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Shah FA, Chen Z, Ni F, Kamal KA, Zhang J, Chen J, Ren J. ArNAC148 induces Acer rubrum leaf senescence by activating the transcription of the ABA receptor gene ArPYR13. Int J Biol Macromol 2024; 279:134950. [PMID: 39226982 DOI: 10.1016/j.ijbiomac.2024.134950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 08/20/2024] [Accepted: 08/20/2024] [Indexed: 09/05/2024]
Abstract
Acer rubrum, an ornamental tree known for its stunning autumn colors, has an elusive molecular mechanism that governs its leaf senescence. We performed the genome-wide analysis of NAC transcription factor genes and PYRABACTIN RESISTANCE1-LIKE (PYLs) and found that ArNAC148 and ArPYL13 were significantly upregulated in senescing leaves as compared to mature leaves. Subcellular localization studies confirmed the nuclear localization of ArNAC148 and the cytoplasmic localization of ArPYL13. Electrophoretic mobility shift assay and yeast one-hybrid assay demonstrated that ArNAC148 directly binds to the promoter of ArPYL13. Luciferase reporter assays further showed that ArNAC148 activates the transcription of ArPYL13. The transient expression of ArNAC148 and ArPYL13 in tobacco leaves promoted chlorophyll degradation, increased H2O2 level, MDA contents, and electrolyte leakage in response to abscisic acid (ABA). Moreover, the virus-induced gene silencing of ArNAC148 and ArPYL13 in A. rubrum produced results that were opposite to those observed in transient expression experiments. Our findings suggest that ArNAC148 induces leaf senescence by directly activating the transcription of ArPYL13, providing insights into the ABA-mediated regulatory mechanisms governing leaf senescence in A. rubrum. This study offers new perspectives for researchers to explore the roles of NAC and PYL genes in regulating leaf senescence in woody ornamental plants.
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Affiliation(s)
- Faheem Afzal Shah
- Institute of Agricultural Engineering, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Zhu Chen
- Institute of Agricultural Engineering, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Fang Ni
- Anhui Wenda University of Information Engineering, Anhui Province, Anhui 230032, China
| | - Khan Arif Kamal
- Institute of Agricultural Engineering, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Jimei Zhang
- Institute of Agricultural Engineering, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Jinhuan Chen
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Jie Ren
- Institute of Agricultural Engineering, Anhui Academy of Agricultural Sciences, Hefei 230031, China.
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2
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Wang Q, Zhou L, Yuan M, Peng F, Zhu X, Wang Y. Genome-Wide Identification of NAC Gene Family Members of Tree Peony ( Paeonia suffruticosa Andrews) and Their Expression under Heat and Waterlogging Stress. Int J Mol Sci 2024; 25:9312. [PMID: 39273263 PMCID: PMC11395581 DOI: 10.3390/ijms25179312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/14/2024] [Accepted: 08/26/2024] [Indexed: 09/15/2024] Open
Abstract
An important family of transcription factors (TFs) in plants known as NAC (NAM, ATAF1/2, and CUC2) is crucial for the responses of plants to environmental stressors. In this study, we mined the NAC TF family members of tree peony (Paeonia suffruticosa Andrews) from genome-wide data and analyzed their response to heat and waterlogging stresses in conjunction with transcriptome data. Based on tree peony's genomic information, a total of 48 PsNAC genes were discovered. Based on how similar their protein sequences were, these PsNAC genes were divided into 14 branches. While the gene structures and conserved protein motifs of the PsNAC genes within each branch were largely the same, the cis-acting elements in the promoter region varied significantly. Transcriptome data revealed the presence of five PsNAC genes (PsNAC06, PsNAC23, PsNAC38, PsNAC41, PsNAC47) and one PsNAC gene (PsNAC37) in response to heat and waterlogging stresses, respectively. qRT-PCR analysis reconfirmed the response of these five PsNAC genes to heat stress and one PsNAC gene to waterlogging stress. This study lays a foundation for the study of the functions and regulatory mechanisms of NAC TFs in tree peony. Meanwhile, the NAC TFs of tree peony in response to heat and waterlogging stress were excavated, which is of great significance for the selection and breeding of new tree peony varieties with strong heat and waterlogging tolerance.
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Affiliation(s)
- Qun Wang
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Lin Zhou
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Meng Yuan
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Fucheng Peng
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Xiangtao Zhu
- College of Jiyang, Zhejiang A&F University, Zhuji 311800, China
| | - Yan Wang
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
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He M, Chen P, Li M, Lei F, Lu W, Jiang C, Liu J, Li Y, Xiao J, Zheng Y. Physiological and transcriptome analysis of changes in endogenous hormone and sugar content during the formation of tender asparagus stems. BMC PLANT BIOLOGY 2024; 24:581. [PMID: 38898382 PMCID: PMC11186092 DOI: 10.1186/s12870-024-05277-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
Asparagus is a nutritionally dense stem vegetable whose growth and development are correlated with its quality and yield. To investigate the dynamic changes and underlying mechanisms during the elongation and growth process of asparagus stems, we documented the growth pattern of asparagus and selected stem segments from four consecutive elongation stages using physiological and transcriptome analyses. Notably, the growth rate of asparagus accelerated at a length of 25 cm. A significant decrease in the concentration of sucrose, fructose, glucose, and additional sugars was observed in the elongation region of tender stems. Conversely, the levels of auxin and gibberellins(GAs) were elevated along with increased activity of enzymes involved in sucrose degradation. A significant positive correlation existed between auxin, GAs, and enzymes involved in sucrose degradation. The ABA content gradually increased with stem elongation. The tissue section showed that cell elongation is an inherent manifestation of stem elongation. The differential genes screened by transcriptome analysis were enriched in pathways such as starch and sucrose metabolism, phytohormone synthesis metabolism, and signal transduction. The expression levels of genes such as ARF, GA20ox, NCED, PIF4, and otherswere upregulated during stem elongation, while DAO, GA2ox, and other genes were downregulated. The gene expression level was consistent with changes in hormone content and influenced the cell length elongation. Additionally, the expression results of RT-qPCR were consistent with RNA-seq. The observed variations in gene expression levels, endogenous hormones and sugar changes during the elongation and growth of asparagus tender stems offer valuable insights for future investigations into the molecular mechanisms of asparagus stem growth and development and provide a theoretical foundation for cultivation and production practices.
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Affiliation(s)
- Maolin He
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Peiran Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Fengyun Lei
- Agricultural Equipment Research Institute, Chengdu Academy of Agricultural and Forest Sciences, Chengdu, 611130, China
| | - Wei Lu
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chengyao Jiang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Junting Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yanwen Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiachang Xiao
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yangxia Zheng
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China.
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4
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Guo L, Liao Y, Deng S, Li J, Bu X, Zhu C, Zhang W, Cong X, Cheng S, Chen Q, Xu F. Genome-wide analysis of NAC transcription factors and exploration of candidate genes regulating selenium metabolism in Broussonetia papyrifera. PLANTA 2024; 260:1. [PMID: 38753175 DOI: 10.1007/s00425-024-04438-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 05/09/2024] [Indexed: 07/03/2024]
Abstract
MAIN CONCLUSION Genome-wide identification revealed 79 BpNAC genes belonging to 16 subfamilies, and their gene structures and evolutionary relationships were characterized. Expression analysis highlighted their importance in plant selenium stress responses. Paper mulberry (Broussonetia papyrifera), a deciduous arboreal plant of the Moraceae family, is distinguished by its leaves, which are abundant in proteins, polysaccharides, and flavonoids, positioning it as a novel feedstock. NAC transcription factors, exclusive to plant species, are crucial in regulating growth, development, and response to biotic and abiotic stress. However, extensive characterization of the NAC family within paper mulberry is lacking. In this study, 79 BpNAC genes were identified from the paper mulberry genome, with an uneven distribution across 13 chromosomes. A comprehensive, genome-wide analysis of BpNACs was performed, including investigating gene structures, promoter regions, and chromosomal locations. Phylogenetic tree analysis, alongside comparisons with Arabidopsis thaliana NACs, allowed for categorizing these genes into 16 subfamilies in alignment with gene structure and motif conservation. Collinearity analysis suggested a significant homologous relationship between the NAC genes of paper mulberry and those in Morus notabilis, Ficus hispida, Antiaris toxicaria, and Cannabis sativa. Integrating transcriptome data and Se content revealed that 12 BpNAC genes were associated with selenium biosynthesis. Subsequent RT-qPCR analysis corroborated the correlation between BpNAC59, BpNAC62 with sodium selenate, and BpNAC55 with sodium selenite. Subcellular localization experiments revealed the nuclear functions of BpNAC59 and BpNAC62. This study highlights the potential BpNAC transcription factors involved in selenium metabolism, providing a foundation for strategically breeding selenium-fortified paper mulberry.
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Affiliation(s)
- Longfei Guo
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Yongling Liao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Shiming Deng
- Hubei Key Laboratory of Selenium Resource Research and Biological Application, Hubei Minzu University, Enshi, 445000, Hubei, China
| | - Jitao Li
- Hubei Key Laboratory of Selenium Resource Research and Biological Application, Hubei Minzu University, Enshi, 445000, Hubei, China
| | - Xianchen Bu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Changye Zhu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
- Hubei Key Laboratory of Selenium Resource Research and Biological Application, Hubei Minzu University, Enshi, 445000, Hubei, China
| | - Xin Cong
- Enshi Se-Run Material Engineering Technology Co., Ltd., Enshi, 445000, Hubei, China
| | - Shuiyuan Cheng
- National R&D Center for Se-rich Agricultural Products Processing, Wuhan Polytechnic University, Wuhan, 430023, Hubei, China
| | - Qiangwen Chen
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China.
- Hubei Key Laboratory of Selenium Resource Research and Biological Application, Hubei Minzu University, Enshi, 445000, Hubei, China.
- Enshi Se-Run Material Engineering Technology Co., Ltd., Enshi, 445000, Hubei, China.
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China.
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Fuertes-Aguilar J, Matilla AJ. Transcriptional Control of Seed Life: New Insights into the Role of the NAC Family. Int J Mol Sci 2024; 25:5369. [PMID: 38791407 PMCID: PMC11121595 DOI: 10.3390/ijms25105369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Transcription factors (TFs) regulate gene expression by binding to specific sequences on DNA through their DNA-binding domain (DBD), a universal process. This update conveys information about the diverse roles of TFs, focusing on the NACs (NAM-ATAF-CUC), in regulating target-gene expression and influencing various aspects of plant biology. NAC TFs appeared before the emergence of land plants. The NAC family constitutes a diverse group of plant-specific TFs found in mosses, conifers, monocots, and eudicots. This update discusses the evolutionary origins of plant NAC genes/proteins from green algae to their crucial roles in plant development and stress response across various plant species. From mosses and lycophytes to various angiosperms, the number of NAC proteins increases significantly, suggesting a gradual evolution from basal streptophytic green algae. NAC TFs play a critical role in enhancing abiotic stress tolerance, with their function conserved in angiosperms. Furthermore, the modular organization of NACs, their dimeric function, and their localization within cellular compartments contribute to their functional versatility and complexity. While most NAC TFs are nuclear-localized and active, a subset is found in other cellular compartments, indicating inactive forms until specific cues trigger their translocation to the nucleus. Additionally, it highlights their involvement in endoplasmic reticulum (ER) stress-induced programmed cell death (PCD) by activating the vacuolar processing enzyme (VPE) gene. Moreover, this update provides a comprehensive overview of the diverse roles of NAC TFs in plants, including their participation in ER stress responses, leaf senescence (LS), and growth and development. Notably, NACs exhibit correlations with various phytohormones (i.e., ABA, GAs, CK, IAA, JA, and SA), and several NAC genes are inducible by them, influencing a broad spectrum of biological processes. The study of the spatiotemporal expression patterns provides insights into when and where specific NAC genes are active, shedding light on their metabolic contributions. Likewise, this review emphasizes the significance of NAC TFs in transcriptional modules, seed reserve accumulation, and regulation of seed dormancy and germination. Overall, it effectively communicates the intricate and essential functions of NAC TFs in plant biology. Finally, from an evolutionary standpoint, a phylogenetic analysis suggests that it is highly probable that the WRKY family is evolutionarily older than the NAC family.
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Affiliation(s)
| | - Angel J. Matilla
- Departamento de Biología Funcional, Universidad de Santiago de Compostela, 14971 Santiago de Compostela, Spain
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Chen J, Hou S, Zhang Q, Meng J, Zhang Y, Du J, Wang C, Liang D, Guo Y. Genome-Wide Identification and Analysis of the WRKY Gene Family in Asparagus officinalis. Genes (Basel) 2023; 14:1704. [PMID: 37761844 PMCID: PMC10530708 DOI: 10.3390/genes14091704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
In recent years, the related research of the WRKY gene family has been gradually promoted, which is mainly reflected in the aspects of environmental stress and hormone response. However, to make the study of the WRKY gene family more complete, we also need to focus on the whole-genome analysis and identification of the family. In previous studies, the whole WRKY gene family of Arabidopsis, legumes and other plants has been thoroughly studied. However, since the publication of Asparagus officinalis genome-wide data, there has never been an analysis of the whole WRKY gene family. To understand more broadly the function of the WRKY gene family, the whole genome and salt stress transcriptome data of asparagus were used for comprehensive analysis in this study, including WRKY gene family identification, phylogenetic tree construction, analysis of conserved mods and gene domains, extraction of cis-acting elements, intron/exon analysis, species collinearity analysis, and WRKY expression analysis under salt stress. The results showed that a total of 70 genes were selected and randomly distributed on 10 chromosomes and one undefined chromosome. According to the functional classification of Arabidopsis thaliana, the WRKY family of asparagus was divided into 11 subgroups (C1-C9, U1, U2). It is worth considering that the distribution rules of gene-conserved motifs, gene domains and introns/exons in the same subfamily are similar, which suggests that genes in the same subfamily may regulate similar physiological processes. In this study, 11 cis-acting elements of WRKY family were selected, among which auxin, gibberellin, abscisic acid, salicylic acid and other hormone-regulated induction elements were involved. In addition, environmental stress (such as drought stress and low-temperature response) also accounted for a large proportion. Interestingly, we analyzed a total of two tandem duplicate genes and 13 segmental duplication genes, suggesting that this is related to the amplification of the WRKY gene family. Transcriptome data analysis showed that WRKY family genes could regulate plant growth and development by up-regulating and down-regulating gene expression under salt stress. Volcanic maps showed that 3 and 15 AoWRKY genes were significantly up-regulated or down-regulated in NI&NI+S and AMF&AMF+S, respectively. These results provide a new way to analyze the evolution and function of the WRKY gene family, and can provide a reference for the production and research of asparagus.
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Affiliation(s)
- Jing Chen
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
| | - Sijia Hou
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
| | - Qianqian Zhang
- Chinese Institute for Brain Research, Beijing 102206, China;
- College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jianqiao Meng
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
| | - Yingying Zhang
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
| | - Junhong Du
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
| | - Cong Wang
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
| | - Dan Liang
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
| | - Yunqian Guo
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
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Fu C, Liu M. Genome-wide identification and molecular evolution of NAC gene family in Dendrobium nobile. FRONTIERS IN PLANT SCIENCE 2023; 14:1232804. [PMID: 37670854 PMCID: PMC10475575 DOI: 10.3389/fpls.2023.1232804] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/31/2023] [Indexed: 09/07/2023]
Abstract
NAC transcription factors are an important genes that regulate plant growth and development, and can regulate functions such as fruit ripening in plants. Based on genome data of Dendrobium nobile, the NAC gene family was identified and analyzed by bioinformatics methods. In this study, we identified 85 NAC genes in Dendrobium nobile genome, and systematically analyzed the NAC gene family. We found that they were distributed unevenly in the nineteen chromosomes. The amino acid length of D. nobile NAC gene family (DnoNACs) ranged from 80 to 1065, molecular weight ranged from 22.17 to 119.02 kD, and isoelectric point ranged from 4.61~9.26. Its promoter region contains multiple stress responsive elements, including light responsive, gibberellin-responsive, abscisic acid responsiveness, MeJA-responsiveness and drought-inducibility elements. Phylogenetic analysis indicates that the D. nobile NAC gene family is most closely related to Dendrobium catenatum and Dendrobium chrysotoxum. Analysis of SSR loci indicates that the fraction of mononucleotide repeats was the largest, as was the frequency of A/T. Non-coding RNA analysis showed that these 85 NAC genes contain 397 miRNAs. The collinearity analysis shows that 9 collinear locis were found on the chromosomes of D. nobile with Arabidopsis thaliana, and 75 collinear locis with D.chrysotoxum. QRT-PCR experiment under different salt concentration and temperature conditions verified the response mechanism of DnoNAC gene family under stress conditions. Most DnoNAC genes are sensitive to salt stress and temperature stress. The results of this study provide a reference for further understanding the function of NAC gene in D. nobile.
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Wang Z, Zhang Z, Wang P, Qin C, He L, Kong L, Ren W, Liu X, Ma W. Genome-wide identification of the NAC transcription factor family and regulation of metabolites under salt stress in Isatis indigotica. Int J Biol Macromol 2023; 240:124436. [PMID: 37068542 DOI: 10.1016/j.ijbiomac.2023.124436] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 03/28/2023] [Accepted: 04/03/2023] [Indexed: 04/19/2023]
Abstract
NAC (NAM, ATAF1/2 and CUC2) transcription factors (TFs) are a class of TFs families unique to plants, which not only play an important role in the growth and developmental stages of plants but also function in response to stress and regulation of secondary metabolite biosynthesis. However, there are few studies on NAC genes in the medicinal plant Isatis indigotica. In this study, 96 IiNAC genes were identified based on the whole-genome data of I. indigotica, distributed in seven chromosomes and three contigs. IiNAC genes were structurally conserved and divided into 15 subgroups. Cis-elements were identified in the promoter region of the IiNAC gene in response to plant growth and development, abiotic stresses and hormones. In addition, transcriptome and metabolome data of I. indigotica leaves under salt stress were analyzed to construct a network of IiNAC gene co-expression and metabolite association. Ten differentially expressed IiNAC genes were co-expressed with 109 TFs, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that most of these genes were associated with plant growth and development and abiotic stress responses. Eleven IiNAC genes were positively associated with 72 metabolites. Eleven IiNAC genes were positively or negatively associated with 47 metabolites through 37 TFs. Commonly associated secondary metabolites include two terpenoids, abscisic acid and bilobalide, two flavonoids, dihydrokaempferol and syringaldehyde, a coumarin, 7-methoxycoumarin, an alkaloid, lupinine, and quinone dihydrotanshinone I. This study provides important data to support the identification of the NAC gene family in I. indigotica and the regulatory functions of IiNAC genes in metabolites under salt stress.
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Affiliation(s)
- Zhen Wang
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Zhanping Zhang
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Panpan Wang
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Chen Qin
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Lianqing He
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Lingyyang Kong
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Weichhao Ren
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Xiubo Liu
- College of Jiamusi, Heilongjiang University of Chinese Medicine, Harbin, China.
| | - Wei Ma
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China.
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9
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Sun MM, Liu X, Huang XJ, Yang JJ, Qin PT, Zhou H, Jiang MG, Liao HZ. Genome-Wide Identification and Expression Analysis of the NAC Gene Family in Kandelia obovata, a Typical Mangrove Plant. Curr Issues Mol Biol 2022; 44:5622-5637. [PMID: 36421665 PMCID: PMC9689236 DOI: 10.3390/cimb44110381] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/15/2023] Open
Abstract
The NAC (NAM, ATAF1/2, and CUC2) gene family, one of the largest transcription factor families in plants, acts as positive or negative regulators in plant response and adaption to various environmental stresses, including cold stress. Multiple reports on the functional characterization of NAC genes in Arabidopsis thaliana and other plants are available. However, the function of the NAC genes in the typical woody mangrove (Kandelia obovata) remains poorly understood. Here, a comprehensive analysis of NAC genes in K. obovata was performed with a pluri-disciplinary approach including bioinformatic and molecular analyses. We retrieved a contracted NAC family with 68 genes from the K. obovata genome, which were unevenly distributed in the chromosomes and classified into ten classes. These KoNAC genes were differentially and preferentially expressed in different organs, among which, twelve up-regulated and one down-regulated KoNAC genes were identified. Several stress-related cis-regulatory elements, such as LTR (low-temperature response), STRE (stress response element), ABRE (abscisic acid response element), and WUN (wound-responsive element), were identified in the promoter regions of these 13 KoNAC genes. The expression patterns of five selected KoNAC genes (KoNAC6, KoNAC15, KoNAC20, KoNAC38, and KoNAC51) were confirmed by qRT-PCR under cold treatment. These results strongly implied the putative important roles of KoNAC genes in response to chilling and other stresses. Collectively, our findings provide valuable information for further investigations on the function of KoNAC genes.
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Affiliation(s)
- Man-Man Sun
- Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Marine Sciences and Biotechnology, Guangxi Minzu University, 158 West Daxue Road, Nanning 530008, China
| | - Xiu Liu
- Guangxi Key Laboratory of Special Non-Wood Forest Cultivation and Utilization, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning 530002, China
| | - Xiao-Juan Huang
- Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Marine Sciences and Biotechnology, Guangxi Minzu University, 158 West Daxue Road, Nanning 530008, China
| | - Jing-Jun Yang
- Guangxi Key Laboratory of Special Non-Wood Forest Cultivation and Utilization, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning 530002, China
| | - Pei-Ting Qin
- Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Marine Sciences and Biotechnology, Guangxi Minzu University, 158 West Daxue Road, Nanning 530008, China
| | - Hao Zhou
- Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Marine Sciences and Biotechnology, Guangxi Minzu University, 158 West Daxue Road, Nanning 530008, China
| | - Ming-Guo Jiang
- Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Marine Sciences and Biotechnology, Guangxi Minzu University, 158 West Daxue Road, Nanning 530008, China
| | - Hong-Ze Liao
- Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Marine Sciences and Biotechnology, Guangxi Minzu University, 158 West Daxue Road, Nanning 530008, China
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Genome-Wide Identification, Characterization, and Expression Analysis Related to Low-Temperature Stress of the CmGLP Gene Family in Cucumis melo L. Int J Mol Sci 2022; 23:ijms23158190. [PMID: 35897766 PMCID: PMC9330424 DOI: 10.3390/ijms23158190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 01/25/2023] Open
Abstract
Germin-like protein (GLP) participates in plant growth and development and plays an important role in plant stress. In the present study, 22 CmGLPs belonging to five classes were identified in the melon genome. Each member of the CmGLPs family contains a typical Cupin_1 domain. We conducted a genome-wide analysis of the melon GLP gene family characterization. CmGLPs were randomly distributed in the melon chromosomes, with the largest number on chromosome 8, having eight family members. Gene duplication events drive the evolution and expansion of the melon GLP gene family. Based on the phylogenetic tree analysis of GLP proteins in melon, rice, Arabidopsis, and cucumber, it was found that the GLP gene families of different species have diverged in evolution. Based on qRT-PCR results, all members of the CmGLP gene family could be expressed in different tissues of melon. Most CmGLP genes were up-regulated after low-temperature stress. The relative expression of CmGLP2-5 increased by 157.13 times at 48 h after low-temperature treatment. This finding suggests that the CmGLP2-5 might play an important role in low-temperature stress in melon. Furthermore, quantitative dual LUC assays indicated that CmMYB23 and CmWRKY33 can bind the promoter fragment of the CmGLP2-5. These results were helpful in understanding the functional succession and evolution of the melon GLP gene family and further revealed the response of CmGLPs to low-temperature stress in melon.
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