Molecular structures and functional exploration of NDA family genes respond tolerant to alkaline stress in Gossypium hirsutum L.
Abstract Background The internal NAD(P)H dehydrogenase (NDA) gene family was a member of the NAD(P)H dehydrogenase (ND) gene family, mainly involved in the non-phosphorylated respiratory pathways in mitochondria and played crucial roles in response to abiotic stress. Methods The whole genome identif...
| Main Authors: | , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-01-01
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| Series: | Biological Research |
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| Online Access: | https://doi.org/10.1186/s40659-022-00372-8 |
| _version_ | 1798024935409451008 |
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| author | Yapeng Fan Yuexin Zhang Cun Rui Hong Zhang Nan Xu Jing Wang Mingge Han Xuke Lu Xiugui Chen Delong Wang Shuai Wang Lixue Guo Lanjie Zhao Hui Huang Junjuan Wang Liangqing Sun Chao Chen Wuwei Ye |
| author_facet | Yapeng Fan Yuexin Zhang Cun Rui Hong Zhang Nan Xu Jing Wang Mingge Han Xuke Lu Xiugui Chen Delong Wang Shuai Wang Lixue Guo Lanjie Zhao Hui Huang Junjuan Wang Liangqing Sun Chao Chen Wuwei Ye |
| author_sort | Yapeng Fan |
| collection | DOAJ |
| description | Abstract Background The internal NAD(P)H dehydrogenase (NDA) gene family was a member of the NAD(P)H dehydrogenase (ND) gene family, mainly involved in the non-phosphorylated respiratory pathways in mitochondria and played crucial roles in response to abiotic stress. Methods The whole genome identification, structure analysis and expression pattern of NDA gene family were conducted to analyze the NDA gene family. Results There were 51, 52, 26, and 24 NDA genes identified in G. hirsutum, G. barbadense, G. arboreum and G. raimondii, respectively. According to the structural characteristics of genes and traits of phylogenetic tree, we divided the NDA gene family into 8 clades. Gene structure analysis showed that the NDA gene family was relatively conservative. The four Gossypium species had good collinearity, and segmental duplication played an important role in the evolution of the NDA gene family. Analysis of cis-elements showed that most GhNDA genes contained cis-elements related to light response and plant hormones (ABA, MeJA and GA). The analysis of the expression patterns of GhNDA genes under different alkaline stress showed that GhNDA genes were actively involved in the response to alkaline stress, possibly through different molecular mechanisms. By analyzing the existing RNA-Seq data after alkaline stress, it was found that an NDA family gene GhNDA32 was expressed, and then theGhNDA32 was silenced by virus-induced gene silencing (VIGS). By observing the phenotype, we found that the wilting degree of silenced plants was much higher than that of the control plant after alkaline treatment, suggesting that GhNDA32 gene was involved in the response to alkaline stress. Conclusions In this study, GhNDAs participated in response to alkaline stress, especially NaHCO3 stress. It was of great significance for the future research on the molecular mechanism of NDA gene family in responding to abiotic stresses. |
| first_indexed | 2024-04-11T18:10:51Z |
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| id | doaj.art-646265f8483d4260a2f86eab05357a54 |
| institution | Directory Open Access Journal |
| issn | 0717-6287 |
| language | English |
| last_indexed | 2024-04-11T18:10:51Z |
| publishDate | 2022-01-01 |
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| spelling | doaj.art-646265f8483d4260a2f86eab05357a542022-12-22T04:10:07ZengBMCBiological Research0717-62872022-01-0155111910.1186/s40659-022-00372-8Molecular structures and functional exploration of NDA family genes respond tolerant to alkaline stress in Gossypium hirsutum L.Yapeng Fan0Yuexin Zhang1Cun Rui2Hong Zhang3Nan Xu4Jing Wang5Mingge Han6Xuke Lu7Xiugui Chen8Delong Wang9Shuai Wang10Lixue Guo11Lanjie Zhao12Hui Huang13Junjuan Wang14Liangqing Sun15Chao Chen16Wuwei Ye17State Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University Research Base, Zhengzhou University / Key Laboratory for Cotton Genetic Improvement, MOAState Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University Research Base, Zhengzhou University / Key Laboratory for Cotton Genetic Improvement, MOAState Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University Research Base, Zhengzhou University / Key Laboratory for Cotton Genetic Improvement, MOAState Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University Research Base, Zhengzhou University / Key Laboratory for Cotton Genetic Improvement, MOAState Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University Research Base, Zhengzhou University / Key Laboratory for Cotton Genetic Improvement, MOAState Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University Research Base, Zhengzhou University / Key Laboratory for Cotton Genetic Improvement, MOAState Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University Research Base, Zhengzhou University / Key Laboratory for Cotton Genetic Improvement, MOAState Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University Research Base, Zhengzhou University / Key Laboratory for Cotton Genetic Improvement, MOAState Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University Research Base, Zhengzhou University / Key Laboratory for Cotton Genetic Improvement, MOAState Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University Research Base, Zhengzhou University / Key Laboratory for Cotton Genetic Improvement, MOAState Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University Research Base, Zhengzhou University / Key Laboratory for Cotton Genetic Improvement, MOAState Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University Research Base, Zhengzhou University / Key Laboratory for Cotton Genetic Improvement, MOAState Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University Research Base, Zhengzhou University / Key Laboratory for Cotton Genetic Improvement, MOAState Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University Research Base, Zhengzhou University / Key Laboratory for Cotton Genetic Improvement, MOAState Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University Research Base, Zhengzhou University / Key Laboratory for Cotton Genetic Improvement, MOAState Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University Research Base, Zhengzhou University / Key Laboratory for Cotton Genetic Improvement, MOAState Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University Research Base, Zhengzhou University / Key Laboratory for Cotton Genetic Improvement, MOAState Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University Research Base, Zhengzhou University / Key Laboratory for Cotton Genetic Improvement, MOAAbstract Background The internal NAD(P)H dehydrogenase (NDA) gene family was a member of the NAD(P)H dehydrogenase (ND) gene family, mainly involved in the non-phosphorylated respiratory pathways in mitochondria and played crucial roles in response to abiotic stress. Methods The whole genome identification, structure analysis and expression pattern of NDA gene family were conducted to analyze the NDA gene family. Results There were 51, 52, 26, and 24 NDA genes identified in G. hirsutum, G. barbadense, G. arboreum and G. raimondii, respectively. According to the structural characteristics of genes and traits of phylogenetic tree, we divided the NDA gene family into 8 clades. Gene structure analysis showed that the NDA gene family was relatively conservative. The four Gossypium species had good collinearity, and segmental duplication played an important role in the evolution of the NDA gene family. Analysis of cis-elements showed that most GhNDA genes contained cis-elements related to light response and plant hormones (ABA, MeJA and GA). The analysis of the expression patterns of GhNDA genes under different alkaline stress showed that GhNDA genes were actively involved in the response to alkaline stress, possibly through different molecular mechanisms. By analyzing the existing RNA-Seq data after alkaline stress, it was found that an NDA family gene GhNDA32 was expressed, and then theGhNDA32 was silenced by virus-induced gene silencing (VIGS). By observing the phenotype, we found that the wilting degree of silenced plants was much higher than that of the control plant after alkaline treatment, suggesting that GhNDA32 gene was involved in the response to alkaline stress. Conclusions In this study, GhNDAs participated in response to alkaline stress, especially NaHCO3 stress. It was of great significance for the future research on the molecular mechanism of NDA gene family in responding to abiotic stresses.https://doi.org/10.1186/s40659-022-00372-8NDAPhylogenetic analysisCis-elementsExpression patternVIGSAlkaline stress |
| spellingShingle | Yapeng Fan Yuexin Zhang Cun Rui Hong Zhang Nan Xu Jing Wang Mingge Han Xuke Lu Xiugui Chen Delong Wang Shuai Wang Lixue Guo Lanjie Zhao Hui Huang Junjuan Wang Liangqing Sun Chao Chen Wuwei Ye Molecular structures and functional exploration of NDA family genes respond tolerant to alkaline stress in Gossypium hirsutum L. Biological Research NDA Phylogenetic analysis Cis-elements Expression pattern VIGS Alkaline stress |
| title | Molecular structures and functional exploration of NDA family genes respond tolerant to alkaline stress in Gossypium hirsutum L. |
| title_full | Molecular structures and functional exploration of NDA family genes respond tolerant to alkaline stress in Gossypium hirsutum L. |
| title_fullStr | Molecular structures and functional exploration of NDA family genes respond tolerant to alkaline stress in Gossypium hirsutum L. |
| title_full_unstemmed | Molecular structures and functional exploration of NDA family genes respond tolerant to alkaline stress in Gossypium hirsutum L. |
| title_short | Molecular structures and functional exploration of NDA family genes respond tolerant to alkaline stress in Gossypium hirsutum L. |
| title_sort | molecular structures and functional exploration of nda family genes respond tolerant to alkaline stress in gossypium hirsutum l |
| topic | NDA Phylogenetic analysis Cis-elements Expression pattern VIGS Alkaline stress |
| url | https://doi.org/10.1186/s40659-022-00372-8 |
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