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 

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 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.

scholarly journals MYB Gene Family in Potato (Solanum tuberosum L.): Genome-Wide Identification of Hormone-Responsive Reveals Their Potential Functions in Growth and Development

2019 ◽  
Vol 20 (19) ◽  
pp. 4847 ◽  
Author(s):  
Wenjun Sun ◽  
Zhaotang Ma ◽  
Hui Chen ◽  
Moyang Liu
Keyword(s):  
Solanum Tuberosum ◽  
Gene Family ◽  
Stress Responses ◽  
Growth And Development ◽  
Solanum Tuberosum L ◽  
Potential Functions ◽  
Anthocyanin Synthesis ◽  
Myb Gene ◽  
Genome Wide ◽  
R2r3 Myb

As an important nongrain crop, the growth and yield of potato (Solanum tuberosum L.) is often affected by an unfavorable external environment in the process of cultivation. The MYB family is one of the largest and most important gene families, participating in the regulation of plant growth and development and response to abiotic stresses. Several MYB genes in potato that regulate anthocyanin synthesis and participate in abiotic stress responses have been identified. To identify all Solanum tuberosum L. MYB (StMYB) genes involved in hormone or stress responses to potentially regulate potato growth and development, we identified the MYB gene family at the genome-wide level. In this work, 158 StMYB genes were found in the potato genome. According to the amino acid sequence of the MYB domain and gene structure, the StMYB genes were divided into R2R3-MYB and R1R2R3-MYB families, and the R2R3-MYB family was divided into 20 subgroups (SGs). The expression of 21 StMYB genes from different SGs in roots, stems, leaves, flowers, shoots, stolons, young tubers, and mature tubers was determined by quantitative real-time polymerase chain reaction (qRT-PCR). The expression patterns of StMYB genes in potatoes treated with abscisic acid (ABA), indole-3-acetic acid (IAA), gibberellin acid 3 (GA3), NaCl, mannitol, and heat were also measured. We have identified several potential candidate genes that regulate the synthesis of potato flavonoids or participate in hormone or stress responses. This work provides a comprehensive understanding of the MYB family in potato and will lay a foundation for the future investigation of the potential functions of StMYB genes in the growth and development of potato.

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 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 Maize R2R3 Myb Genes: Sequence Analysis Reveals Amplification in the Higher Plants

Genetics ◽  
1999 ◽  
Vol 153 (1) ◽  
pp. 427-444 ◽  
Author(s):  
Pablo D Rabinowicz ◽  
Edward L Braun ◽  
Andrea D Wolfe ◽  
Ben Bowen ◽  
Erich Grotewold
Keyword(s):  
Gene Family ◽  
Higher Plants ◽  
Land Plants ◽  
Rt Pcr ◽  
Cellular Functions ◽  
Myb Gene ◽  
History Of ◽  
Myb Genes ◽  
R2r3 Myb ◽  
Recent Duplication

Abstract Transcription factors containing the Myb-homologous DNA-binding domain are widely found in eukaryotes. In plants, R2R3 Myb-domain proteins are involved in the control of form and metabolism. The Arabidopsis genome harbors >100 R2R3 Myb genes, but few have been found in monocots, animals, and fungi. Using RT-PCR from different maize organs, we cloned 480 fragments corresponding to a 42–44 residue-long sequence spanning the region between the conserved DNA-recognition helices (MybBRH) of R2R3 Myb domains. We determined that maize expresses >80 different R2R3 Myb genes, and evolutionary distances among maize MybBRH sequences indicate that most of the amplification of the R2R3 Myb gene family occurred after the origin of land plants but prior to the separation of monocots and dicots. In addition, evidence is provided for the very recent duplication of particular classes of R2R3 Myb genes in the grasses. Together, these findings render a novel line of evidence for the amplification of the R2R3 Myb gene family in the early history of land plants and suggest that maize provides a possible model system to examine the hypothesis that the expansion of Myb genes is associated with the regulation of novel plant cellular functions.

scholarly journals The R2R3-MYB gene family in banana (Musa acuminata): Genome-wide identification, classification and expression patterns

PLoS ONE ◽  
2020 ◽  
Vol 15 (10) ◽  
pp. e0239275
Author(s):  
Boas Pucker ◽  
Ashutosh Pandey ◽  
Bernd Weisshaar ◽  
Ralf Stracke
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Musa Acuminata ◽  
Myb Gene ◽  
Genome Wide ◽  
R2r3 Myb

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.

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