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.

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 Genome-Wide Identification and Expression Analysis of MYB Transcription Factor Superfamily in Dendrobium catenatum

2021 ◽  
Vol 12 ◽  
Author(s):  
Tingting Zhang ◽  
Zheng Cui ◽  
Yuxin Li ◽  
Yuqian Kang ◽  
Xiqiang Song ◽  
...  
Keyword(s):  
Abiotic Stresses ◽  
Molecular Breeding ◽  
Theoretical Foundation ◽  
Expression Profiles ◽  
Myb Transcription Factor ◽  
Rna Seq ◽  
Genome Wide ◽  
Gene Structures ◽  
Myb Proteins ◽  
R2r3 Myb

Dendrobium catenatum is an important traditional Chinese medicine and naturally grows on tree trunks and cliffs, where it can encounter diverse environmental stimuli. MYB transcription factors are widely involved in response to abiotic stresses. However, the MYB gene family has not yet been systematically cataloged in D. catenatum. In this study, a total of 133 MYB proteins were identified in D. catenatum, including 32 MYB-related, 99 R2R3-MYB, 1 3R-MYB, and 1 4R-MYB proteins. Phylogenetic relationships, conserved motifs, gene structures, and expression profiles in response to abiotic stresses were then analyzed. Phylogenetic analysis revealed MYB proteins in D. catenatum could be divided into 14 subgroups, which was supported by the conserved motif compositions and gene structures. Differential DcMYB gene expression and specific responses were analyzed under drought, heat, cold, and salt stresses using RNA-seq and validated by qRT-PCR. Forty-two MYB genes were differentially screened following exposure to abiotic stresses. Five, 12, 11, and 14 genes were specifically expressed in response to drought, heat, cold, and salt stress, respectively. This study identified candidate MYB genes with possible roles in abiotic tolerance and established a theoretical foundation for molecular breeding of D. catenatum.

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 Genome-wide analysis and expression profiles of PdeMYB transcription factors in colored-leaf poplar (Populus deltoids)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Weibing Zhuang ◽  
Xiaochun Shu ◽  
Xinya Lu ◽  
Tao Wang ◽  
Fengjiao Zhang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Green Leaf ◽  
Myb Transcription Factor ◽  
Pcr Analysis ◽  
Genome Wide ◽  
Populus Deltoids

Abstract Background MYB transcription factors, comprising one of the largest transcription factor families in plants, play many roles in secondary metabolism, especially in anthocyanin biosynthesis. However, the functions of the PdeMYB transcription factor in colored-leaf poplar remain elusive. Results In the present study, genome-wide characterization of the PdeMYB genes in colored-leaf poplar (Populus deltoids) was conducted. A total of 302 PdeMYB transcription factors were identified, including 183 R2R3-MYB, five R1R2R3-MYB, one 4R-MYB, and 113 1R-MYB transcription factor genes. Genomic localization and paralogs of PdeMYB genes mapped 289 genes on 19 chromosomes, with collinearity relationships among genes. The conserved domain, gene structure, and evolutionary relationships of the PdeMYB genes were also established and analyzed. The expression levels of PdeMYB genes were obtained from previous data in green leaf poplar (L2025) and colored leaf poplar (QHP) as well as our own qRT-PCR analysis data in green leaf poplar (L2025) and colored leaf poplar (CHP), which provide valuable clues for further functional characterization of PdeMYB genes. Conclusions The above results provide not only comprehensive insights into the structure and functions of PdeMYB genes but also provide candidate genes for the future improvement of leaf colorization in Populus deltoids.

scholarly journals Genome-Wide Identification and Analysis of the MYB Transcription Factor Gene Family in Chili Pepper (Capsicum spp.)

2021 ◽  
Vol 22 (5) ◽  
pp. 2229
Author(s):  
Magda L. Arce-Rodríguez ◽  
Octavio Martínez ◽  
Neftalí Ochoa-Alejo
Keyword(s):  
Transcription Factor ◽  
Expression Profiles ◽  
Chemical Properties ◽  
Chili Pepper ◽  
Myb Transcription Factor ◽  
Specific Expression ◽  
Genome Wide ◽  
Capsicum Spp ◽  
Myb Proteins ◽  
Functionally Diverse

The MYB transcription factor family is very large and functionally diverse in plants, however, only a few members of this family have been reported and characterized in chili pepper (Capsicum spp.). In the present study, we performed genome-wide analyses of the MYB family in Capsicum annuum, including phylogenetic relationships, conserved domain, gene structure organization, motif protein arrangement, chromosome distribution, chemical properties predictions, RNA-seq expression, and RT-qPCR expression assays. A total of 235 non-redundant MYB proteins were identified from C. annuum, including R2R3-MYB, 3R-MYB, atypical MYB, and MYB-related subclasses. The sequence analysis of CaMYBs compared with other plant MYB proteins revealed gene conservation, but also potential specialized genes. Tissue-specific expression profiles showed that CaMYB genes were differentially expressed, suggesting that they are functionally divergent. Furthermore, the integration of our data allowed us to propose strong CaMYBs candidates to be regulating phenylpropanoid, lignin, capsaicinoid, carotenoid, and vitamin C biosynthesis, providing new insights into the role of MYB transcription factors in secondary metabolism. This study adds valuable knowledge about the functions of CaMYB genes in various processes in the Capsicum genus.

scholarly journals Genome-Wide Identification and Comparative Analysis of MYB Transcription Factor Family in Musa acuminata and Musa balbisiana

Plants ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 413
Author(s):  
Lin Tan ◽  
Usman Ijaz ◽  
Haron Salih ◽  
Zhihao Cheng ◽  
Nwe Ni Win Htet ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Expression Patterns ◽  
Musa Acuminata ◽  
Protein Domain ◽  
Myb Transcription Factor ◽  
Segmental Duplications ◽  
Musa Balbisiana ◽  
Functional Studies ◽  
Myb Genes ◽  
Gain Loss

MYB transcription factors (TFs) make up one of the most important TF families in plants. These proteins play crucial roles in processes related to development, metabolism, and stimulus-response; however, very few studies have been reported for the characterization of MYB TFs from banana. The current study identified 305 and 251 MYB genes from Musa acuminata and Musa balbisiana, respectively. Comprehensive details of MYBs are reported in terms of gene structure, protein domain, chromosomal localization, phylogeny, and expression patterns. Based on the exon–intron arrangement, these genes were classified into 12 gene models. Phylogenetic analysis of MYBs involving both species of banana, Oryza sativa, and Arabidopsis thaliana distributed these genes into 27 subfamilies. This highlighted not only the conservation, but also the gain/loss of MYBs in banana. Such genes are important candidates for future functional investigations. The MYB genes in both species exhibited a random distribution on chromosomes with variable densities. Estimation of gene duplication events revealed that segmental duplications represented the major factor behind MYB gene family expansion in banana. Expression profiles of MYB genes were also explored for their potential involvement in acetylene response or development. Collectively, the current comprehensive analysis of MYB genes in both species of banana will facilitate future functional studies.

scholarly journals Genome-wide identification and characterisation of R2R3-MYB genes in sugar beet (Beta vulgaris)

2014 ◽  
Vol 14 (1) ◽  
Author(s):  
Ralf Stracke ◽  
Daniela Holtgräwe ◽  
Jessica Schneider ◽  
Boas Pucker ◽  
Thomas Rosleff Sörensen ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Beta Vulgaris ◽  
Genome Wide ◽  
Myb Genes ◽  
R2r3 Myb

scholarly journals Genome-Wide Identification of R2R3-MYB Genes and Expression Analyses During Abiotic Stress in Gossypium raimondii

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Qiuling He ◽  
Don C. Jones ◽  
Wei Li ◽  
Fuliang Xie ◽  
Jun Ma ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Genome Wide ◽  
Gossypium Raimondii ◽  
Myb Genes ◽  
R2r3 Myb

scholarly journals  Genome-Wide Analysis of R2R3-MYB Transcription Factors Family in The Autopolyploid Saccharum Spontaneum: An Exploration of Dominance Expression and Stress Response 

2021 ◽  
Author(s):  
Yuan Yuan ◽  
Xiping Yang ◽  
Mengfang Feng ◽  
Hongyan Ding ◽  
Khan Muhammad Tahir ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Stress Response ◽  
Gene Family ◽  
Expression Analysis ◽  
Expression Profiling ◽  
Saccharum Spontaneum ◽  
Myb Gene ◽  
Genome Wide ◽  
Myb Genes ◽  
R2r3 Myb

Abstract Background: Sugarcane (Saccharum) is the most important sugar crop in the world. As one of the most enriched transcription factor families in plants, MYB genes display a great potential to contribute to sugarcane improvement by trait modification. We have identified the sugarcane MYB gene family at a whole-genome level through systematic evolution analyses and expression profiling. R2R3-MYB is a large subfamily involved in many plant-specific processes. Results: A total of 202 R2R3-MYB genes (356 alleles) were identified in the polyploid Saccharum spontaneum genome and classified into 15 subgroups by phylogenetic analysis. The sugarcane MYB family had more members by a comparative analysis in sorghum and significant advantages among most plants, especially grasses. Collinearity analysis revealed that 70% of the SsR2R3-MYB genes had experienced duplication events, logically suggesting the contributors to the MYB gene family expansion. Functional characterization was performed to identify 56 SsR2R3-MYB genes involved in various plant bioprocesses with expression profiling analysis on 60 RNA-seq databases. We identified 22 MYB genes specifically expressed in the stem, of which MYB43, MYB53, MYB65, MYB78, and MYB99 were validated by qPCR. Allelic expression dominance in the stem was more significant than that in the leaf, implying the differential expression of alleles may be responsible for the high expression of MYB in the stem. MYB169, MYB181, MYB192 were identified as candidate C4 photosynthetic regulators by C4 expression pattern and robust circadian oscillations. Furthermore, stress expression analysis showed that MYB36, MYB48, MYB54, MYB61 actively responded to drought treatment; 19 and 10 MYB genes were involved in response to the sugarcane pokkah boeng and mosaic disease, respectively. Conclusions: A Genome-wide expression analysis demonstrated that SsMYB genes were involved in stem development and stress response. This study largely contributed to understanding the extent to which MYB transcription factors investigate regulatory mechanisms and functional divergence in sugarcane.

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