Genome-wide analysis of the basic Helix-Loop-Helix (bHLH) transcription factor family in maize
Abstract Background In plants, the basic helix-loop-helix (bHLH) transcription factors play key roles in diverse biological processes. Genome-wide comprehensive and systematic analyses of bHLH proteins have been well conducted in Arabidopsis, rice, tomato and other plant species. However, only few o...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2018-10-01
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| Series: | BMC Plant Biology |
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| Online Access: | http://link.springer.com/article/10.1186/s12870-018-1441-z |
| _version_ | 1818948927486951424 |
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| author | Tingting Zhang Wei Lv Haisen Zhang Lin Ma Pinghua Li Lei Ge Gang Li |
| author_facet | Tingting Zhang Wei Lv Haisen Zhang Lin Ma Pinghua Li Lei Ge Gang Li |
| author_sort | Tingting Zhang |
| collection | DOAJ |
| description | Abstract Background In plants, the basic helix-loop-helix (bHLH) transcription factors play key roles in diverse biological processes. Genome-wide comprehensive and systematic analyses of bHLH proteins have been well conducted in Arabidopsis, rice, tomato and other plant species. However, only few of bHLH family genes have been functional characterized in maize. Results In this study, our genome-wide analysis identified 208 putative bHLH family proteins (ZmbHLH proteins) in maize (Zea mays). We classified these proteins into 18 subfamilies by comparing the ZmbHLHs with Arabidopsis thaliana bHLH proteins. Phylogenetic analysis, conserved protein motifs, and exon-intron patterns further supported the evolutionary relationships among these bHLH proteins. Genome distribution analysis found that the 208 ZmbHLH loci were located non-randomly on the ten maize chromosomes. Further, analysis of conserved cis-elements in the promoter regions, protein interaction networks, and expression patterns in roots, leaves, and seeds across developmental stages, suggested that bHLH family proteins in maize are probably involved in multiple physiological processes in plant growth and development. Conclusion We performed a genome-wide, systematic analysis of bHLH proteins in maize. This comprehensive analysis provides a useful resource that enables further investigation of the physiological roles and molecular functions of the ZmbHLH transcription factors. |
| first_indexed | 2024-12-20T08:54:34Z |
| format | Article |
| id | doaj.art-ecaa6d0f75d74483b3074f4b4f7bc9be |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-20T08:54:34Z |
| publishDate | 2018-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-ecaa6d0f75d74483b3074f4b4f7bc9be2022-12-21T19:46:02ZengBMCBMC Plant Biology1471-22292018-10-0118111410.1186/s12870-018-1441-zGenome-wide analysis of the basic Helix-Loop-Helix (bHLH) transcription factor family in maizeTingting Zhang0Wei Lv1Haisen Zhang2Lin Ma3Pinghua Li4Lei Ge5Gang Li6State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural UniversityState Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural UniversityState Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural UniversityState Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural UniversityState Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural UniversityState Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural UniversityState Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural UniversityAbstract Background In plants, the basic helix-loop-helix (bHLH) transcription factors play key roles in diverse biological processes. Genome-wide comprehensive and systematic analyses of bHLH proteins have been well conducted in Arabidopsis, rice, tomato and other plant species. However, only few of bHLH family genes have been functional characterized in maize. Results In this study, our genome-wide analysis identified 208 putative bHLH family proteins (ZmbHLH proteins) in maize (Zea mays). We classified these proteins into 18 subfamilies by comparing the ZmbHLHs with Arabidopsis thaliana bHLH proteins. Phylogenetic analysis, conserved protein motifs, and exon-intron patterns further supported the evolutionary relationships among these bHLH proteins. Genome distribution analysis found that the 208 ZmbHLH loci were located non-randomly on the ten maize chromosomes. Further, analysis of conserved cis-elements in the promoter regions, protein interaction networks, and expression patterns in roots, leaves, and seeds across developmental stages, suggested that bHLH family proteins in maize are probably involved in multiple physiological processes in plant growth and development. Conclusion We performed a genome-wide, systematic analysis of bHLH proteins in maize. This comprehensive analysis provides a useful resource that enables further investigation of the physiological roles and molecular functions of the ZmbHLH transcription factors.http://link.springer.com/article/10.1186/s12870-018-1441-zMaizeGenome-wide analysisBasic helix-loop-helix transcription factorsExpression analysisDevelopment |
| spellingShingle | Tingting Zhang Wei Lv Haisen Zhang Lin Ma Pinghua Li Lei Ge Gang Li Genome-wide analysis of the basic Helix-Loop-Helix (bHLH) transcription factor family in maize BMC Plant Biology Maize Genome-wide analysis Basic helix-loop-helix transcription factors Expression analysis Development |
| title | Genome-wide analysis of the basic Helix-Loop-Helix (bHLH) transcription factor family in maize |
| title_full | Genome-wide analysis of the basic Helix-Loop-Helix (bHLH) transcription factor family in maize |
| title_fullStr | Genome-wide analysis of the basic Helix-Loop-Helix (bHLH) transcription factor family in maize |
| title_full_unstemmed | Genome-wide analysis of the basic Helix-Loop-Helix (bHLH) transcription factor family in maize |
| title_short | Genome-wide analysis of the basic Helix-Loop-Helix (bHLH) transcription factor family in maize |
| title_sort | genome wide analysis of the basic helix loop helix bhlh transcription factor family in maize |
| topic | Maize Genome-wide analysis Basic helix-loop-helix transcription factors Expression analysis Development |
| url | http://link.springer.com/article/10.1186/s12870-018-1441-z |
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