.3390/plants11151928/s1, Figure S1: Multiple sequence alignments of Os2R_MYB proteins; Figure S2: Relative gene expression of 20 Os2R_MYBs under PEG and CdCl 2 stress treatments; Table S1: Physicochemical Properties of the 2R-MYB Type Proteins; Table S2: Statistical Analysis of the Intron Numbers of 99 Os2R_MYB Genes; Table S3: R2R3_MYB proteins interaction network construct; Table S4: R2R3_MYB proteins interaction network protein annotations; Table S5: R2R3_MYB proteins interaction network functional annotations; Table S6: Statistical Analysis of Os2R_MYB Genes Expression Level under the PEG and CdCl2 Stresses; Table S7: Quantitative RT-PCR Primers. ...
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Citations
... In this study, 52 R2R3-MYB genes were identified using full-length transcriptome sequencing (Fig. 6). The number of R2R3-MYB genes was lower than that of Arabidopsis (126) [39], rice (99) [40], impatiens (73) [41], Chrysanthemum nankingense (183) [42], and Casuarina equisetifolia (107) [43], but it was equivalent to the reported number in Morinda officinalis (51) [44] and Bothriochloa ischaemum (43) [45] (Fig. 7). Because genes clustered in the same branch have close genetic relationships and similar functions, in this study, we predicted the function of RpMYBs based on the phylogenetic tree. ...
Background
Rheum palmatum L. has important medicinal value because it contains biologically active anthraquinones. However, the key genes and TFs involved in anthraquinone biosynthesis and regulation in R. palmatum remain unclear.
Methods
Based on full length transcriptome data, in this study, we screened the differentially expressed genes in the anthraquinone biosynthesis pathway. The R2R3-MYB family genes of R. palmatum were systematically identified based on full-length transcriptome sequencing followed by bioinformatics analyses. The correlation analysis was carried out by using co-expression analysis, protein interaction analysis, and real-time fluorescence quantitative analysis after MeJA treatment. The RpMYB81 and RpMYB98 genes were amplified by RT-PCR, and their subcellular localization and self-activation characteristics were analyzed.
Results
Comparative transcriptome analysis results revealed a total of 3525 upregulated and 6043 downregulated DEGs in the CK versus MeJA group; 28 DEGs were involved in the anthraquinone pathway. Eleven CHS genes that belonged to the PKS family were differentially expressed and involved in anthraquinone biosynthesis. Twelve differentially expressed MYBs genes were found to be co-expressed and interact with CHS genes. Furthermore, 52 MYB genes were identified as positive regulators of anthraquinone biosynthesis and were further characterized . Three MYB genes including RpMYB81 , RpMYB98 , and RpMYB100 responded to MeJA treatment in R. palmatum , and the levels of these genes were verified by qRT-PCR . RpMYB81 was related to anthraquinone biosynthesis. RpMYB98 had an interaction with genes in the anthraquinone biosynthesis pathway. RpMYB81 and RpMYB98 were mainly localized in the nucleus. RpMYB81 had self-activation activity, while RpMYB98 had no self-activation activity.
Conclusion
RpMYB8 1, RpMYB98 , and RpMYB100 were significantly induced by MeJA treatment. RpMYB81 and RpMYB98 are located in the nucleus, and RpMYB81 has transcriptional activity, suggesting that it might be involved in the transcriptional regulation of anthraquinone biosynthesis in R. palmatum .
... In this study, 12 ClHSP70s were identified in watermelon, which was similar to the number in cucumber (13) and grapevine (15), but less than that in tomato (19), maize (28) and rice (31) (Figure 3; Supplementary Table S1). This difference may be related to their genome sizes or evolutionary diversities (Sung et al., 2001;Zhang et al., 2015;Guo et al., 2016;Kang et al., 2022). Gene structure and phylogenetic tree were helpful to analyze the evolutionary relationship among genes . ...
Watermelon (Citrullus lanatus) as a crop with important economic value, is widely cultivated around the world. The heat shock protein 70 (HSP70) family in plant is indispensable under stress conditions. However, no comprehensive analysis of watermelon HSP70 family is reported to date. In this study, 12 ClHSP70 genes were identified from watermelon, which were unevenly located in 7 out of 11 chromosomes and divided into three subfamilies. ClHSP70 proteins were predicted to be localized primarily in cytoplasm, chloroplast, and endoplasmic reticulum. Two pairs of segmental repeats and 1 pair of tandem repeats existed in ClHSP70 genes, and ClHSP70s underwent strong purification selection. There were many abscisic acid (ABA) and abiotic stress response elements in ClHSP70 promoters. Additionally, the transcriptional levels of ClHSP70s in roots, stems, true leaves, and cotyledons were also analyzed. Some of ClHSP70 genes were also strongly induced by ABA. Furthermore, ClHSP70s also had different degrees of response to drought and cold stress. The above data indicate that ClHSP70s may be participated in growth and development, signal transduction and abiotic stress response, laying a foundation for further analysis of the function of ClHSP70s in biological processes.
Cadmium (Cd) is a heavy metal highly toxic to living organisms. Cd pollution of soils has become a serious problem worldwide, posing a severe threat to crop production and human health. When plants are poisoned by Cd, their growth and development are inhibited, chloroplasts are severely damaged, and respiration and photosynthesis are negatively affected. Therefore, elucidating the molecular mechanisms that underlie Cd tolerance in plants is important. Transcription factors can bind to specific plant cis-acting genes. Transcription factors are frequently reported to be involved in various signaling pathways involved in plant growth and development. Their role in the resistance to environmental stress factors, particularly Cd, should not be underestimated. The roles of several transcription factor families in the regulation of plant resistance to Cd stress have been widely demonstrated. In this review, we summarize the mechanisms of five major transcription factor families–WRKY, ERF, MYB, bHLH, and bZIP–in plant resistance to Cd stress to provide useful information for using molecular techniques to solve Cd pollution problems in the future.
Plants often experience abiotic stress, which severely affects their growth. With the advent of global warming, drought stress has become a pivotal factor affecting crop yield and quality. Increasing numbers of studies have focused on elucidating the molecular mechanisms underlying plant responses to drought stress. As molecular switches, transcription factors (TFs) are key participants in drought‐resistance regulatory networks in crops. TFs regulate the transcription of downstream genes and are regulated by various upstream regulatory factors. Therefore, understanding the mechanisms of action of TFs in regulating drought stress can help enhance the adaptive capacity of crops under drought conditions. In this review, we summarize the structural characteristics of several common TFs, their multiple drought‐response pathways, and recently employed research strategies. We describe the application of new technologies such as analysis of stress granule dynamics and function, multi‐omics data, gene editing, and molecular crosstalk between TFs in drought resistance. This review aims to familiarize readers with the regulatory network of TFs in drought resistance and to provide a reference for examining the molecular mechanisms of drought resistance in plants and improving agronomic traits.
Background
Zingiber officinale Roscoe, colloquially known as ginger, is a crop of significant medicinal and culinary value that frequently encounters adversity stemming from inhospitable environmental conditions. The MYB transcription factors have garnered recognition for their pivotal role in orchestrating a multitude of plant biological pathways. Nevertheless, the enumeration and characterization of the MYBs within Z. officinale Roscoe remains unknown. This study embarks on a genome-wide scrutiny of the MYB gene lineage in ginger, with the aim of cataloging all ZoMYB genes implicated in the biosynthesis of gingerols and curcuminoids, and elucidating their potential regulatory mechanisms in counteracting abiotic stress, thereby influencing ginger growth and development.
Results
In this study, we identified an MYB gene family comprising 231 members in ginger genome. This ensemble comprises 74 singular-repeat MYBs (1R-MYB), 156 double-repeat MYBs (R2R3-MYB), and a solitary triple-repeat MYB (R1R2R3-MYB). Moreover, a comprehensive analysis encompassing the sequence features, conserved protein motifs, phylogenetic relationships, chromosome location, and gene duplication events of the ZoMYBs was conducted. We classified ZoMYBs into 37 groups, congruent with the number of conserved domains and gene structure analysis. Additionally, the expression profiles of ZoMYBs during development and under various stresses, including ABA, cold, drought, heat, and salt, were investigated in ginger utilizing both RNA-seq data and qRT-PCR analysis.
Conclusion
This work provides a comprehensive understanding of the MYB family in ginger and lays the foundation for the future investigation of the potential functions of ZoMYB genes in ginger growth, development and abiotic stress tolerance of ginger.
The R2R3-MYB gene family, encoding plant transcriptional regulators, participates in many metabolic pathways of plant physiology and development, including flavonoid metabolism and anthocyanin synthesis. This study proceeded as follows: the JrR2R3-MYB gene family was analyzed genome-wide, and the family members were identified and characterized using the high-quality walnut reference genome “Chandler 2.0”. All 204 JrR2R3-MYBs were established and categorized into 30 subgroups via phylogenetic analysis. JrR2R3-MYBs were unevenly distributed over 16 chromosomes. Most JrR2R3-MYBs had similar structures and conservative motifs. The cis-acting elements exhibit multiple functions of JrR2R3-MYBs such as light response, metabolite response, and stress response. We found that the expansion of JrR2R3-MYBs was mainly caused by WGD or segmental duplication events. Ka/Ks analysis indicated that these genes were in a state of negative purifying selection. Transcriptome results suggested that JrR2R3-MYBs were widely entangled in the process of walnut organ development and differentially expressed in different colored varieties of walnuts. Subsequently, we identified 17 differentially expressed JrR2R3-MYBs, 9 of which may regulate anthocyanin biosynthesis based on the results of a phylogenetic analysis. These genes were present in greater expression levels in ‘Zijing’ leaves than in ‘Lvling’ leaves, as revealed by the results of qRT-PCR experiments. These results contributed to the elucidation of the functions of JrR2R3-MYBs in walnut coloration. Collectively, this work provides a foundation for exploring the functional characteristics of the JrR2R3-MYBs in walnuts and improving the nutritional value and appearance quality of walnuts.
In the context of sustainable agriculture and biomaterial development, understanding and enhancing plant secondary cell wall formation are crucial for improving crop fiber quality and biomass conversion efficiency. This is especially critical for economically important crops like upland cotton (Gossypium hirsutum L.), for which fiber quality and its processing properties are essential. Through comprehensive genome-wide screening and analysis of expression patterns, we identified a particularly high expression of an R2R3 MYB transcription factor, GhMYB52 Like, in the development of the secondary cell wall in cotton fiber cells. Utilizing gene-editing technology to generate a loss-of-function mutant to clarify the role of GhMYB52 Like, we revealed that GhMYB52 Like does not directly contribute to cellulose synthesis in cotton fibers but instead represses a subset of lignin biosynthesis genes, establishing it as a lignin biosynthesis inhibitor. Concurrently, a substantial decrease in the lint index, a critical measure of cotton yield, was noted in parallel with an elevation in lignin levels. This study not only deepens our understanding of the molecular mechanisms underlying cotton fiber development but also offers new perspectives for the molecular improvement of other economically important crops and the enhancement of biomass energy utilization.
In the current study, a MYB (Myeloblastosis) Transcription Factor (TF) gene sequence (WsMYB46) has been retrieved from the transcriptome repertoire of the medicinal plant Withania somnifera and it has been structurally and functionally characterised using different bioinformatics tools. Amino acid sequence comparison of WsMYB46 and MYB TFs from 30 medicinal plants and the model plant Arabidopsis thaliana provided information about the conserved DNA binding domains of WsMYB46. The analysis suggests that WsMYB46 belongs to the R2R3 family of MYB TFs. The in silico prediction of the physicochemical properties of WsMYB46 and the MYB TFs show that they are localized in the nucleus, contain 312–438 amino acid residues, and are hydrophilic and acidic in nature, with a theoretical pI between 5.15 and 6.65. A 3-D model of the WsMYB46 protein has been constructed, and the functional annotation indicates that the WsMYB46 gene is involved in mRNA and cellular processing. The high degree of structural similarity of WsMYB46 with AtMYB46/AtMYB83, which are known to have important roles in the regulation of secondary cell wall biosynthesis, indicates the possible functional role of WsMYB46 in the regulation of secondary cell wall biosynthesis. The in silico gene expression analysis showed its low expression during salt stress. 427 miRNA sequences from A. thaliana were selected to identify the possible miRNA targets in WsMYB46. Six miRNAs with target sites in WsMYB46 were identified. This comprehensive in silico study of WsMYB46 and other MYB TFs from medicinal plants would be helpful to gain a deeper understanding of MYB TFs and their roles in medicinal plants.
