Genome-Wide Identification and Analysis of the <i>MYB</i> Transcription Factor Gene Family in Chili Pepper (<i>Capsicum</i> spp.)
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 (<i>Capsicum</i> spp.). In the present study, we performed genome-wide analyses of the MYB family in <i...
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| Format: | Article |
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MDPI AG
2021-02-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/22/5/2229 |
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| author | Magda L. Arce-Rodríguez Octavio Martínez Neftalí Ochoa-Alejo |
| author_facet | Magda L. Arce-Rodríguez Octavio Martínez Neftalí Ochoa-Alejo |
| author_sort | Magda L. Arce-Rodríguez |
| collection | DOAJ |
| description | 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 (<i>Capsicum</i> spp.). In the present study, we performed genome-wide analyses of the MYB family in <i>Capsicum annuum</i>, 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 <i>C. annuum</i>, 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 <i>CaMYB</i> genes were differentially expressed, suggesting that they are functionally divergent. Furthermore, the integration of our data allowed us to propose strong <i>CaMYBs</i> 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 <i>CaMYB</i> genes in various processes in the <i>Capsicum</i> genus. |
| first_indexed | 2024-03-09T00:35:20Z |
| format | Article |
| id | doaj.art-4911887774444396a7619f699a997408 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T00:35:20Z |
| publishDate | 2021-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-4911887774444396a7619f699a9974082023-12-11T18:12:04ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-02-01225222910.3390/ijms22052229Genome-Wide Identification and Analysis of the <i>MYB</i> Transcription Factor Gene Family in Chili Pepper (<i>Capsicum</i> spp.)Magda L. Arce-Rodríguez0Octavio Martínez1Neftalí Ochoa-Alejo2Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto, Politécnico Nacional, 36824 Irapuato, Guanajuato, MexicoUnidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), 36824 Irapuato, Guanajuato, MexicoDepartamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto, Politécnico Nacional, 36824 Irapuato, Guanajuato, MexicoThe 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 (<i>Capsicum</i> spp.). In the present study, we performed genome-wide analyses of the MYB family in <i>Capsicum annuum</i>, 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 <i>C. annuum</i>, 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 <i>CaMYB</i> genes were differentially expressed, suggesting that they are functionally divergent. Furthermore, the integration of our data allowed us to propose strong <i>CaMYBs</i> 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 <i>CaMYB</i> genes in various processes in the <i>Capsicum</i> genus.https://www.mdpi.com/1422-0067/22/5/2229<i>Capsicum</i>chili pepperMYB transcription factorexpression profilessecondary metabolismcapsaicinoids |
| spellingShingle | Magda L. Arce-Rodríguez Octavio Martínez Neftalí Ochoa-Alejo Genome-Wide Identification and Analysis of the <i>MYB</i> Transcription Factor Gene Family in Chili Pepper (<i>Capsicum</i> spp.) International Journal of Molecular Sciences <i>Capsicum</i> chili pepper MYB transcription factor expression profiles secondary metabolism capsaicinoids |
| title | Genome-Wide Identification and Analysis of the <i>MYB</i> Transcription Factor Gene Family in Chili Pepper (<i>Capsicum</i> spp.) |
| title_full | Genome-Wide Identification and Analysis of the <i>MYB</i> Transcription Factor Gene Family in Chili Pepper (<i>Capsicum</i> spp.) |
| title_fullStr | Genome-Wide Identification and Analysis of the <i>MYB</i> Transcription Factor Gene Family in Chili Pepper (<i>Capsicum</i> spp.) |
| title_full_unstemmed | Genome-Wide Identification and Analysis of the <i>MYB</i> Transcription Factor Gene Family in Chili Pepper (<i>Capsicum</i> spp.) |
| title_short | Genome-Wide Identification and Analysis of the <i>MYB</i> Transcription Factor Gene Family in Chili Pepper (<i>Capsicum</i> spp.) |
| title_sort | genome wide identification and analysis of the i myb i transcription factor gene family in chili pepper i capsicum i spp |
| topic | <i>Capsicum</i> chili pepper MYB transcription factor expression profiles secondary metabolism capsaicinoids |
| url | https://www.mdpi.com/1422-0067/22/5/2229 |
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