In silico genome-wide identification, phylogeny and expression analysis of the R2R3-MYB gene family in Medicago truncatula
The R2R3-MYB genes make up one of the largest transcription factor families in plants, and play regulatory roles in various biological processes such as development, metabolism and defense response. Although genome-wide analyses of this gene family have been conducted in several species, R2R3-MYB ge...
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KeAi Communications Co., Ltd.
2017-07-01
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| Series: | Journal of Integrative Agriculture |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2095311916615216 |
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| author | Xing-wei ZHENG Deng-xia YI Lin-hui SHAO Cong LI |
| author_facet | Xing-wei ZHENG Deng-xia YI Lin-hui SHAO Cong LI |
| author_sort | Xing-wei ZHENG |
| collection | DOAJ |
| description | The R2R3-MYB genes make up one of the largest transcription factor families in plants, and play regulatory roles in various biological processes such as development, metabolism and defense response. Although genome-wide analyses of this gene family have been conducted in several species, R2R3-MYB genes have not been systematically analyzed in Medicago truncatula, a sequenced model legume plant. Here, we performed a comprehensive, genome-wide computational analysis of the structural characteristics, phylogeny, functions and expression patterns of M. truncatula R2R3-MYB genes. DNA binding domains are highly conserved among the 155 putative MtR2R3-MYB proteins that we identified. Chromosomal location analysis revealed that these genes were distributed across all eight chromosomes. Results showed that the expansion of the MtR2R3-MYB family was mainly attributable to segmental duplication and tandem duplication. A comprehensive classification was performed based on phylogenetic analysis of the R2R3-MYB gene families in M. truncatula, Arabidopsis thaliana and other plant species. Evolutionary relationships within clades were supported by clade-specific conserved motifs outside the MYB domain. Species-specific clades have been gained or lost during evolution, resulting in functional divergence. Also, tissue-specific expression patterns were investigated. The functions of stress response-related clades were further verified by the changes in transcript levels of representative R2R3-MYB genes upon treatment with abiotic and biotic stresses. This study is the first report on identification and characterization of R2R3-MYB gene family based on the genome of M. truncatula, and will facilitate functional analysis of this gene family in the future. |
| format | Article |
| id | doaj-art-c6b2f92f89894fe9ba93d4ef5dea7d91 |
| institution | Matheson Library |
| issn | 2095-3119 |
| language | English |
| publishDate | 2017-07-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Journal of Integrative Agriculture |
| spelling | doaj-art-c6b2f92f89894fe9ba93d4ef5dea7d912025-08-02T19:04:24ZengKeAi Communications Co., Ltd.Journal of Integrative Agriculture2095-31192017-07-0116715761591In silico genome-wide identification, phylogeny and expression analysis of the R2R3-MYB gene family in Medicago truncatulaXing-wei ZHENG0Deng-xia YI1Lin-hui SHAO2Cong LI3Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.ChinaInstitute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.ChinaInstitute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.ChinaCorrespondence LI Cong, Tel: +86-10-62815998; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.ChinaThe R2R3-MYB genes make up one of the largest transcription factor families in plants, and play regulatory roles in various biological processes such as development, metabolism and defense response. Although genome-wide analyses of this gene family have been conducted in several species, R2R3-MYB genes have not been systematically analyzed in Medicago truncatula, a sequenced model legume plant. Here, we performed a comprehensive, genome-wide computational analysis of the structural characteristics, phylogeny, functions and expression patterns of M. truncatula R2R3-MYB genes. DNA binding domains are highly conserved among the 155 putative MtR2R3-MYB proteins that we identified. Chromosomal location analysis revealed that these genes were distributed across all eight chromosomes. Results showed that the expansion of the MtR2R3-MYB family was mainly attributable to segmental duplication and tandem duplication. A comprehensive classification was performed based on phylogenetic analysis of the R2R3-MYB gene families in M. truncatula, Arabidopsis thaliana and other plant species. Evolutionary relationships within clades were supported by clade-specific conserved motifs outside the MYB domain. Species-specific clades have been gained or lost during evolution, resulting in functional divergence. Also, tissue-specific expression patterns were investigated. The functions of stress response-related clades were further verified by the changes in transcript levels of representative R2R3-MYB genes upon treatment with abiotic and biotic stresses. This study is the first report on identification and characterization of R2R3-MYB gene family based on the genome of M. truncatula, and will facilitate functional analysis of this gene family in the future.http://www.sciencedirect.com/science/article/pii/S2095311916615216R2R3-MYBMedicago truncatulagene familystress responsefunction prediction |
| spellingShingle | Xing-wei ZHENG Deng-xia YI Lin-hui SHAO Cong LI In silico genome-wide identification, phylogeny and expression analysis of the R2R3-MYB gene family in Medicago truncatula Journal of Integrative Agriculture R2R3-MYB Medicago truncatula gene family stress response function prediction |
| title | In silico genome-wide identification, phylogeny and expression analysis of the R2R3-MYB gene family in Medicago truncatula |
| title_full | In silico genome-wide identification, phylogeny and expression analysis of the R2R3-MYB gene family in Medicago truncatula |
| title_fullStr | In silico genome-wide identification, phylogeny and expression analysis of the R2R3-MYB gene family in Medicago truncatula |
| title_full_unstemmed | In silico genome-wide identification, phylogeny and expression analysis of the R2R3-MYB gene family in Medicago truncatula |
| title_short | In silico genome-wide identification, phylogeny and expression analysis of the R2R3-MYB gene family in Medicago truncatula |
| title_sort | in silico genome wide identification phylogeny and expression analysis of the r2r3 myb gene family in medicago truncatula |
| topic | R2R3-MYB Medicago truncatula gene family stress response function prediction |
| url | http://www.sciencedirect.com/science/article/pii/S2095311916615216 |
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