Genome-wide identification of bHLH transcription factors and their response to salt stress in Cyclocarya paliurus
As a highly valued and multiple function tree species, the leaves of Cyclocarya paliurus are enriched in diverse bioactive substances with healthy function. To meet the requirement for its leaf production and medical use, the land with salt stress would be a potential resource for developing C. pali...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-03-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1117246/full |
| _version_ | 1811155613241049088 |
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| author | Zijie Zhang Jie Fang Lei Zhang Lei Zhang Huiyin Jin Shengzuo Fang Shengzuo Fang |
| author_facet | Zijie Zhang Jie Fang Lei Zhang Lei Zhang Huiyin Jin Shengzuo Fang Shengzuo Fang |
| author_sort | Zijie Zhang |
| collection | DOAJ |
| description | As a highly valued and multiple function tree species, the leaves of Cyclocarya paliurus are enriched in diverse bioactive substances with healthy function. To meet the requirement for its leaf production and medical use, the land with salt stress would be a potential resource for developing C. paliurus plantations due to the limitation of land resources in China. The basic helix-loop-helix (bHLH) transcription factor protein family, the second largest protein family in plants, has been found to play essential roles in the response to multiple abiotic stresses, especially salt stress. However, the bHLH gene family in C.paliurus has not been investigated. In this study, 159 CpbHLH genes were successfully identified from the whole-genome sequence data, and were classified into 26 subfamilies. Meanwhile, the 159 members were also analyzed from the aspects of protein sequences alignment, evolution, motif prediction, promoter cis-acting elements analysis and DNA binding ability. Based on transcriptome profiling under a hydroponic experiment with four salt concentrations (0%, 0.15%, 0.3%, and 0.45% NaCl), 9 significantly up- or down-regulated genes were screened, while 3 genes associated with salt response were selected in term of the GO annotation results. Totally 12 candidate genes were selected in response to salt stress. Moreover, based on expression analysis of the 12 candidate genes sampled from a pot experiment with three salt concentrations (0%, 0.2% and 0.4% NaCl), CpbHLH36/68/146 were further verified to be involved in the regulation of salt tolerance genes, which is also confirmed by protein interaction network analysis. This study was the first analysis of the transcription factor family at the genome-wide level of C. paliurus, and our findings would not only provide insight into the function of the CpbHLH gene family members involved in salt stress but also drive progress in genetic improvement for the salt tolerance of C. paliurus. |
| first_indexed | 2024-04-10T04:37:23Z |
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| id | doaj.art-6099dc64c2854f4481d21df7b961e58e |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-10T04:37:23Z |
| publishDate | 2023-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-6099dc64c2854f4481d21df7b961e58e2023-03-09T14:35:21ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-03-011410.3389/fpls.2023.11172461117246Genome-wide identification of bHLH transcription factors and their response to salt stress in Cyclocarya paliurusZijie Zhang0Jie Fang1Lei Zhang2Lei Zhang3Huiyin Jin4Shengzuo Fang5Shengzuo Fang6College of Forestry, Nanjing Forestry University, Nanjing, ChinaCollege of Forestry, Nanjing Forestry University, Nanjing, ChinaCollege of Forestry, Nanjing Forestry University, Nanjing, ChinaCo-Innovation Center for Sustainable Forestry in Southern China, Nanjing, ChinaCollege of Forestry, Nanjing Forestry University, Nanjing, ChinaCollege of Forestry, Nanjing Forestry University, Nanjing, ChinaCo-Innovation Center for Sustainable Forestry in Southern China, Nanjing, ChinaAs a highly valued and multiple function tree species, the leaves of Cyclocarya paliurus are enriched in diverse bioactive substances with healthy function. To meet the requirement for its leaf production and medical use, the land with salt stress would be a potential resource for developing C. paliurus plantations due to the limitation of land resources in China. The basic helix-loop-helix (bHLH) transcription factor protein family, the second largest protein family in plants, has been found to play essential roles in the response to multiple abiotic stresses, especially salt stress. However, the bHLH gene family in C.paliurus has not been investigated. In this study, 159 CpbHLH genes were successfully identified from the whole-genome sequence data, and were classified into 26 subfamilies. Meanwhile, the 159 members were also analyzed from the aspects of protein sequences alignment, evolution, motif prediction, promoter cis-acting elements analysis and DNA binding ability. Based on transcriptome profiling under a hydroponic experiment with four salt concentrations (0%, 0.15%, 0.3%, and 0.45% NaCl), 9 significantly up- or down-regulated genes were screened, while 3 genes associated with salt response were selected in term of the GO annotation results. Totally 12 candidate genes were selected in response to salt stress. Moreover, based on expression analysis of the 12 candidate genes sampled from a pot experiment with three salt concentrations (0%, 0.2% and 0.4% NaCl), CpbHLH36/68/146 were further verified to be involved in the regulation of salt tolerance genes, which is also confirmed by protein interaction network analysis. This study was the first analysis of the transcription factor family at the genome-wide level of C. paliurus, and our findings would not only provide insight into the function of the CpbHLH gene family members involved in salt stress but also drive progress in genetic improvement for the salt tolerance of C. paliurus.https://www.frontiersin.org/articles/10.3389/fpls.2023.1117246/fullwheel wingnutbHLH family genesCpbHLH genessalt toleranceexpression analysisregulation networks |
| spellingShingle | Zijie Zhang Jie Fang Lei Zhang Lei Zhang Huiyin Jin Shengzuo Fang Shengzuo Fang Genome-wide identification of bHLH transcription factors and their response to salt stress in Cyclocarya paliurus Frontiers in Plant Science wheel wingnut bHLH family genes CpbHLH genes salt tolerance expression analysis regulation networks |
| title | Genome-wide identification of bHLH transcription factors and their response to salt stress in Cyclocarya paliurus |
| title_full | Genome-wide identification of bHLH transcription factors and their response to salt stress in Cyclocarya paliurus |
| title_fullStr | Genome-wide identification of bHLH transcription factors and their response to salt stress in Cyclocarya paliurus |
| title_full_unstemmed | Genome-wide identification of bHLH transcription factors and their response to salt stress in Cyclocarya paliurus |
| title_short | Genome-wide identification of bHLH transcription factors and their response to salt stress in Cyclocarya paliurus |
| title_sort | genome wide identification of bhlh transcription factors and their response to salt stress in cyclocarya paliurus |
| topic | wheel wingnut bHLH family genes CpbHLH genes salt tolerance expression analysis regulation networks |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1117246/full |
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