Comprehensive analysis of the MYB transcription factor gene family in Morus alba
Abstract Background The V-myb myeloblastosis viral oncogene homolog (MYB) family of proteins is large, containing functionally diverse transcription factors. However, MYBs in Morus are still poorly annotated and a comprehensive functional analysis of these transcription factors is lacking. Results I...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-06-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-022-03626-5 |
| _version_ | 1811258092365545472 |
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| author | Li Liu Nan Chao Keermula Yidilisi Xiaoru Kang Xu Cao |
| author_facet | Li Liu Nan Chao Keermula Yidilisi Xiaoru Kang Xu Cao |
| author_sort | Li Liu |
| collection | DOAJ |
| description | Abstract Background The V-myb myeloblastosis viral oncogene homolog (MYB) family of proteins is large, containing functionally diverse transcription factors. However, MYBs in Morus are still poorly annotated and a comprehensive functional analysis of these transcription factors is lacking. Results In the present study, a genome-wide identification of MYBs in Morus alba was performed. In total 166 MaMYBs were identified, including 103 R2R3-MYBs and four 3R-MaMYBs. Comprehensive analyses, including the phylogenetic analysis with putative functional annotation, motif and structure analysis, gene structure organization, promoter analysis, chromosomal localization, and syntenic relationships of R2R3-MaMYBs and 3R-MaMYBs, provided primary characterization for these MaMYBs. R2R3-MaMYBs covered the subgroups reported for R2R3-MYBs in Arabidopsis and Populus, and had two Morus-specific subgroups, indicating the high retention of MYBs in Morus. Motif analysis revealed high conservative residues at the start and end of each helix and residues consisting of the third helix in R2 and R3 repeats. Thirteen intron/exon patterns (a–m) were summarized, and the intron/exon pattern of two introns with phase numbers of 0 and 2 was the prevalent pattern for R2R3-MaMYBs. Various cis-elements in promoter regions were identified, and were mainly related to light response, development, phytohormone response, and abiotic and biotic stress response and secondary metabolite production. Expression patterns of R2R3-MaMYBs in different organs showed that MaMYBs involved in secondary cell wall components and stress responsiveness were preferentially expressed in roots or stems. R2R3-MaMYBs involved in flavonoid biosynthesis and anthocyanin accumulation were identified and characterized based on functional annotation and correlation of their expression levels with anthocyanin contents. Conclusion Based on a comprehensive analysis, this work provided functional annotation for R2R3-MYBs and an informative reference for further functional dissection of MYBs in Morus. |
| first_indexed | 2024-04-12T18:07:51Z |
| format | Article |
| id | doaj.art-1db0bcdc116b4548a88eb796ecf5e3fa |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-04-12T18:07:51Z |
| publishDate | 2022-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-1db0bcdc116b4548a88eb796ecf5e3fa2022-12-22T03:21:55ZengBMCBMC Plant Biology1471-22292022-06-0122111710.1186/s12870-022-03626-5Comprehensive analysis of the MYB transcription factor gene family in Morus albaLi Liu0Nan Chao1Keermula Yidilisi2Xiaoru Kang3Xu Cao4Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and TechnologyJiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and TechnologyJiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and TechnologyJiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and TechnologyJiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and TechnologyAbstract Background The V-myb myeloblastosis viral oncogene homolog (MYB) family of proteins is large, containing functionally diverse transcription factors. However, MYBs in Morus are still poorly annotated and a comprehensive functional analysis of these transcription factors is lacking. Results In the present study, a genome-wide identification of MYBs in Morus alba was performed. In total 166 MaMYBs were identified, including 103 R2R3-MYBs and four 3R-MaMYBs. Comprehensive analyses, including the phylogenetic analysis with putative functional annotation, motif and structure analysis, gene structure organization, promoter analysis, chromosomal localization, and syntenic relationships of R2R3-MaMYBs and 3R-MaMYBs, provided primary characterization for these MaMYBs. R2R3-MaMYBs covered the subgroups reported for R2R3-MYBs in Arabidopsis and Populus, and had two Morus-specific subgroups, indicating the high retention of MYBs in Morus. Motif analysis revealed high conservative residues at the start and end of each helix and residues consisting of the third helix in R2 and R3 repeats. Thirteen intron/exon patterns (a–m) were summarized, and the intron/exon pattern of two introns with phase numbers of 0 and 2 was the prevalent pattern for R2R3-MaMYBs. Various cis-elements in promoter regions were identified, and were mainly related to light response, development, phytohormone response, and abiotic and biotic stress response and secondary metabolite production. Expression patterns of R2R3-MaMYBs in different organs showed that MaMYBs involved in secondary cell wall components and stress responsiveness were preferentially expressed in roots or stems. R2R3-MaMYBs involved in flavonoid biosynthesis and anthocyanin accumulation were identified and characterized based on functional annotation and correlation of their expression levels with anthocyanin contents. Conclusion Based on a comprehensive analysis, this work provided functional annotation for R2R3-MYBs and an informative reference for further functional dissection of MYBs in Morus.https://doi.org/10.1186/s12870-022-03626-5AnthocyaninFruit ripeningFunctional annotationMorus albaMYBPhenylpropanoid |
| spellingShingle | Li Liu Nan Chao Keermula Yidilisi Xiaoru Kang Xu Cao Comprehensive analysis of the MYB transcription factor gene family in Morus alba BMC Plant Biology Anthocyanin Fruit ripening Functional annotation Morus alba MYB Phenylpropanoid |
| title | Comprehensive analysis of the MYB transcription factor gene family in Morus alba |
| title_full | Comprehensive analysis of the MYB transcription factor gene family in Morus alba |
| title_fullStr | Comprehensive analysis of the MYB transcription factor gene family in Morus alba |
| title_full_unstemmed | Comprehensive analysis of the MYB transcription factor gene family in Morus alba |
| title_short | Comprehensive analysis of the MYB transcription factor gene family in Morus alba |
| title_sort | comprehensive analysis of the myb transcription factor gene family in morus alba |
| topic | Anthocyanin Fruit ripening Functional annotation Morus alba MYB Phenylpropanoid |
| url | https://doi.org/10.1186/s12870-022-03626-5 |
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