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Rehman S, Bahadur S, Xia W. Unlocking nature's secrets: The pivotal role of WRKY transcription factors in plant flowering and fruit development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112150. [PMID: 38857658 DOI: 10.1016/j.plantsci.2024.112150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024]
Abstract
The WRKY transcription factor family is a key player in the regulatory mechanisms of flowering plants, significantly influencing both their biotic and abiotic response systems as well as being vital to numerous physiological and biological functions. Over the past two decades, the functionality of WRKY proteins has been the subject of extensive research in over 50 plant species, with a strong focus on their roles in responding to various stresses. Despite this extensive research, there remains a notable gap in comprehensive studies aimed at understanding how specific WRKY genes directly influence the timing of flowering and fruit development. This review offers an up-to-date look at WRKY family genes and provides insights into the key genes of WRKY to control flowering, enhance fruit ripening and secondary metabolism synthesis, and maintain fruit quality of various plants, including annuals, perennials, medicinal, and crop plants. The WRKY transcription factors serve as critical regulators within the transcriptional regulatory network, playing a crucial role in the precise enhancement of flowering processes. It is also involved in the up-regulation of fruit ripening was strongly demonstrated by combined transcriptomics and metabolomic investigation. Therefore, we speculated that the WRKY family is known to be a key regulator of flowering and fruiting in plants. This detailed insight will enable the identification of the series of molecular occurrences featuring WRKY proteins throughout the stages of flowering and fruiting.
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Affiliation(s)
- Shazia Rehman
- Sanya Nanfan Research Institution, Hainan University, Sanya, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Saraj Bahadur
- College of Forestry, Hainan University, Haikou 570228, China; College of Life and Health Sciences, Hainan University, Haikou 570228, China.
| | - Wei Xia
- Sanya Nanfan Research Institution, Hainan University, Sanya, China; College of Tropical Crops, Hainan University, Haikou 570228, China.
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Qin Z, Yan C, Yang K, Wang Q, Wang Z, Gou C, Feng H, Jin Q, Dai X, Maitikadir Z, Hao H, Wang L. Genome-wide identification of walnut (Juglans regia) PME gene family members and expression analysis during infection with Cryptosphaeria pullmanensis pathogens. Genomics 2024; 116:110860. [PMID: 38776985 DOI: 10.1016/j.ygeno.2024.110860] [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: 02/17/2024] [Revised: 05/14/2024] [Accepted: 05/18/2024] [Indexed: 05/25/2024]
Abstract
Walnuts exhibit a higher resistance to diseases, though they are not completely immune. This study focuses on the Pectin methylesterase (PME) gene family to investigate whether it is involved in disease resistance in walnuts. These 21 genes are distributed across 12 chromosomes, with four pairs demonstrating homology. Variations in conserved motifs and gene structures suggest diverse functions within the gene family. Phylogenetic and collinear gene pairs of the PME family indicate that the gene family has evolved in a relatively stable way. The cis-acting elements and gene ontology enrichment of these genes, underscores their potential role in bolstering walnuts' defense mechanisms. Transcriptomic analyses were conducted under conditions of Cryptosphaeria pullmanensis infestation and verified by RT-qPCR. The results showed that certain JrPME family genes were activated in response, leading to the hypothesis that some members may confer resistance to the disease.
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Affiliation(s)
- Ze Qin
- Scientific Observing and Experimental Station of Crop Pests in Alar, Ministry of Agriculture/ Key Laboratory of Integrated Pest Management (IPM) of Xinjiang Production and Construction Corps in Southern Xinjiang, College of Agronomy, Tarim University, Alar, Xinjiang 843300, China
| | - Chengcai Yan
- Scientific Observing and Experimental Station of Crop Pests in Alar, Ministry of Agriculture/ Key Laboratory of Integrated Pest Management (IPM) of Xinjiang Production and Construction Corps in Southern Xinjiang, College of Agronomy, Tarim University, Alar, Xinjiang 843300, China
| | - Kaiying Yang
- Scientific Observing and Experimental Station of Crop Pests in Alar, Ministry of Agriculture/ Key Laboratory of Integrated Pest Management (IPM) of Xinjiang Production and Construction Corps in Southern Xinjiang, College of Agronomy, Tarim University, Alar, Xinjiang 843300, China
| | - Qinpeng Wang
- Scientific Observing and Experimental Station of Crop Pests in Alar, Ministry of Agriculture/ Key Laboratory of Integrated Pest Management (IPM) of Xinjiang Production and Construction Corps in Southern Xinjiang, College of Agronomy, Tarim University, Alar, Xinjiang 843300, China
| | - Zhe Wang
- Scientific Observing and Experimental Station of Crop Pests in Alar, Ministry of Agriculture/ Key Laboratory of Integrated Pest Management (IPM) of Xinjiang Production and Construction Corps in Southern Xinjiang, College of Agronomy, Tarim University, Alar, Xinjiang 843300, China
| | - Changqing Gou
- Scientific Observing and Experimental Station of Crop Pests in Alar, Ministry of Agriculture/ Key Laboratory of Integrated Pest Management (IPM) of Xinjiang Production and Construction Corps in Southern Xinjiang, College of Agronomy, Tarim University, Alar, Xinjiang 843300, China
| | - Hongzu Feng
- Scientific Observing and Experimental Station of Crop Pests in Alar, Ministry of Agriculture/ Key Laboratory of Integrated Pest Management (IPM) of Xinjiang Production and Construction Corps in Southern Xinjiang, College of Agronomy, Tarim University, Alar, Xinjiang 843300, China
| | - Qiming Jin
- Scientific Observing and Experimental Station of Crop Pests in Alar, Ministry of Agriculture/ Key Laboratory of Integrated Pest Management (IPM) of Xinjiang Production and Construction Corps in Southern Xinjiang, College of Agronomy, Tarim University, Alar, Xinjiang 843300, China
| | - Xianxing Dai
- Scientific Observing and Experimental Station of Crop Pests in Alar, Ministry of Agriculture/ Key Laboratory of Integrated Pest Management (IPM) of Xinjiang Production and Construction Corps in Southern Xinjiang, College of Agronomy, Tarim University, Alar, Xinjiang 843300, China
| | - Zulihumar Maitikadir
- Scientific Observing and Experimental Station of Crop Pests in Alar, Ministry of Agriculture/ Key Laboratory of Integrated Pest Management (IPM) of Xinjiang Production and Construction Corps in Southern Xinjiang, College of Agronomy, Tarim University, Alar, Xinjiang 843300, China
| | - Haiting Hao
- Scientific Observing and Experimental Station of Crop Pests in Alar, Ministry of Agriculture/ Key Laboratory of Integrated Pest Management (IPM) of Xinjiang Production and Construction Corps in Southern Xinjiang, College of Agronomy, Tarim University, Alar, Xinjiang 843300, China.
| | - Lan Wang
- Scientific Observing and Experimental Station of Crop Pests in Alar, Ministry of Agriculture/ Key Laboratory of Integrated Pest Management (IPM) of Xinjiang Production and Construction Corps in Southern Xinjiang, College of Agronomy, Tarim University, Alar, Xinjiang 843300, China.
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Babaei S, Bhalla PL, Singh MB. Identifying long non-coding RNAs involved in heat stress response during wheat pollen development. FRONTIERS IN PLANT SCIENCE 2024; 15:1344928. [PMID: 38379952 PMCID: PMC10876783 DOI: 10.3389/fpls.2024.1344928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/17/2024] [Indexed: 02/22/2024]
Abstract
Introduction Wheat is a staple food crop for over one-third of the global population. However, the stability of wheat productivity is threatened by heat waves associated with climate change. Heat stress at the reproductive stage can result in pollen sterility and failure of grain development. Methods This study used transcriptome data analysis to explore the specific expression of long non-coding RNAs (lncRNAs) in response to heat stress during pollen development in four wheat cultivars. Results and discussion We identified 11,054 lncRNA-producing loci, of which 5,482 lncRNAs showed differential expression in response to heat stress. Heat-responsive lncRNAs could target protein-coding genes in cis and trans and in lncRNA-miRNA-mRNA regulatory networks. Gene ontology analysis predicted that target protein-coding genes of lncRNAs regulate various biological processes such as hormonal responses, protein modification and folding, response to stress, and biosynthetic and metabolic processes. We also noted some paired lncRNA/protein-coding gene modules and some lncRNA-miRNA-mRNA regulatory modules shared in two or more wheat cultivars. These modules were related to regulating plant responses to heat stress, such as heat-shock proteins and transcription factors, and protein domains, such as MADS-box, Myc-type, and Alpha crystallin/Hsp20 domain. Conclusion Our results provide the basic knowledge and molecular resources for future functional studies investigating wheat reproductive development under heat stress.
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Affiliation(s)
| | | | - Mohan B. Singh
- Plant Molecular Biology and Biotechnology Laboratory, School of Agriculture, Food and Ecosystem Sciences, The University of Melbourne, Melbourne, VIC, Australia
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Javed T, Gao SJ. WRKY transcription factors in plant defense. Trends Genet 2023; 39:787-801. [PMID: 37633768 DOI: 10.1016/j.tig.2023.07.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 08/28/2023]
Abstract
Environmental stressors caused by climate change are fundamental barriers to agricultural sustainability. Enhancing the stress resilience of crops is a key strategy in achieving global food security. Plants perceive adverse environmental conditions and initiate signaling pathways to activate precise responses that contribute to their survival. WRKY transcription factors (TFs) are essential players in several signaling cascades and regulatory networks that have crucial implications for defense responses in plants. This review summarizes advances in research concerning how WRKY TFs mediate various signaling cascades and metabolic adjustments as well as how epigenetic modifications involved in environmental stress responses in plants can modulate WRKYs and/or their downstream genes. Emerging research shows that clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas)-mediated genome editing of WRKYs could be used to improve crop resilience.
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Affiliation(s)
- Talha Javed
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - San-Ji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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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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Wang C, Ye D, Li Y, Hu P, Xu R, Wang X. Genome-wide identification and bioinformatics analysis of the WRKY transcription factors and screening of candidate genes for anthocyanin biosynthesis in azalea ( Rhododendron simsii). Front Genet 2023; 14:1172321. [PMID: 37234867 PMCID: PMC10206045 DOI: 10.3389/fgene.2023.1172321] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/02/2023] [Indexed: 05/28/2023] Open
Abstract
WRKY transcription factors have been demonstrated to influence the anthocyanin biosynthesis in many plant species. However, there is limited knowledge about the structure and function of WRKY genes in the major ornamental plant azalea (Rhododendron simsii). In this study, we identified 57 RsWRKY genes in the R. simsii genome and classified them into three main groups and several subgroups based on their structural and phylogenetic characteristics. Comparative genomic analysis suggested WRKY gene family has significantly expanded during plant evolution from lower to higher species. Gene duplication analysis indicated that the expansion of the RsWRKY gene family was primarily due to whole-genome duplication (WGD). Additionally, selective pressure analysis (Ka/Ks) suggested that all RsWRKY duplication gene pairs underwent purifying selection. Synteny analysis indicated that 63 and 24 pairs of RsWRKY genes were orthologous to Arabidopsis thaliana and Oryza sativa, respectively. Furthermore, RNA-seq data was used to investigate the expression patterns of RsWRKYs, revealing that 17 and 9 candidate genes may be associated with anthocyanin synthesis at the bud and full bloom stages, respectively. These findings provide valuable insights into the molecular mechanisms underlying anthocyanin biosynthesis in Rhododendron species and lay the foundation for future functional studies of WRKY genes.
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Affiliation(s)
- Cheng Wang
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, China
| | - Dan Ye
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, China
| | - Yan Li
- Department of Biology and Chemical Engineering, Weihai Vocational College, Weihai, China
| | - Peiling Hu
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, China
| | - Run Xu
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, China
| | - Xiaojing Wang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, China
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Yang X, Zhao S, Ge W, Wang T, Fan Z, Wang Y. Genome-wide identification and expression analysis of the WRKY gene family in cabbage ( Brassica oleracea var. capitata L.). BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2110518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Affiliation(s)
- Xuyan Yang
- Department of Horticulture, College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, PR China
| | - Shuang Zhao
- Department of Horticulture, College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, PR China
| | - Wendong Ge
- Department of Horticulture, College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, PR China
| | - Tenghui Wang
- Department of Horticulture, College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, PR China
| | - Zhenyu Fan
- Department of Horticulture, College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, PR China
| | - Yushu Wang
- Department of Horticulture, College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar, PR China
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Guo H, Sun X, Wang B, Wu D, Sun H, Wang Y. The upstream regulatory mechanism of BplMYB46 and the function of upstream regulatory factors that mediate resistance to stress in Betula platyphylla. FRONTIERS IN PLANT SCIENCE 2022; 13:1030459. [PMID: 36388548 PMCID: PMC9640943 DOI: 10.3389/fpls.2022.1030459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Previously, we have shown that the transcription factor BplMYB46 in Betula platyphylla can enhance tolerance to salt and osmotic stress and promote secondary cell wall deposition, and we characterized its downstream regulatory mechanism. However, its upstream regulatory mechanism remains unclear. Here, the promoter activity and upstream regulatory factors of BplMYB46 were studied. Analyses of β-glucuronidase (GUS) staining and activity indicated that BplMYB46 promoter was specific temporal and spatial expression, and its expression can be induced by salt and osmotic stress. We identified three upstream regulatory factors of BplMYB46: BpDof1, BpWRKY3, and BpbZIP3. Yeast-one hybrid assays, GUS activity, chromatin immunoprecipitation, and quantitative real-time polymerase chain reaction revealed that BpDof1, BpWRKY3, and BpbZIP3 can directly regulate the expression of BplMYB46 by specifically binding to Dof, W-box, and ABRE elements in the BplMYB46 promoter, respectively. BpDof1, BpWRKY3, and BpbZIP3 were all localized to the nucleus, and their expressions can be induced by stress. Overexpression of BpDof1, BpWRKY3, and BpbZIP3 conferred the resistance of transgenic birch plants to salt and osmotic stress. Our findings provide new insights into the upstream regulatory mechanism of BplMYB46 and reveal new upstream regulatory genes that mediate resistance to adverse environments. The genes identified in our study provide novel targets for the breeding of forest tree species.
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Affiliation(s)
- Huiyan Guo
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
- The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Xiaomeng Sun
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
- The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Bo Wang
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
- The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Di Wu
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
- The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Hu Sun
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
- The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Yucheng Wang
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
- The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
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Genome-Wide Identification and Characterization of the Oat ( Avena sativa L.) WRKY Transcription Factor Family. Genes (Basel) 2022; 13:genes13101918. [PMID: 36292803 PMCID: PMC9601435 DOI: 10.3390/genes13101918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/11/2022] [Accepted: 10/20/2022] [Indexed: 11/04/2022] Open
Abstract
The WRKY family is widely involved in the regulation of plant growth and stress response and is one of the largest gene families related to plant environmental adaptation. However, no systematic studies on the WRKY family in oat (Avena sativa L.) have been conducted to date. The recently published complete genome sequence of oat enables the systematic analysis of the AsWRKYs. Based on a genome-wide study of oat, we identified 162 AsWRKYs that were unevenly distributed across 21 chromosomes; a phylogenetic tree of WRKY domains divided these genes into three groups (I, II, and III). We also analyzed the gene duplication events and identified a total of 111 gene pairs that showed strong purifying selection during the evolutionary process. Surprisingly, almost all genes evolved after the completion of subgenomic differentiation of hexaploid oat. Further studies on the functional analysis indicated that AsWRKYs were widely involved in various biological processes. Notably, expression patterns of 16 AsWRKY genes revealed that the response of AsWRKYs were affected by stress level and time. In conclusion, this study provides a reference for further analysis of the role of WRKY transcription factors in species evolution and functional differentiation.
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Li G, Chen Y, Zhao X, Yang J, Wang X, Li X, Hu S, Hou H. Genome-Wide Analysis of the Growth-Regulating Factor (GRF) Family in Aquatic Plants and Their Roles in the ABA-Induced Turion Formation of Spirodela polyrhiza. Int J Mol Sci 2022; 23:ijms231810485. [PMID: 36142399 PMCID: PMC9499638 DOI: 10.3390/ijms231810485] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 01/16/2023] Open
Abstract
Growth-regulating factors (GRFs) are plant-specific transcription factors that play essential roles in regulating plant growth and stress response. The GRF gene families have been described in several terrestrial plants, but a comprehensive analysis of these genes in diverse aquatic species has not been reported yet. In this study, we identified 130 GRF genes in 13 aquatic plants, including floating plants (Azolla filiculoides, Wolffia australiana, Lemna minuta, Spirodela intermedia, and Spirodela polyrhiza), floating-leaved plants (Nymphaea colorata and Euryale ferox), submersed plants (Zostera marina, Ceratophyllum demersum, Aldrovanda vesiculosa, and Utricularia gibba), an emergent plant (Nelumbo nucifera), and an amphibious plant (Cladopus chinensis). The gene structures, motifs, and cis-acting regulatory elements of these genes were analyzed. Phylogenetic analysis divided these GRFs into five clusters, and ABRE cis-elements were highly enriched in the promoter region of the GRFs in floating plants. We found that abscisic acid (ABA) is efficient at inducing the turion of Spirodela polyrhiza (giant duckweed), accompanied by the fluctuated expression of SpGRF genes in their fronds. Our results provide information about the GRF gene family in aquatic species and lay the foundation for future studies on the functions of these genes.
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Affiliation(s)
- Gaojie Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yan Chen
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuyao Zhao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Jingjing Yang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- Correspondence: (J.Y.); (H.H.)
| | - Xiaoyu Wang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaozhe Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Shiqi Hu
- Zhejiang Marine Development Research Institute, Zhoushan 316021, China
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (J.Y.); (H.H.)
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Lv M, Dong T, Wang J, Zuo K. Genome-wide identification of nitrate transporter genes from Spirodela polyrhiza and characterization of SpNRT1.1 function in plant development. FRONTIERS IN PLANT SCIENCE 2022; 13:945470. [PMID: 36061775 PMCID: PMC9436390 DOI: 10.3389/fpls.2022.945470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
Nitrate transporter (NRT) genes that participate in nitrate transport and distribution are indispensable for plant growth, development, and stress tolerance. Spirodela polyrhiza has the smallest genome among monocotyledon plants, and it has strong nitrate absorbance and phytoremediation abilities. However, the evolutionary history, expression patterns, and functions of the NRT gene family in S. polyrhiza are not well understood. Here, we identified 29 NRT members in the S. polyrhiza genome. Gene structure and phylogeny analyses showed that S. polyrhiza nitrate transporter (SpNRTs) genes were divided into eight clades without gene expansion compared with that in Arabidopsis. Transcriptomic analysis showed that SpNRT genes have spatiotemporal expression patterns and respond to abiotic stress. Functional analysis revealed that in S. polyrhiza, SpNRT1.1 expression was strongly induced by treatment with nitrate and ammonium. Overexpression of SpNRT1.1 significantly repressed primary root length, and the number and total length of lateral roots. This was more pronounced in high ammonium concentration medium. Overexpressed SpNRT1.1 in Arabidopsis significantly improved biomass and delayed flowering time, indicating that the nitrate transport ability of SpNRT1.1 differs from AtNRT1.1. In conclusion, our results provide valuable information about the evolution of the NRT family in higher plants and the function of SpNRT1.1.
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Affiliation(s)
- Mengli Lv
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Tiantian Dong
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kaijing Zuo
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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12
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Rozman U, Jemec Kokalj A, Dolar A, Drobne D, Kalčíková G. Long-term interactions between microplastics and floating macrophyte Lemna minor: The potential for phytoremediation of microplastics in the aquatic environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 831:154866. [PMID: 35351508 DOI: 10.1016/j.scitotenv.2022.154866] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/20/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
The presence of microplastics (MPs) in the environment has raised many concerns, and therefore approaches and technologies to remove them in situ are of high interest. In this context, we investigated the interactions between polyethylene MPs (fragments with a mean size of 149 ± 75 μm) and an aquatic floating macrophyte Lemna minor in order to assess its potential use for in situ phytoremediation. We first investigated the long-term effects of a high (100 mg/L = 9600 MPs/L), but still environmentally relevant concentration of MPs on L. minor. Subsequently bioadhesion of MPs was studied and the number and strength of MPs adhering to plant biomass were assessed. MPs did not adversely affect various parameters of plants (e.g., specific growth rate, chlorophyll contents, total antioxidant capacity, electron transport system activity, and contents of energy-rich molecules) throughout the duration of the experiment (12 weeks), except for the first week of the experiment, when protein content and total antioxidant capacity were affected. On the other hand, MPs affected the root length of L. minor during the first eight weeks of the experiment, while further exposure resulted in a decrease in the effects, indicating the ability of L. minor to tolerate the presence of MPs for a long period of time. MPs adhered rapidly to the plant biomass and the average percentages of strongly and weakly adhered particles were 6.5% and 20.0%, respectively, of the total MPs applied. In summary, results of this study suggest that L. minor can tolerate hotspot concentrations of MPs and can collect MPs from the water surface. Therefore, phytoremediation using floating plants could be considered as a potential method for in situ removal of MPs from the aquatic environment.
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Affiliation(s)
- Ula Rozman
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, 113 Večna pot, SI-1000 Ljubljana, Slovenia
| | - Anita Jemec Kokalj
- University of Ljubljana, Biotechnical Faculty, 101 Jamnikarjeva, SI-1000 Ljubljana, Slovenia
| | - Andraž Dolar
- University of Ljubljana, Biotechnical Faculty, 101 Jamnikarjeva, SI-1000 Ljubljana, Slovenia
| | - Damjana Drobne
- University of Ljubljana, Biotechnical Faculty, 101 Jamnikarjeva, SI-1000 Ljubljana, Slovenia
| | - Gabriela Kalčíková
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, 113 Večna pot, SI-1000 Ljubljana, Slovenia.
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13
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Zhao X, Yang J, Li X, Li G, Sun Z, Chen Y, Chen Y, Xia M, Li Y, Yao L, Hou H. Identification and expression analysis of GARP superfamily genes in response to nitrogen and phosphorus stress in Spirodela polyrhiza. BMC PLANT BIOLOGY 2022; 22:308. [PMID: 35751022 PMCID: PMC9233324 DOI: 10.1186/s12870-022-03696-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/13/2022] [Indexed: 06/12/2023]
Abstract
BACKGROUND GARP transcription factors perform critical roles in plant development and response to environmental stimulus, especially in the phosphorus (P) and nitrogen (N) sensing and uptake. Spirodela polyrhiza (giant duckweed) is widely used for phytoremediation and biomass production due to its rapid growth and efficient N and P removal capacities. However, there has not yet been a comprehensive analysis of the GRAP gene family in S. polyrhiza. RESULTS We conducted a comprehensive study of GRAP superfamily genes in S. polyrhiza. First, we investigated 35 SpGARP genes which have been classified into three groups based on their gene structures, conserved motifs, and phylogenetic relationship. Then, we identified the duplication events, performed the synteny analysis, and calculated the Ka/Ks ratio in these SpGARP genes. The regulatory and co-expression networks of SpGARPs were further constructed using cis-acting element analysis and weighted correlation network analysis (WGCNA). Finally, the expression pattern of SpGARP genes were analyzed using RNA-seq data and qRT-PCR, and several NIGT1 transcription factors were found to be involved in both N and P starvation responses. CONCLUSIONS The study provides insight into the evolution and function of GARP superfamily in S. polyrhiza, and lays the foundation for the further functional verification of SpGARP genes.
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Affiliation(s)
- Xuyao Zhao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jingjing Yang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiaozhe Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Gaojie Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zuoliang Sun
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Chen
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yimeng Chen
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Manli Xia
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yixian Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lunguang Yao
- Henan Key Laboratory of Ecological Security for Water Source Region of Mid-Line of South-to-North Diversion Project of Henan Province, Collaborative Innovation Center of Water Security for Water Source Region of Mid-Line of South-to-North Diversion Project of Henan Province, Nanyang Normal University, Nanyang, 473061, China
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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14
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Systematic Identification and Expression Analysis of the Auxin Response Factor (ARF) Gene Family in Ginkgo biloba L. Int J Mol Sci 2022; 23:ijms23126754. [PMID: 35743196 PMCID: PMC9223646 DOI: 10.3390/ijms23126754] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/04/2022] [Accepted: 06/14/2022] [Indexed: 12/10/2022] Open
Abstract
Auxin participates in various physiological and molecular response-related developmental processes and is a pivotal hormone that regulates phenotypic formation in plants. Auxin response factors (ARFs) are vital transcription factors that mediate downstream auxin signaling by explicitly binding to auxin-responsive genes' promoters. Here, to investigate the possible developmental regulatory functions of ARFs in Ginkgo biloba, through employing comprehensive bioinformatics, we recognized 15 putative GbARF members. Conserved domains and motifs, gene and protein structure, gene duplication, GO enrichment, transcriptome expression profiles, and qRT-PCR all showed that Group I and III members were highly conserved. Among them, GbARF10b and GbARF10a were revealed as transcriptional activators in the auxin response for the development of Ginkgo male flowers through sequences alignment, cis-elements analysis and GO annotation; the results were corroborated for the treatment of exogenous SA. Moreover, the GbARFs expansion occurred predominantly by segmental duplication, and most GbARFs have undergone purifying selection. The Ka/Ks ratio test identified the functional consistence of GbARF2a and GbARF2c, GbARF10b, and GbARF10a in tissue expression profiles and male flower development. In summary, our study established a new research basis for exploring Ginkgo GbARF members' roles in floral organ development and hormone response.
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15
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Genome-Wide Analysis of the WRKY Gene Family in Malus domestica and the Role of MdWRKY70L in Response to Drought and Salt Stresses. Genes (Basel) 2022; 13:genes13061068. [PMID: 35741830 PMCID: PMC9222762 DOI: 10.3390/genes13061068] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 02/05/2023] Open
Abstract
The WRKY transcription factors are unique regulatory proteins in plants, which are important in the stress responses of plants. In this study, 113 WRKY genes were identified from the apple genome GDDH13 and a comprehensive analysis was performed, including chromosome mapping, and phylogenetic, motif and collinearity analysis. MdWRKYs are expressed in different tissues, such as seeds, flowers, stems and leaves. We analyzed seven WRKY proteins in different groups and found that all of them were localized in the nucleus. Among the 113 MdWRKYs, MdWRKY70L was induced by both drought and salt stresses. Overexpression of it in transgenic tobacco plants conferred enhanced stress tolerance to drought and salt. The malondialdehyde content and relative electrolyte leakage values were lower, while the chlorophyll content was higher in transgenic plants than in the wild-type under stressed conditions. In conclusion, this study identified the WRKY members in the apple genome GDDH13, and revealed the function of MdWRKY70L in the response to drought and salt stresses.
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16
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Yang J, Zhao X, Chen Y, Li G, Li X, Xia M, Sun Z, Chen Y, Li Y, Yao L, Hou H. Identification, Structural, and Expression Analyses of SPX Genes in Giant Duckweed (Spirodela polyrhiza) Reveals Its Role in Response to Low Phosphorus and Nitrogen Stresses. Cells 2022; 11:cells11071167. [PMID: 35406731 PMCID: PMC8997716 DOI: 10.3390/cells11071167] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 01/25/2023] Open
Abstract
SPX genes play important roles in the coordinated utilization of nitrogen (N) and phosphorus (P) in plants. However, a genome-wide analysis of the SPX family is still lacking. In this study, the gene structure and phylogenetic relationship of 160 SPX genes were systematically analyzed at the genome-wide level. Results revealed that SPX genes were highly conserved in plants. All SPX genes contained the conserved SPX domain containing motifs 2, 3, 4, and 8. The 160 SPX genes were divided into five clades and the SPX genes within the same clade shared a similar motif composition. P1BS cis–elements showed a high frequency in the promoter region of SPXs, indicating that SPX genes could interact with the P signal center regulatory gene Phosphate Starvation Response1 (PHR1) in response to low P stress. Other cis–elements were also involved in plant development and biotic/abiotic stress, suggesting the functional diversity of SPXs. Further studies were conducted on the interaction network of three SpSPXs, revealing that these genes could interact with important components of the P signaling network. The expression profiles showed that SpSPXs responded sensitively to N and P deficiency stresses, thus playing a key regulatory function in P and N metabolism. Furthermore, the expression of SpSPXs under P and N deficiency stresses could be affected by environmental factors such as ABA treatment, osmotic, and LT stresses. Our study suggested that SpSPXs could be good candidates for enhancing the uptake ability of Spirodela polyrhiza for P nutrients in wastewater. These findings could broaden the understanding of the evolution and biological function of the SPX family and offer a foundation to further investigate this family in plants.
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Affiliation(s)
- Jingjing Yang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (J.Y.); (X.Z.); (Y.C.); (G.L.); (X.L.); (M.X.); (Z.S.); (Y.C.); (Y.L.)
| | - Xuyao Zhao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (J.Y.); (X.Z.); (Y.C.); (G.L.); (X.L.); (M.X.); (Z.S.); (Y.C.); (Y.L.)
| | - Yan Chen
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (J.Y.); (X.Z.); (Y.C.); (G.L.); (X.L.); (M.X.); (Z.S.); (Y.C.); (Y.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gaojie Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (J.Y.); (X.Z.); (Y.C.); (G.L.); (X.L.); (M.X.); (Z.S.); (Y.C.); (Y.L.)
| | - Xiaozhe Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (J.Y.); (X.Z.); (Y.C.); (G.L.); (X.L.); (M.X.); (Z.S.); (Y.C.); (Y.L.)
| | - Manli Xia
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (J.Y.); (X.Z.); (Y.C.); (G.L.); (X.L.); (M.X.); (Z.S.); (Y.C.); (Y.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zuoliang Sun
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (J.Y.); (X.Z.); (Y.C.); (G.L.); (X.L.); (M.X.); (Z.S.); (Y.C.); (Y.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yimeng Chen
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (J.Y.); (X.Z.); (Y.C.); (G.L.); (X.L.); (M.X.); (Z.S.); (Y.C.); (Y.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yixian Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (J.Y.); (X.Z.); (Y.C.); (G.L.); (X.L.); (M.X.); (Z.S.); (Y.C.); (Y.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lunguang Yao
- Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North Diversion Project of Henan Province, Nanyang 473061, China;
- Collaborative Innovation Center of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project of Henan Province, Nanyang Normal University, Nanyang 473061, China
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (J.Y.); (X.Z.); (Y.C.); (G.L.); (X.L.); (M.X.); (Z.S.); (Y.C.); (Y.L.)
- Correspondence: ; Tel.: +86-2768788691; Fax: +86-2768780123
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17
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Feng X, Abubakar AS, Yu C, Zhu A, Chen J, Chen K, Gao G, Wang X, Mou P, Shao D, Chen P. Analysis of WRKY Resistance Gene Family in Boehmeria nivea (L.) Gaudich: Crosstalk Mechanisms of Secondary Cell Wall Thickening and Cadmium Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:812988. [PMID: 35432436 PMCID: PMC9010656 DOI: 10.3389/fpls.2022.812988] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
A total of 60 WRKY family genes of ramie were identified in the ramie. The genes were unevenly distributed across 14 chromosomes in the specie and highly concentrated (72%) in the distal telomeric region. Phylogenetic analysis placed these genes into seven distinct subfamilies groups: I, II (a, b, c, d, e), and III, with group IIc containing only the variant of heptapetide sequence (WRKYGKK). Segmental duplication events (41.7%) was found to be the main driver of BnGWRKY evolution. Thirty eight from among the genes showed collinear relationships with WRKY genes from Arabidopsis thaliana, Cannabis sativa, Oryza sativa, and Zea mays. The number and density of stress and hormone responsives cis-acting elements were comparably higher than other elements, with abundant ARE and rare LTR cis-acting elements indicating the long-standing adaptability of ramie to its natural environment. GO and KEGG enrichment analysis of the WRKY target genes revealed their involvement in response to stimuli, immune system processes, transporter protein activity and antioxidant activity. Expression analysis show that most WRKYs were activated by the cadmium stress, more especially the BnGWRKY2, BnGWRKY15, BnGWRKY20, BnGWRKY50 and BnGWRKY58. Combining transcriptome, orthologous gene relationships and qPCR result, we established the possible involvement of BnGWRKY50 and BnGWRKY58 in crosstalk mechanism between secondary cell wall thickening and Cd2+ stress. This provided information into the role of BnGWRKY proteins in ramie secondary wall development and cadmium stress response to, and could serve as basis for improvement of the ramie.
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Affiliation(s)
- Xinkang Feng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Aminu Shehu Abubakar
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- Department of Agronomy, Bayero University Kano, Kano, Nigeria
| | - Chunming Yu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Aiguo Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jikang Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Kunmei Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Gang Gao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Xiaofei Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Pan Mou
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Deyi Shao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Ping Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
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18
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Zhao X, Yang J, Li G, Sun Z, Chen Y, Guo W, Li Y, Chen Y, Hou H. Identification, structure analysis, and transcript profiling of phosphate transporters under Pi deficiency in duckweeds. Int J Biol Macromol 2021; 188:595-608. [PMID: 34389388 DOI: 10.1016/j.ijbiomac.2021.08.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/04/2021] [Accepted: 08/04/2021] [Indexed: 11/16/2022]
Abstract
Phosphate transporters (PHTs) mediate the uptake and translocation of phosphate in plants. A comprehensive analysis of the PHT family in aquatic plant is still lacking. In this study, we identified 73 PHT members of six major PHT families from four duckweed species. The phylogenetic analysis, gene structure and protein characteristics analysis revealed that PHT genes are highly conserved among duckweeds. Interaction network and miRNA target prediction showed that SpPHTs could interact with the important components of the nitrate/phosphate signaling pathway, and spo-miR399 might be a central regulator that mediates phosphate signal network in giant duckweed (Spirodela polyrhiza). The modeled 3D structure of SpPHT proteins shared a high level of homology with template structures, which provide information to understand their functions at proteomic level. The expression profiles derived from transcriptome data and quantitative real-time PCR revealed that SpPHT genes are respond to exogenous stimuli and remarkably induced by phosphate starvation, phosphate is absorbed from aquatic environment by the whole duckweed plant. This study lays the foundation for further functional studies on PHT genes for genetic improvement and the promotion of phosphate uptake efficiency in duckweeds.
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Affiliation(s)
- Xuyao Zhao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China; College of Environment and Chemical Engineering, Pingdingshan University, Pingdingshan 467000, Henan, China
| | - Jingjing Yang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gaojie Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zuoliang Sun
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Chen
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjun Guo
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yixian Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yimeng Chen
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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