Comprehensive analysis of the NAC transcription factor gene family in Kandelia obovata reveals potential members related to chilling tolerance
BackgroundKandelia obovata is an important mangrove species extensively distributed in Eastern Asia that is susceptible to low-temperature stress. NAC (NAM, ATAF1/2 and CUC2) domain proteins are transcription factors (TFs) that play various roles in plant growth and development and in the plant resp...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-11-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.1048822/full |
| _version_ | 1811307440042409984 |
|---|---|
| author | Zhaokui Du Shixian You Dang Yang Yutian Tao Yunxiao Zhu Wen Sun Zhengman Chen Junmin Li |
| author_facet | Zhaokui Du Shixian You Dang Yang Yutian Tao Yunxiao Zhu Wen Sun Zhengman Chen Junmin Li |
| author_sort | Zhaokui Du |
| collection | DOAJ |
| description | BackgroundKandelia obovata is an important mangrove species extensively distributed in Eastern Asia that is susceptible to low-temperature stress. NAC (NAM, ATAF1/2 and CUC2) domain proteins are transcription factors (TFs) that play various roles in plant growth and development and in the plant response to environmental stresses. Nevertheless, genome-wide analyses of K. obovata NAC genes (KoNACs) and their responses to chilling stress have rarely been studied.MethodsThe KoNAC gene family was identified and characterized using bioinformatic analysis, the subcellular location of some NAC proteins was confirmed using confocal microscopy analysis, and the KoNACs that responded to chilling stress were screened using RNA-seq and qRT-PCR analysis.ResultsA total of 79 KoNACs were identified, and they were unequally distributed across all 18 chromosomes of K. obovata. The KoNAC proteins could be divided into 16 subgroups according to the phylogenetic tree based on NAC family members of Arabidopsis thaliana. The KoNACs exhibited greater synteny with A. thaliana sequences than with Oryza sativa sequences, indicating that KoNACs underwent extensive evolution after the divergence of dicotyledons and monocotyledons. Segmental duplication was the main driving force of the expansions of KoNAC genes. Confocal microscopy analysis verified that the four randomly selected KoNACs localized to the nucleus, indicating the accuracy of the bioinformatic predictions. Tissue expression pattern analysis demonstrated that some KoNAC genes showed tissue-specific expression, suggesting that these KoNACs might be important for plant development and growth. Additionally, the expression levels of 19 KoNACs were significantly (15 positively and 4 negatively) induced by cold treatment, demonstrating that these KoNACs might play important roles during cold stress responses and might be candidate genes for the genetic engineering of K. obovata with enhanced chilling stress tolerance. Coexpression network analysis revealed that 381 coexpressed pairs (between 13 KoNACs and 284 other genes) were significantly correlated.ConclusionsSeventy-nine KoNACs were identified in K. obovata, nineteen of which displayed chilling-induced expression patterns. These genes may serve as candidates for functional analyses of KoNACs engaged in chilling stress. Our results lay the foundation for evolutionary analyses of KoNACs and their molecular mechanisms in response to environmental stress. |
| first_indexed | 2024-04-13T09:04:26Z |
| format | Article |
| id | doaj.art-7b4566f9794246d3a503b204b39523e4 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-13T09:04:26Z |
| publishDate | 2022-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-7b4566f9794246d3a503b204b39523e42022-12-22T02:53:01ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-11-011310.3389/fpls.2022.10488221048822Comprehensive analysis of the NAC transcription factor gene family in Kandelia obovata reveals potential members related to chilling toleranceZhaokui Du0Shixian You1Dang Yang2Yutian Tao3Yunxiao Zhu4Wen Sun5Zhengman Chen6Junmin Li7Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, ChinaSection of Maritime Space and Island Management, Yuhuan Municipal Bureau of Natural Resources and Planning, Yuhuan, ChinaZhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, ChinaZhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, ChinaZhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, ChinaZhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, ChinaDepartment of Security Production Management, Taizhou Circular Economy Development Co., Ltd., Taizhou, ChinaZhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, ChinaBackgroundKandelia obovata is an important mangrove species extensively distributed in Eastern Asia that is susceptible to low-temperature stress. NAC (NAM, ATAF1/2 and CUC2) domain proteins are transcription factors (TFs) that play various roles in plant growth and development and in the plant response to environmental stresses. Nevertheless, genome-wide analyses of K. obovata NAC genes (KoNACs) and their responses to chilling stress have rarely been studied.MethodsThe KoNAC gene family was identified and characterized using bioinformatic analysis, the subcellular location of some NAC proteins was confirmed using confocal microscopy analysis, and the KoNACs that responded to chilling stress were screened using RNA-seq and qRT-PCR analysis.ResultsA total of 79 KoNACs were identified, and they were unequally distributed across all 18 chromosomes of K. obovata. The KoNAC proteins could be divided into 16 subgroups according to the phylogenetic tree based on NAC family members of Arabidopsis thaliana. The KoNACs exhibited greater synteny with A. thaliana sequences than with Oryza sativa sequences, indicating that KoNACs underwent extensive evolution after the divergence of dicotyledons and monocotyledons. Segmental duplication was the main driving force of the expansions of KoNAC genes. Confocal microscopy analysis verified that the four randomly selected KoNACs localized to the nucleus, indicating the accuracy of the bioinformatic predictions. Tissue expression pattern analysis demonstrated that some KoNAC genes showed tissue-specific expression, suggesting that these KoNACs might be important for plant development and growth. Additionally, the expression levels of 19 KoNACs were significantly (15 positively and 4 negatively) induced by cold treatment, demonstrating that these KoNACs might play important roles during cold stress responses and might be candidate genes for the genetic engineering of K. obovata with enhanced chilling stress tolerance. Coexpression network analysis revealed that 381 coexpressed pairs (between 13 KoNACs and 284 other genes) were significantly correlated.ConclusionsSeventy-nine KoNACs were identified in K. obovata, nineteen of which displayed chilling-induced expression patterns. These genes may serve as candidates for functional analyses of KoNACs engaged in chilling stress. Our results lay the foundation for evolutionary analyses of KoNACs and their molecular mechanisms in response to environmental stress.https://www.frontiersin.org/articles/10.3389/fpls.2022.1048822/fullchilling stressexpression profilesgene duplicationKandelia obovataNAC gene familyphylogenetic analysis |
| spellingShingle | Zhaokui Du Shixian You Dang Yang Yutian Tao Yunxiao Zhu Wen Sun Zhengman Chen Junmin Li Comprehensive analysis of the NAC transcription factor gene family in Kandelia obovata reveals potential members related to chilling tolerance Frontiers in Plant Science chilling stress expression profiles gene duplication Kandelia obovata NAC gene family phylogenetic analysis |
| title | Comprehensive analysis of the NAC transcription factor gene family in Kandelia obovata reveals potential members related to chilling tolerance |
| title_full | Comprehensive analysis of the NAC transcription factor gene family in Kandelia obovata reveals potential members related to chilling tolerance |
| title_fullStr | Comprehensive analysis of the NAC transcription factor gene family in Kandelia obovata reveals potential members related to chilling tolerance |
| title_full_unstemmed | Comprehensive analysis of the NAC transcription factor gene family in Kandelia obovata reveals potential members related to chilling tolerance |
| title_short | Comprehensive analysis of the NAC transcription factor gene family in Kandelia obovata reveals potential members related to chilling tolerance |
| title_sort | comprehensive analysis of the nac transcription factor gene family in kandelia obovata reveals potential members related to chilling tolerance |
| topic | chilling stress expression profiles gene duplication Kandelia obovata NAC gene family phylogenetic analysis |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.1048822/full |
| work_keys_str_mv | AT zhaokuidu comprehensiveanalysisofthenactranscriptionfactorgenefamilyinkandeliaobovatarevealspotentialmembersrelatedtochillingtolerance AT shixianyou comprehensiveanalysisofthenactranscriptionfactorgenefamilyinkandeliaobovatarevealspotentialmembersrelatedtochillingtolerance AT dangyang comprehensiveanalysisofthenactranscriptionfactorgenefamilyinkandeliaobovatarevealspotentialmembersrelatedtochillingtolerance AT yutiantao comprehensiveanalysisofthenactranscriptionfactorgenefamilyinkandeliaobovatarevealspotentialmembersrelatedtochillingtolerance AT yunxiaozhu comprehensiveanalysisofthenactranscriptionfactorgenefamilyinkandeliaobovatarevealspotentialmembersrelatedtochillingtolerance AT wensun comprehensiveanalysisofthenactranscriptionfactorgenefamilyinkandeliaobovatarevealspotentialmembersrelatedtochillingtolerance AT zhengmanchen comprehensiveanalysisofthenactranscriptionfactorgenefamilyinkandeliaobovatarevealspotentialmembersrelatedtochillingtolerance AT junminli comprehensiveanalysisofthenactranscriptionfactorgenefamilyinkandeliaobovatarevealspotentialmembersrelatedtochillingtolerance |