Characterization of the basic helix–loop–helix gene family and its tissue-differential expression in response to salt stress in poplar
The basic helix–loop–helix (bHLH) transcription factor gene family is one of the largest gene families and extensively involved in plant growth, development, and stress responses. However, limited studies are available on the gene family in poplar. In this study, we focused on 202 bHLH genes, explor...
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| Format: | Article |
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PeerJ Inc.
2018-03-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/4502.pdf |
| _version_ | 1827605495258546176 |
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| author | Kai Zhao Shuxuan Li Wenjing Yao Boru Zhou Renhua Li Tingbo Jiang |
| author_facet | Kai Zhao Shuxuan Li Wenjing Yao Boru Zhou Renhua Li Tingbo Jiang |
| author_sort | Kai Zhao |
| collection | DOAJ |
| description | The basic helix–loop–helix (bHLH) transcription factor gene family is one of the largest gene families and extensively involved in plant growth, development, and stress responses. However, limited studies are available on the gene family in poplar. In this study, we focused on 202 bHLH genes, exploring their DNA and protein sequences and physicochemical properties. According to their protein sequence similarities, we classified the genes into 25 groups with specific motif structures. In order to explore their expressions, we performed gene expression profiling using RNA-Seq and identified 19 genes that display tissue-differential expression patterns without treatment. Furthermore, we also performed gene expression profiling under salt stress. We found 74 differentially expressed genes (DEGs), which are responsive to the treatment. A total of 18 of the 19 genes correspond well to the DEGs. We validated the results using reverse transcription quantitative real-time PCR. This study lays the foundation for future studies on gene cloning, transgenes, and biological mechanisms. |
| first_indexed | 2024-03-09T06:22:34Z |
| format | Article |
| id | doaj.art-2ba621e3da4c4a87aac9c240d2c5c0b1 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:22:34Z |
| publishDate | 2018-03-01 |
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| spelling | doaj.art-2ba621e3da4c4a87aac9c240d2c5c0b12023-12-03T11:33:55ZengPeerJ Inc.PeerJ2167-83592018-03-016e450210.7717/peerj.4502Characterization of the basic helix–loop–helix gene family and its tissue-differential expression in response to salt stress in poplarKai Zhao0Shuxuan Li1Wenjing Yao2Boru Zhou3Renhua Li4Tingbo Jiang5State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, ChinaState Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, ChinaState Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, ChinaState Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, ChinaState Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, ChinaState Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, ChinaThe basic helix–loop–helix (bHLH) transcription factor gene family is one of the largest gene families and extensively involved in plant growth, development, and stress responses. However, limited studies are available on the gene family in poplar. In this study, we focused on 202 bHLH genes, exploring their DNA and protein sequences and physicochemical properties. According to their protein sequence similarities, we classified the genes into 25 groups with specific motif structures. In order to explore their expressions, we performed gene expression profiling using RNA-Seq and identified 19 genes that display tissue-differential expression patterns without treatment. Furthermore, we also performed gene expression profiling under salt stress. We found 74 differentially expressed genes (DEGs), which are responsive to the treatment. A total of 18 of the 19 genes correspond well to the DEGs. We validated the results using reverse transcription quantitative real-time PCR. This study lays the foundation for future studies on gene cloning, transgenes, and biological mechanisms.https://peerj.com/articles/4502.pdfGene and protein structureSalt stressPoplar bHLH gene familyTissue-differential expression |
| spellingShingle | Kai Zhao Shuxuan Li Wenjing Yao Boru Zhou Renhua Li Tingbo Jiang Characterization of the basic helix–loop–helix gene family and its tissue-differential expression in response to salt stress in poplar PeerJ Gene and protein structure Salt stress Poplar bHLH gene family Tissue-differential expression |
| title | Characterization of the basic helix–loop–helix gene family and its tissue-differential expression in response to salt stress in poplar |
| title_full | Characterization of the basic helix–loop–helix gene family and its tissue-differential expression in response to salt stress in poplar |
| title_fullStr | Characterization of the basic helix–loop–helix gene family and its tissue-differential expression in response to salt stress in poplar |
| title_full_unstemmed | Characterization of the basic helix–loop–helix gene family and its tissue-differential expression in response to salt stress in poplar |
| title_short | Characterization of the basic helix–loop–helix gene family and its tissue-differential expression in response to salt stress in poplar |
| title_sort | characterization of the basic helix loop helix gene family and its tissue differential expression in response to salt stress in poplar |
| topic | Gene and protein structure Salt stress Poplar bHLH gene family Tissue-differential expression |
| url | https://peerj.com/articles/4502.pdf |
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