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 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 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 Identification and expression analysis under abiotic stress of the R2R3-MYB genes in Ginkgo biloba L.

2017 ◽  
Vol 23 (3) ◽  
pp. 503-516 ◽  
Author(s):  
Xinliang Liu ◽  
Wanwen Yu ◽  
Xuhui Zhang ◽  
Guibin Wang ◽  
Fuliang Cao ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Expression Analysis ◽  
Ginkgo Biloba ◽  
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.

scholarly journals Genome-wide identification and characterization of R2R3-MYB genes in Medicago truncatula

2019 ◽  
Vol 42 (3) ◽  
pp. 611-623 ◽  
Author(s):  
Wei Li ◽  
Ying Liu ◽  
Jinyue Zhao ◽  
Xin Zhen ◽  
Changhong Guo ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Genome Wide ◽  
Myb Genes ◽  
R2r3 Myb ◽  
Identification And Characterization

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 the StR2R3-MYB transcription factor superfamily in Solanum Tuberosum

2019 ◽  
Author(s):  
Yuanming Li ◽  
Kui Lin-Wang ◽  
Zhen Liu ◽  
Andrew C. Allan ◽  
Junlian Zhang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Solanum Tuberosum ◽  
Drought Stress ◽  
Anthocyanin Biosynthesis ◽  
Rna Seq ◽  
Genome Wide ◽  
Ear Motif ◽  
Myb Genes ◽  
Myb Proteins

Abstract Background: MYB transcription factors comprise one of the largest families in plant kingdom, which play a variety of functions in plant developmental processes and defence responses. However, it has not been systematically studied in Potato (Solanum tuberosum), which is the most important non-cereal crop world-wide. Results: In the present study, a total of 108 StR2R3-MYB transcription factors were identified and further phylogenetically classified into 28 subfamilies, as supported by highly conserved gene structures and motifs. Collinearity analysis showed that the segmental duplication events played a crucial role in the expansion of StR2R3-MYB gene family. Synteny analysis indicated that 37 and 13 StR2R3-MYB genes were orthologous to Arabidopsis and wheat, respectively, and these gene pairs have evolved under strong purifying selection. RNA-seq data from different tissues and abiotic stresses revealed tissue-preferential and abiotic stress-responsive StR2R3-MYB genes. We further analyzed StR2R3-MYB genes might be involved in anthocyanin biosynthesis and drought stress by using RNA-seq data of pigmented tetraploid potato cultivars and drought-sensitive and -tolerant tetraploid potato cultivars under drought stress, respectively. Moreover, EAR motifs were found in 21 StR2R3-MYB proteins and 446 pairs of proteins were predicted to interact with 21 EAR motif-containing StR2R3-MYB proteins by constructing the interaction network with medium confidence (0.4). Additionally, Gene Ontology (GO) analysis of the 21 EAR motif-containing StR2R3-MYB proteins was performed to further investigate their functions. Conclusions: In this work, we systematically identified StR2R3-MYB genes by analyzing the potato genome sequence using a set of bioinformatics approaches. Genome-wide comparative analysis of StR2R3-MYB genes and their expression analysis identified members of this superfamily may be involved in tissue-specific development, anthocyanin biosynthesis and abiotic stress responses.

scholarly journals Genome-Wide Comparative Analysis of R2R3 MYB Gene Family in Populus and Salix and Identification of Male Flower Bud Development-Related Genes

2021 ◽  
Vol 12 ◽  
Author(s):  
Fangwei Zhou ◽  
Yingnan Chen ◽  
Huaitong Wu ◽  
Tongming Yin
Keyword(s):  
Transcription Factor ◽  
Comparative Analysis ◽  
Gene Family ◽  
Pollen Development ◽  
Male Flower ◽  
Flower Bud ◽  
Myb Gene ◽  
Genome Wide ◽  
Myb Genes ◽  
R2r3 Myb

The MYB transcription factor (TF) family is one of the largest plant transcription factor gene family playing vital roles in plant growth and development, including defense, cell differentiation, secondary metabolism, and responses to biotic and abiotic stresses. As a model tree species of woody plants, in recent years, the identification and functional prediction of certain MYB family members in the poplar genome have been reported. However, to date, the characterization of the gene family in the genome of the poplar’s sister species willow has not been done, nor are the differences and similarities between the poplar and willow genomes understood. In this study, we conducted the first genome-wide investigation of the R2R3 MYB subfamily in the willow, identifying 216 R2R3 MYB gene members, and combined with the poplar R2R3 MYB genes, performed the first comparative analysis of R2R3 MYB genes between the poplar and willow. We identified 81 and 86 pairs of R2R3 MYB paralogs in the poplar and willow, respectively. There were 17 pairs of tandem repeat genes in the willow, indicating active duplication of willow R2R3 MYB genes. A further 166 pairs of poplar and willow orthologs were identified by collinear and synonymous analysis. The findings support the duplication of R2R3 MYB genes in the ancestral species, with most of the R2R3 MYB genes being retained during the evolutionary process. The phylogenetic trees of the R2R3 MYB genes of 10 different species were drawn. The functions of the poplar and willow R2R3 MYB genes were predicted using reported functional groupings and clustering by OrthoFinder. Identified 5 subgroups in general expanded in woody species, three subgroups were predicted to be related to lignin synthesis, and we further speculate that the other two subgroups also play a role in wood formation. We analyzed the expression patterns of the GAMYB gene of subgroup 18 (S18) related to pollen development in the male flower buds of poplar and willow at different developmental stages by qRT-PCR. The results showed that the GAMYB gene was specifically expressed in the male flower bud from pollen formation to maturity, and that the expression first increased and then decreased. Both the specificity of tissue expression specificity and conservation indicated that GAMYB played an important role in pollen development in both poplar and willow and was an ideal candidate gene for the analysis of male flower development-related functions of the two species.

scholarly journals Genome-wide analysis of R2R3-MYB transcription factors family in the autopolyploid Saccharum spontaneum: an exploration of dominance expression and stress response

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yuan Yuan ◽  
Xiping Yang ◽  
Mengfan Feng ◽  
Hongyan Ding ◽  
Muhammad Tahir Khan ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Gene Family ◽  
Expression Profiling ◽  
Saccharum Spontaneum ◽  
Myb Transcription Factors ◽  
Genome Wide Analysis ◽  
Myb Gene ◽  
Genome Wide ◽  
Myb Genes ◽  
R2r3 Myb

Abstract Background Sugarcane (Saccharum) is the most critical sugar crop worldwide. 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 genomic sequence 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 RT-qPCR validated MYB43, MYB53, MYB65, MYB78, and MYB99. Allelic expression dominance analysis implied the differential expression of alleles might 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 This is the first report on genome-wide analysis of the MYB gene family in sugarcane. SsMYBs probably played an essential role in stem development and the adaptation of various stress conditions. The results will provide detailed insights and rich resources to understand the functional diversity of MYB transcription factors and facilitate the breeding of essential traits in sugarcane.

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