Genome-Wide Identification, Characterization, and Expression Pattern of <i>MYB</i> Gene Family in <i>Melastoma candidum</i>
The <i>MYB</i> gene family is significant in plants, playing a role in numerous plant development processes, including metabolism, hormone signal transduction, cell identity, and biotic and abiotic stresses. Due to the recent availability of the <i>Melastoma candidum</i> geno...
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| Format: | Article |
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MDPI AG
2023-06-01
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| Series: | Horticulturae |
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| Online Access: | https://www.mdpi.com/2311-7524/9/6/708 |
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| author | Hui Li Xiaoxia Wen Mingke Wei Xiong Huang Seping Dai Lin Ruan Yixun Yu |
| author_facet | Hui Li Xiaoxia Wen Mingke Wei Xiong Huang Seping Dai Lin Ruan Yixun Yu |
| author_sort | Hui Li |
| collection | DOAJ |
| description | The <i>MYB</i> gene family is significant in plants, playing a role in numerous plant development processes, including metabolism, hormone signal transduction, cell identity, and biotic and abiotic stresses. Due to the recent availability of the <i>Melastoma candidum</i> genome, this is the first time that the <i>MYB</i> gene family has been identified in this species. This study identified 421 <i>MYB</i> gene members in the <i>M. candidum</i> genome using the HMMER search and BLASTp method. These <i>MYBs</i> were further divided into 10 sub-types, including R2R3, R-R, CPC-like, CCA1-like, TBP-like, R1R2R3, I-box, atypical MYB, MYB-CC, and MYB-like. Domain and conservation analyses revealed that each type of MYB was characterized by a different number and combination of SANTs/myb DNA-binding domains. Collinearity analysis revealed several gene duplication events within the <i>MYB</i> gene family. The Ka to Ks ratio suggested that most of the <i>MYB</i> genes underwent purifying selection during the evolution process. Phylogenetic analysis among three species confirmed our findings and displayed the evolutionary relationship of <i>MYB</i> genes in different species. RNA-seq of three developmental stages of flowers and WGCNA analysis identified <i>McMYB113h</i>, <i>McMYB21b</i>, and <i>McGLK1c</i> as playing a pivotal role during flower development in <i>M. candidum</i>. Finally, we conducted qRT-PCR experiments for 20 flower-development-related <i>MYBs</i> across 9 tissues to illustrate their expression patterns in <i>M. candidum</i>. This study establishes a foundation for exploring <i>MYB</i> gene resources and their potential applications in related industries of <i>M. candidum</i>. |
| first_indexed | 2024-03-11T02:23:08Z |
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| id | doaj.art-0dc30b7e552648108a57668d9d6dfc1a |
| institution | Directory Open Access Journal |
| issn | 2311-7524 |
| language | English |
| last_indexed | 2024-03-11T02:23:08Z |
| publishDate | 2023-06-01 |
| publisher | MDPI AG |
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| series | Horticulturae |
| spelling | doaj.art-0dc30b7e552648108a57668d9d6dfc1a2023-11-18T10:41:31ZengMDPI AGHorticulturae2311-75242023-06-019670810.3390/horticulturae9060708Genome-Wide Identification, Characterization, and Expression Pattern of <i>MYB</i> Gene Family in <i>Melastoma candidum</i>Hui Li0Xiaoxia Wen1Mingke Wei2Xiong Huang3Seping Dai4Lin Ruan5Yixun Yu6College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, ChinaFaculty of Electronic Information Engineering, Guangdong Baiyun University, Guangzhou 510450, ChinaState Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, ChinaCollege of Forestry, Sichuan Agricultural University, Chengdu 611130, ChinaGuangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, ChinaGuangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, ChinaCollege of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, ChinaThe <i>MYB</i> gene family is significant in plants, playing a role in numerous plant development processes, including metabolism, hormone signal transduction, cell identity, and biotic and abiotic stresses. Due to the recent availability of the <i>Melastoma candidum</i> genome, this is the first time that the <i>MYB</i> gene family has been identified in this species. This study identified 421 <i>MYB</i> gene members in the <i>M. candidum</i> genome using the HMMER search and BLASTp method. These <i>MYBs</i> were further divided into 10 sub-types, including R2R3, R-R, CPC-like, CCA1-like, TBP-like, R1R2R3, I-box, atypical MYB, MYB-CC, and MYB-like. Domain and conservation analyses revealed that each type of MYB was characterized by a different number and combination of SANTs/myb DNA-binding domains. Collinearity analysis revealed several gene duplication events within the <i>MYB</i> gene family. The Ka to Ks ratio suggested that most of the <i>MYB</i> genes underwent purifying selection during the evolution process. Phylogenetic analysis among three species confirmed our findings and displayed the evolutionary relationship of <i>MYB</i> genes in different species. RNA-seq of three developmental stages of flowers and WGCNA analysis identified <i>McMYB113h</i>, <i>McMYB21b</i>, and <i>McGLK1c</i> as playing a pivotal role during flower development in <i>M. candidum</i>. Finally, we conducted qRT-PCR experiments for 20 flower-development-related <i>MYBs</i> across 9 tissues to illustrate their expression patterns in <i>M. candidum</i>. This study establishes a foundation for exploring <i>MYB</i> gene resources and their potential applications in related industries of <i>M. candidum</i>.https://www.mdpi.com/2311-7524/9/6/708<i>MYB</i> gene familyphylogenetic analysiscollinearity analysisGO and KEGG analysisRNA-seq<i>Melastoma candidum</i> |
| spellingShingle | Hui Li Xiaoxia Wen Mingke Wei Xiong Huang Seping Dai Lin Ruan Yixun Yu Genome-Wide Identification, Characterization, and Expression Pattern of <i>MYB</i> Gene Family in <i>Melastoma candidum</i> Horticulturae <i>MYB</i> gene family phylogenetic analysis collinearity analysis GO and KEGG analysis RNA-seq <i>Melastoma candidum</i> |
| title | Genome-Wide Identification, Characterization, and Expression Pattern of <i>MYB</i> Gene Family in <i>Melastoma candidum</i> |
| title_full | Genome-Wide Identification, Characterization, and Expression Pattern of <i>MYB</i> Gene Family in <i>Melastoma candidum</i> |
| title_fullStr | Genome-Wide Identification, Characterization, and Expression Pattern of <i>MYB</i> Gene Family in <i>Melastoma candidum</i> |
| title_full_unstemmed | Genome-Wide Identification, Characterization, and Expression Pattern of <i>MYB</i> Gene Family in <i>Melastoma candidum</i> |
| title_short | Genome-Wide Identification, Characterization, and Expression Pattern of <i>MYB</i> Gene Family in <i>Melastoma candidum</i> |
| title_sort | genome wide identification characterization and expression pattern of i myb i gene family in i melastoma candidum i |
| topic | <i>MYB</i> gene family phylogenetic analysis collinearity analysis GO and KEGG analysis RNA-seq <i>Melastoma candidum</i> |
| url | https://www.mdpi.com/2311-7524/9/6/708 |
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