scholarly journals Genome-wide characterization and expression analyses of the MYB superfamily genes during developmental stages in Chinese jujube

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6353 ◽  
Author(s):  
Ji Qing ◽  
Wang Dawei ◽  
Zhou Jun ◽  
Xu Yulan ◽  
Shen Bingqi ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Total Flavonoid ◽  
Myb Transcription Factor ◽  
Phenylpropanoid Metabolism ◽  
Sequencing Data ◽  
Chinese Jujube ◽  
Physiological Processes ◽  
Jujube Fruit ◽  
Myb Genes ◽  
R2r3 Myb

The MYB transcription factor (TF) superfamily, one of the largest gene superfamilies, regulates a variety of physiological processes in plants. Although many MYB superfamily genes have been identified in plants, the MYB TFs in Chinese jujube (Ziziphus jujuba Mill.) have not been fully identified and characterized. Additionally, the functions of these genes remain unclear. In total, we identified 171 MYB superfamily genes in jujube and divided them into five subfamilies containing 99 genes of the R2R3-MYB subfamily, 58 genes of the MYB-related subfamily, four genes of the R1R2R3-MYB subfamily, one gene of the 4R-MYB subfamily, and nine genes of the atypical MYB subfamily. The 99 R2R3-MYB genes of jujube were divided into 35 groups, C1–C35, and the 58 MYB-related genes were divided into the following groups: the R-R-type, CCA1-like, I-box-binding-like, TBP-like, CPC-like, and Chinese jujube-specific groups. ZjMYB genes in jujube were well supported by additional highly conserved motifs and exon/intron structures. Most R1 repeats of MYB-related proteins comprised the R2 repeat and had highly conserved EED and EEE residue groups in jujube. Three tandem duplicated gene pairs were found on 12 chromosomes in jujube. According to an expression analysis of 126 ZjMYB genes, MYB-related genes played important roles in jujube development and fruit-related biological processes. The total flavonoid content of jujube fruit decreased as ripening progressed. A total of 93 expressed genes were identified in the RNA-sequencing data from jujube fruit, and 56 ZjMYB members presented significant correlations with total flavonoid contents by correlation analysis. Five pairs of paralogous MYB genes within jujube were composed of nine jujube MYB genes. A total of 14 ZjMYB genes had the same homology to the MYB genes of Arabidopsis and peach, indicating that these 14 MYB genes and their orthologs probably existed before the ancestral divergence of the MYB superfamily. We used a synteny analysis of MYB genes between jujube and Arabidopsis to predict that the functions of the ZjMYBs involve flavonoid/phenylpropanoid metabolism, the light signaling pathway, auxin signal transduction, and responses to various abiotic stresses (cold, drought, and salt stresses). Additionally, we speculate that ZjMYB108 is an important TF involved in the flavonoid metabolic pathway. This comprehensive analysis of MYB superfamily genes in jujube lay a solid foundation for future comprehensive analyses of ZjMYB gene functions.

scholarly journals Dissecting the Genome-Wide Evolution and Function of R2R3-MYB Transcription Factor Family in Rosa chinensis

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 823 ◽  
Author(s):  
Yu Han ◽  
Jiayao Yu ◽  
Tao Zhao ◽  
Tangren Cheng ◽  
Jia Wang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Gene Evolution ◽  
Myb Transcription Factor ◽  
Phenylpropanoid Metabolism ◽  
Transcription Factor Family ◽  
Rosa Chinensis ◽  
Myb Gene ◽  
Myb Genes ◽  
And Function ◽  
R2r3 Myb

Rosa chinensis, an important ancestor species of Rosa hybrida, the most popular ornamental plant species worldwide, produces flowers with diverse colors and fragrances. The R2R3-MYB transcription factor family controls a wide variety of plant-specific metabolic processes, especially phenylpropanoid metabolism. Despite their importance for the ornamental value of flowers, the evolution of R2R3-MYB genes in plants has not been comprehensively characterized. In this study, 121 predicted R2R3-MYB gene sequences were identified in the rose genome. Additionally, a phylogenomic synteny network (synnet) was applied for the R2R3-MYB gene families in 35 complete plant genomes. We also analyzed the R2R3-MYB genes regarding their genomic locations, Ka/Ks ratio, encoded conserved motifs, and spatiotemporal expression. Our results indicated that R2R3-MYBs have multiple synteny clusters. The RcMYB114a gene was included in the Rosaceae-specific Cluster 54, with independent evolutionary patterns. On the basis of these results and an analysis of RcMYB114a-overexpressing tobacco leaf samples, we predicted that RcMYB114a functions in the phenylpropanoid pathway. We clarified the relationship between R2R3-MYB gene evolution and function from a new perspective. Our study data may be relevant for elucidating the regulation of floral metabolism in roses at the transcript level.

scholarly journals Genome-Wide Analysis of the MYB Transcription Factor Superfamily in Physcomitrella patens

2020 ◽  
Vol 21 (3) ◽  
pp. 975 ◽  
Author(s):  
Xiaojun Pu ◽  
Lixin Yang ◽  
Lina Liu ◽  
Xiumei Dong ◽  
Silin Chen ◽  
...  
Keyword(s):  
Stress Responses ◽  
Physcomitrella Patens ◽  
Myb Transcription Factor ◽  
Rna Seq ◽  
Genome Wide ◽  
Terrestrial Environments ◽  
Gene Structures ◽  
Myb Genes ◽  
Myb Proteins ◽  
R2r3 Myb

MYB transcription factors (TFs) are one of the largest TF families in plants to regulate numerous biological processes. However, our knowledge of the MYB family in Physcomitrella patens is limited. We identified 116 MYB genes in the P. patens genome, which were classified into the R2R3-MYB, R1R2R3-MYB, 4R-MYB, and MYB-related subfamilies. Most R2R3 genes contain 3 exons and 2 introns, whereas R1R2R3 MYB genes contain 10 exons and 9 introns. N3R-MYB (novel 3RMYB) and NR-MYBs (novel RMYBs) with complicated gene structures appear to be novel MYB proteins. In addition, we found that the diversity of the MYB domain was mainly contributed by domain shuffling and gene duplication. RNA-seq analysis suggested that MYBs exhibited differential expression to heat and might play important roles in heat stress responses, whereas CCA1-like MYB genes might confer greater flexibility to the circadian clock. Some R2R3-MYB and CCA1-like MYB genes are preferentially expressed in the archegonium and during the transition from the chloronema to caulonema stage, suggesting their roles in development. Compared with that of algae, the numbers of MYBs have significantly increased, thus our study lays the foundation for further exploring the potential roles of MYBs in the transition from aquatic to terrestrial environments.

scholarly journals MdMYB4, an R2R3-Type MYB Transcription Factor, Plays a Crucial Role in Cold and Salt Stress in Apple Calli

2017 ◽  
Vol 142 (3) ◽  
pp. 209-216 ◽  
Author(s):  
Ruigang Wu ◽  
Yi Wang ◽  
Ting Wu ◽  
Xuefeng Xu ◽  
Zhenhai Han
Keyword(s):  
Salt Stress ◽  
Cold Stress ◽  
Stress Responses ◽  
Transcriptional Activation ◽  
Myb Transcription Factor ◽  
Abiotic Stress Response ◽  
Physiological Processes ◽  
In The Wild ◽  
Polymerase Chain ◽  
R2r3 Myb

MYB (v-myb avian myeloblastosis viral oncogene homologs) transcription factors (TFs) are involved in diverse physiological processes, including cell shape determination, cell differentiation, and secondary metabolism, as well as abiotic stress response. In the present study, MdMYB4, an R2R3-MYB protein that is a homolog of Arabidopsis thaliana MYB4, was identified and characterized. Quantitative real-time polymerase chain reaction (qRT-PCR) expression analysis demonstrated that MdMYB4 is extensively expressed in various apple (Malus domestica) tissues and that its expression is induced by cold, osmotic, and salt stress. An MdMYB4-GFP fusion protein was localized in the nucleus of transformed onion (Allium cepa) epidermal cells and had a certain transcriptional activation activity by yeast one-hybrid assay. Overexpression of the MdMYB4 gene remarkably enhanced the tolerance of stably transgenic apple calli to severe salt and cold stress, and both the relative conductivity and malondialdehyde (MDA) accumulation of transgenic calli under salt and cold stress were significantly lower than in the wild type control. Taken together, these results suggest that MdMYB4 may play a positive regulatory role in both cold and salt stress responses.

scholarly journals The R2R3-MYB transcription factor family in Taxus chinensis: identification, characterization, expression profiling and posttranscriptional regulation analysis

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8473
Author(s):  
Xinling Hu ◽  
Lisha Zhang ◽  
Iain Wilson ◽  
Fenjuan Shao ◽  
Deyou Qiu
Keyword(s):  
Transcription Factor ◽  
Posttranscriptional Regulation ◽  
Gene Families ◽  
Myb Transcription Factor ◽  
Taxus Chinensis ◽  
Transcription Factor Family ◽  
Myb Genes ◽  
And Function ◽  
R2r3 Myb

The MYB transcription factor family is one of the largest gene families playing regulatory roles in plant growth and development. The MYB family has been studied in a variety of plant species but has not been reported in Taxus chinensis. Here we identified 72 putative R2R3-MYB genes in T. chinensis using a comprehensive analysis. Sequence features, conversed domains and motifs were characterized. The phylogenetic analysis showed TcMYBs and AtMYBs were clustered into 36 subgroups, of which 24 subgroups included members from T. chinensis and Arabidopsis thaliana, while 12 subgroups were specific to one species. This suggests the conservation and specificity in structure and function of plant R2R3-MYBs. The expression of TcMYBs in various tissues and different ages of xylem were investigated. Additionally, miRNA-mediated posttranscriptional regulation analysis revealed that TcMYBs were the targets of miR858, miR159 and miR828, suggesting the posttranscriptional regulation of MYBs is highly conserved in plants. The results provide a basis for further study the role of TcMYBs in the regulation of secondary metabolites of T. chinensis.

scholarly journals Genome Wide Identification and Analysis of the R2R3-MYB Transcription Factor Gene Family in the Mangrove Avicennia marina

Agronomy ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 123
Author(s):  
Seema Pradhan ◽  
P Sushree Shyamli ◽  
Sandhya Suranjika ◽  
Ajay Parida
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
High Salinity ◽  
Avicennia Marina ◽  
Myb Transcription Factor ◽  
Transcription Factor Gene ◽  
Genome Wide ◽  
Myb Genes ◽  
R2r3 Myb ◽  
Transcription Factor Gene Family

Drought and salinity stress have become the major factors for crop yield loss in recent years. Drastically changing climatic conditions will only add to the adverse effects of such abiotic stresses in the future. Hence, it is necessary to conduct extensive research to elucidate the molecular mechanisms that regulate plants’ response to abiotic stress. Halophytes are plants that can grow in conditions of high salinity and are naturally resistant to a number of abiotic stresses. Avicennia marina is one such halophyte, which grows in tropical regions of the world in areas of high salinity. In this study, we have analysed the role of R2R3-MYB transcription factor gene family in response abiotic stress, as a number of transcription factors have been reported to have a definite role in stress manifestation. We identified 185 R2R3 MYB genes at genome-wide level in A. marina and classified them based on the presence of conserved motifs in the protein sequences. Cis-regulatory elements (CREs) present in the promoter region of these genes were analysed to identify stress responsive elements. Comparative homology with genes from other plants provided an insight into the evolutionary changes in the A. marinaR2R3 MYB genes. In silico expression analysis revealed 34 AmR2R3 MYB genes that were differentially regulated in the leaves and root tissue of A. marina subjected to drought and salinity stress. This study is the first report of the R2R3 MYB gene family in the A. marina genome and will help in selecting candidates for further functional characterisation.

scholarly journals Identification of the Eutrema Salsugineum EsMYB90 gene important for anthocyanin biosynthesis

2020 ◽  
Author(s):  
Yuting Qi ◽  
Caihong Gu ◽  
Xingjun Wang ◽  
Shiqing Gao ◽  
Changsheng Li ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transgenic Plants ◽  
Anthocyanin Biosynthesis ◽  
Ectopic Expression ◽  
Myb Transcription Factor ◽  
Anthocyanin Synthesis ◽  
Eutrema Salsugineum ◽  
Tobacco Transgenic Plants ◽  
Myb Genes ◽  
R2r3 Myb

Abstract Abstract Background: Anthocyanins contribute to coloration and antioxidation effects in different plant tissues. MYB transcription factors have been demonstrated to be a key regulator for anthocyanin synthesis in many plants. However, little information was available about the MYB genes in the halophyte species Eutrema salsugineum . Result: Here we report the identification of an important anthocyanin biosynthesis regulator Es MYB90 from Eutrema salsugineum , which is a halophyte tolerant to multiple abiotic stresses. Our phylogenetic and localization analyses supported that Es MYB90 is an R2R3 type of MYB transcription factor. Ectopic expression of EsMYB90 in tobacco and Arabidopsis enhanced pigmentation and anthocyanin accumulation in various organs. The transcriptome analysis revealed that 42 genes upregulated by Es MYB90 in 35S : EsMYB90 tobacco transgenic plants are required for anthocyanin biosynthesis. Moreover, our qRT-PCR results showed that Es MYB90 promoted expression of early ( PAL , CHS , and CHI ) and late ( DFR , ANS , and UFGT ) anthocyanin biosynthesis genes in stems, leaves, and flowers of 35S : EsMYB90 tobacco transgenic plants. Conclusions: Our results indicated that Es MYB90 is a MYB transcription factor, which regulates anthocyanin biosynthesis genes to control anthocyanin biosynthesis. Our work provides a new tool to enhance anthocyanin production in various plants. Keywords : Anthocyanin, flavonoid, Eutrema salsugineum , R2R3 MYB transcription factor, Es MYB90, transcriptional regulation, anthocyanin biosynthesis genes.

scholarly journals Evolution of the Subgroup 6 R2R3-MYB Genes and Their Contribution to Floral Color in the Perianth-Bearing Piperales

2021 ◽  
Vol 12 ◽  
Author(s):  
Sarita Muñoz-Gómez ◽  
Harold Suárez-Baron ◽  
Juan F. Alzate ◽  
Favio González ◽  
Natalia Pabón-Mora
Keyword(s):  
Biosynthetic Pathway ◽  
Developmental Stages ◽  
Regulatory Genes ◽  
Rna Seq ◽  
Floral Color ◽  
Floral Diversity ◽  
Core Eudicots ◽  
Myb Genes ◽  
Species Specific ◽  
R2r3 Myb

Flavonoids, carotenoids, betalains, and chlorophylls are the plant pigments responsible for floral color. Anthocyanins, a class of flavonoids, are largely responsible for the red, purple, pink, and blue colors. R2R3-MYB genes belonging to subgroup 6 (SG6) are the upstream regulatory factors of the anthocyanin biosynthetic pathway. The canonical members of these genes in Arabidopsis include AtMYB75, AtMYB90, AtMYB113, and AtMYB114. The Aristolochiaceae is an angiosperm lineage with diverse floral groundplans and perianth colors. Saruma henryi exhibits a biseriate perianth with green sepals and yellow petals. All other genera have sepals only, with colors ranging from green (in Lactoris) to a plethora of yellow to red and purple mixtures. Here, we isolated and reconstructed the SG6 R2R3-MYB gene lineage evolution in angiosperms with sampling emphasis in Aristolochiaceae. We found numerous species-specific duplications of this gene lineage in core eudicots and local duplications in Aristolochiaceae for Saruma and Asarum. Expression of SG6 R2R3-MYB genes examined in different developmental stages and plant organs of four Aristolochiaceae species, largely overlaps with red and purple pigments, suggesting a role in anthocyanin and flavonoid synthesis and accumulation. A directed RNA-seq analysis corroborated our RT-PCR analyses, by showing that these structural enzymes activate during perianth development in Aristolochia fimbriata and that the regulatory genes are expressed in correlation with color phenotype. Finally, the reconstruction of the flavonoid and anthocyanin metabolic pathways using predicted peptides from transcriptomic data show that all pivotal enzymes are present in the analyzed species. We conclude that the regulatory genes as well as the biosynthetic pathway are largely conserved across angiosperms. In addition, the Aristolochiaceae emerges as a remarkable group to study the genetic regulatory network for floral color, as their members exhibit an outstanding floral diversity with elaborate color patterns and the genetic complement for SG6 R2R3-MYB genes is simpler than in core eudicot model species.

scholarly journals Genome-wide organization and expression profiling of the R2R3-MYB transcription factor family in sea buckthorn (Hippophae rhamnoides L.)

2020 ◽  
Author(s):  
Hong Liu ◽  
Guoyun Zhang ◽  
Zhongrui Lv ◽  
Songfeng Diao ◽  
Caiyun He ◽  
...  
Keyword(s):  
Gene Family ◽  
Gene Structure ◽  
Sea Buckthorn ◽  
Hippophae Rhamnoides ◽  
Myb Transcription Factor ◽  
Hippophaë Rhamnoides ◽  
Myb Gene ◽  
Myb Genes ◽  
Hippophae Rhamnoïdes L ◽  
R2r3 Myb

Abstract Background MYB transcription factor family involved in multifarious stages of plant growth and development until death, which is one of the largest and most versatile gene families in plants, therefore it is an important regulatory factor in plants. Sea buckthorn (Hippophae rhamnoides L.) is rich in many secondary metabolites and has high nutritional and medicinal value. With the completion of sea buckthorn genome sequencing, it has laid the foundation for us to explore the gene structure, evolutionary relationship and function prediction of sea buckthorn MYB gene family from the whole genome perspective. Results In this study, 161 R2R3-MYB genes were identified from the sea buckthorn genome. We systematically analyzed their gene structure, collinearity, phylogenetic relationships and expression pattern. According to the gene structure, conserved motifs and phylogenetic relationship of 161 HrMYB genes, all the HrMYB genes were divided into 28 subgroups. The phylogenetic tree of Hippophae rhamnoides L. and Arabidopsis thaliana R2R3-MYB genes showed that the sea buckthorn MYB gene family showed functional differentiation during evolution. Chromosomal localization results showed that the distribution of HrMYB genes were random. RNA-seq data from seven different tissues indicated that the HrMYB genes have significant spatiotemporal and tissue expression differences. QRT-PCR analysis showed that the selected genes which relate to flavonoid biosynthesis of sea buckthorn fruit expressed different degrees in different developmental stages of the fruit. Conclusion The sea buckthorn R2R3-MYB gene family was successfully identified from the whole genome sequence by a series of bioinformatics methods. The results firstly provide a more comprehensive insight for the phylogenetic relationships and expression patterns of the HrMYB genes. It will help us to further study their specific functions in the growth and development of sea buckthorn.

scholarly journals Identification of Anthocyanins Compositions and Functional Analysis of An Anthocyanin Activator in Solanum nigrum Fruits

2017 ◽  
Author(s):  
Shaoli Wang ◽  
Zhaohui Chu ◽  
Mingxing Ren ◽  
Ru Jia ◽  
Changbao Zhao ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Antioxidant Activities ◽  
Solanum Nigrum ◽  
Myb Transcription Factor ◽  
Purification Method ◽  
Hplc Profiles ◽  
Total Antioxidant ◽  
Race Pcr ◽  
R2r3 Myb ◽  
First Time

Solanum nigrum fruits have been conventionally available as a material of beverage due to its nutritional substances such as minerals, vitamins, amino acids, proteins, sugars, polyphenols and anthocyanins. Here has rarely reported on the characterizaton of the components and the regulatory mechanism of Anthocyanins in S. nigrum. In this study, we determined that the peel and flesh of S. nigrum fruits shared the similar HPLC profiles, but the different contents and total antioxidant activities for Anthocyanins. After an efficient purification method mainly including extraction with pH 1.0 distilled water and then desorption with pH 1.0 95% ethanol after a DM-130 resin adsorption step to obtain more pure anthocyanins extracts, the purity of anthocyanins extract from S. nigrum fruits reached to 56.1%. Moreover, eight anthocyanins from S. nigrum fruit were identified with HPLC-MS/MS for the first time. A typical R2R3-MYB transcription factor gene, SnMYB, was also cloned for the first time by RACE-PCR from S. nigrum. Moreover, the contents of anthocyanins was shown a good correlation (r = 0.93) with the expression levels of SnMYB  during the fruits developmental stages. Most significantly, SnMYB successfully produced high anthocyanins contents (1.03 mg/g) when SnMYB was transiently expressed in tobacco leaves. Taken together, S. nigrum fruits are a promising resource for anthocyanins extraction and SnMYB is an activator that positively regulates anthocyanins biosynthesis in S. nigrum.

scholarly journals Genome-Wide Identification and Expression Analysis of R2R3-MYB Family Genes Associated with Petal Pigment Synthesis in Liriodendron

2021 ◽  
Vol 22 (20) ◽  
pp. 11291
Author(s):  
Lichun Yang ◽  
Huanhuan Liu ◽  
Ziyuan Hao ◽  
Yaxian Zong ◽  
Hui Xia ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Functional Characterization ◽  
Myb Transcription Factor ◽  
Pigment Synthesis ◽  
Genome Wide ◽  
Liriodendron Chinense ◽  
Myb Genes ◽  
Myb Proteins ◽  
Ornamental Trees ◽  
R2r3 Myb

The MYB transcription factor family is one of the largest families in plants, and its members have various biological functions. R2R3-MYB genes are involved in the synthesis of pigments that yield petal colors. Liriodendron plants are widely cultivated as ornamental trees owing to their peculiar leaves, tulip-like flowers, and colorful petals. However, the mechanism underlying petal coloring in this species is unknown, and minimal information about MYB genes in Liriodendron is available. Herein, this study aimed to discern gene(s) involved in petal coloration in Liriodendron via genome-wide identification, HPLC, and RT-qPCR assays. In total, 204 LcMYB superfamily genes were identified in the Liriodendron chinense genome, and 85 R2R3-MYB genes were mapped onto 19 chromosomes. Chromosome 4 contained the most (10) R2R3-MYB genes, and chromosomes 14 and 16 contained the fewest (only one). MEME analysis showed that R2R3-MYB proteins in L. chinense were highly conserved and that their exon-intron structures varied. The HPLC results showed that three major carotenoids were uniformly distributed in the petals of L. chinense, while lycopene and β-carotene were concentrated in the orange band region in the petals of Liriodendron tulipifera. Furthermore, the expression profiles via RT-qPCR assays revealed that four R2R3-MYB genes were expressed at the highest levels at the S3P/S4P stage in L. tulipifera. This result combined with the HPLC results showed that these four R2R3-MYB genes might participate in carotenoid synthesis in the petals of L. tulipifera. This work laid a cornerstone for further functional characterization of R2R3-MYB genes in Liriodendron plants.

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