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Li J, Hu L, Luan Q, Zhang J, Feng X, Li H, Wang Z, He W. Mining key genes associated with phosphorus deficiency through genome-wide identification and characterization of cucumber SPX family genes. BMC PLANT BIOLOGY 2024; 24:699. [PMID: 39044149 PMCID: PMC11267760 DOI: 10.1186/s12870-024-05436-3] [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: 10/23/2023] [Accepted: 07/18/2024] [Indexed: 07/25/2024]
Abstract
BACKGROUND Proteins harboring the SPX domain are crucial for the regulation of phosphate (Pi) homeostasis in plants. This study aimed to identify and analyze the entire SPX gene family within the cucumber genome. RESULTS The cucumber genome encompassed 16 SPX domain-containing genes, which were distributed across six chromosomes and categorized into four distinct subfamilies: SPX, SPX-MFS, SPX-EXS and SPX-RING, based on their structure characteristics. Additionally, gene duplications and synteny analysis were conducted for CsSPXs, revealing that their promoter regions were enriched with a variety of hormone-responsive, biotic/abiotic stress and typical P1BS-related elements. Tissue expression profiling of CsSPX genes revealed that certain members were specifically expressed in particular organs, suggesting essential roles in cucumber growth and development. Under low Pi stress, CsSPX1 and CsSPX2 exhibited a particularly strong response to Pi starvation. It was observed that the cucumber cultivar Xintaimici displayed greater tolerance to low Pi compared to black-spined cucumber under low Pi stress conditions. Protein interaction networks for the 16 CsSPX proteins were predicted, and yeast two-hybrid assay revealed that CsPHR1 interacted with CsSPX2, CsSPX3, CsSPX4 and CsSPX5, implying their involvement in the Pi signaling pathway in conjunction with CsPHR1. CONCLUSION This research lays the foundation for further exploration of the function of the CsSPX genes in response to low Pi stress and for elucidating the underlying mechanism.
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Affiliation(s)
- Jialin Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Linyue Hu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Qianqian Luan
- Gansu Agricultural Engineering Technology Research Institute, Lanzhou, 730000, China
| | - Jingdan Zhang
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Xueru Feng
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Hongmei Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Zenghui Wang
- Shandong Institute of Pomology, Tai'an, Shandong, 271000, China.
| | - Wenxing He
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China.
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2
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Sganzerla Martinez G, Dutt M, Kumar A, Kelvin DJ. Multiple Protein Profiler 1.0 (MPP): A Webserver for Predicting and Visualizing Physiochemical Properties of Proteins at the Proteome Level. Protein J 2024:10.1007/s10930-024-10214-z. [PMID: 38980536 DOI: 10.1007/s10930-024-10214-z] [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] [Accepted: 06/04/2024] [Indexed: 07/10/2024]
Abstract
Determining the physicochemical properties of a protein can reveal important insights in their structure, biological functions, stability, and interactions with other molecules. Although tools for computing properties of proteins already existed, we could not find a comprehensive tool that enables the calculations of multiple properties for multiple input proteins on the proteome level at once. Facing this limitation, we developed Multiple Protein Profiler (MPP) 1.0 as an integrated tool that allows the profiling of 12 individual properties of multiple proteins in a significant manner. MPP provides a tabular and graphic visualization of properties of multiple proteins. The tool is freely accessible at https://mproteinprofiler.microbiologyandimmunology.dal.ca/ .
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Affiliation(s)
- Gustavo Sganzerla Martinez
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, B3H4H7, Canada
- Department of Pediatrics, Izaak Walton Killam (IWK) Health Center, Canadian Center for Vaccinology (CCfV), Halifax, NS, B3H4H7, Canada
- BioForge Canada Limited, Halifax, NS, Canada
| | - Mansi Dutt
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, B3H4H7, Canada
- Department of Pediatrics, Izaak Walton Killam (IWK) Health Center, Canadian Center for Vaccinology (CCfV), Halifax, NS, B3H4H7, Canada
- BioForge Canada Limited, Halifax, NS, Canada
| | - Anuj Kumar
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, B3H4H7, Canada
- Department of Pediatrics, Izaak Walton Killam (IWK) Health Center, Canadian Center for Vaccinology (CCfV), Halifax, NS, B3H4H7, Canada
- BioForge Canada Limited, Halifax, NS, Canada
| | - David J Kelvin
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, B3H4H7, Canada.
- Department of Pediatrics, Izaak Walton Killam (IWK) Health Center, Canadian Center for Vaccinology (CCfV), Halifax, NS, B3H4H7, Canada.
- BioForge Canada Limited, Halifax, NS, Canada.
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3
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Luo B, Sahito JH, Zhang H, Zhao J, Yang G, Wang W, Guo J, Zhang S, Ma P, Nie Z, Zhang X, Liu D, Wu L, Gao D, Gao S, Su S, Gishkori ZGN, Gao S. SPX family response to low phosphorus stress and the involvement of ZmSPX1 in phosphorus homeostasis in maize. FRONTIERS IN PLANT SCIENCE 2024; 15:1385977. [PMID: 39040504 PMCID: PMC11260721 DOI: 10.3389/fpls.2024.1385977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 06/17/2024] [Indexed: 07/24/2024]
Abstract
Phosphorus (P) is a crucial macronutrient for plant growth and development, and low-Pi stress poses a significant limitation to maize production. While the role of the SPX domain in encoding proteins involved in phosphate (Pi) homeostasis and signaling transduction has been extensively studied in other model plants, the molecular and functional characteristics of the SPX gene family members in maize remain largely unexplored. In this study, we identified six SPX members, and the phylogenetic analysis of ZmSPXs revealed a close relationship with SPX genes in rice. The promoter regions of ZmSPXs were abundant in biotic and abiotic stress-related elements, particularly associated with various hormone signaling pathways, indicating potential intersections between Pi signaling and hormone signaling pathways. Additionally, ZmSPXs displayed tissue-specific expression patterns, with significant and differential induction in anthers and roots, and were localized to the nucleus and cytoplasm. The interaction between ZmSPXs and ZmPHRs was established via yeast two-hybrid assays. Furthermore, overexpression of ZmSPX1 enhanced root sensitivity to Pi deficiency and high-Pi conditions in Arabidopsis thaliana. Phenotypic identification of the maize transgenic lines demonstrated the negative regulatory effect on the P concentration of stems and leaves as well as yield. Notably, polymorphic sites including 34 single-nucleotide polymorphisms (SNPs) and seven insertions/deletions (InDels) in ZmSPX1 were significantly associated with 16 traits of low-Pi tolerance index. Furthermore, significant sites were classified into five haplotypes, and haplotype5 can enhance biomass production by promoting root development. Taken together, our results suggested that ZmSPX family members possibly play a pivotal role in Pi stress signaling in plants by interacting with ZmPHRs. Significantly, ZmSPX1 was involved in the Pi-deficiency response verified in transgenic Arabidopsis and can affect the Pi concentration of maize tissues and yield. This work lays the groundwork for deeper exploration of the maize SPX family and could inform the development of maize varieties with improved Pi efficiency.
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Affiliation(s)
- Bowen Luo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Javed Hussain Sahito
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henen Agricultural University, Zhengzhou, China
| | - Haiying Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Jin Zhao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Guohui Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Wei Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Jianyong Guo
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Shuhao Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Peng Ma
- Maize Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, Sichuan, China
| | - Zhi Nie
- Sichuan Academy of Agricultural Sciences, Biotechnology and Nuclear Technology Research Institute, Chengdu, Sichuan, China
| | - Xiao Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Dan Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Ling Wu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Duojiang Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Shiqiang Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Shunzong Su
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | | | - Shibin Gao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
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4
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Zhuomeng L, Ji T, Chen Q, Xu C, Liu Y, Yang X, Li J, Yang F. Genome-wide identification and characterization of SPXdomain-containing genes family in eggplant. PeerJ 2024; 12:e17341. [PMID: 38827281 PMCID: PMC11141551 DOI: 10.7717/peerj.17341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 04/15/2024] [Indexed: 06/04/2024] Open
Abstract
Phosphorus is one of the lowest elements absorbed and utilized by plants in the soil. SPX domain-containing genes family play an important role in plant response to phosphate deficiency signaling pathway, and related to seed development, disease resistance, absorption and transport of other nutrients. However, there are no reports on the mechanism of SPX domain-containing genes in response to phosphorus deficiency in eggplant. In this study, the whole genome identification and functional analysis of SPX domain-containing genes family in eggplant were carried out. Sixteen eggplant SPX domain-containing genes were identified and divided into four categories. Subcellular localization showed that these proteins were located in different cell compartments, including nucleus and membrane system. The expression patterns of these genes in different tissues as well as under phosphate deficiency with auxin were explored. The results showed that SmSPX1, SmSPX5 and SmSPX12 were highest expressed in roots. SmSPX1, SmSPX4, SmSPX5 and SmSPX14 were significantly induced by phosphate deficiency and may be the key candidate genes in response to phosphate starvation in eggplant. Among them, SmSPX1 and SmSPX5 can be induced by auxin under phosphate deficiency. In conclusion, our study preliminary identified the SPX domain genes in eggplant, and the relationship between SPX domain-containing genes and auxin was first analyzed in response to phosphate deficiency, which will provide theoretical basis for improving the absorption of phosphorus in eggplants through molecular breeding technology.
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Affiliation(s)
- Li Zhuomeng
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai an, China
| | - Tuo Ji
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai an, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Tai an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai an, China
| | - Qi Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai an, China
| | - Chenxiao Xu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai an, China
| | - Yuqing Liu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai an, China
| | - Xiaodong Yang
- Weifang Academy of Agricultural Science, Weifang, China
| | - Jing Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai an, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Tai an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai an, China
| | - Fengjuan Yang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai an, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Tai an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai an, China
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5
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Wang M, Wang L, Wang S, Zhang J, Fu Z, Wu P, Yang A, Wu D, Sun G, Wang C. Identification and Analysis of lncRNA and circRNA Related to Wheat Grain Development. Int J Mol Sci 2024; 25:5484. [PMID: 38791522 PMCID: PMC11122269 DOI: 10.3390/ijms25105484] [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: 04/14/2024] [Revised: 05/04/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
The role of lncRNA and circRNA in wheat grain development is still unclear. The objectives of this study were to characterize the lncRNA and circRNA in the wheat grain development and to construct the interaction network among lncRNA, circRNA, and their target miRNA to propose a lncRNA-circRNA-miRNA module related to wheat grain development. Full transcriptome sequencing on two wheat varieties (Annong 0942 and Anke 2005) with significant differences in 1000-grain weight at 10 d (days after pollination), 20 d, and 30 d of grain development were conducted. We detected 650, 736, and 609 differentially expressed lncRNA genes, and 769, 1054, and 1062 differentially expressed circRNA genes in the grains of 10 days, 20 days and 30 days after pollination between Annong 0942 and Anke 2005, respectively. An analysis of the lncRNA-miRNA and circRNA-miRNA targeting networks reveals that circRNAs exhibit a more complex and extensive interaction network in the development of cereal grains and the formation of grain shape. Central to these interactions are tae-miR1177, tae-miR1128, and tae-miR1130b-3p. In contrast, lncRNA genes only form a singular network centered around tae-miR1133 and tae-miR5175-5p when comparing between varieties. Further analysis is conducted on the underlying genes of all target miRNAs, we identified TaNF-YB1 targeted by tae-miR1122a and TaTGW-7B targeted by miR1130a as two pivotal regulatory genes in the development of wheat grains. The quantitative real-time PCR (qRT-PCR) and dual-luciferase reporter assays confirmed the target regulatory relationships between miR1130a-TaTGW-7B and miR1122a-TaNF-YB1. We propose a network of circRNA and miRNA-mediated gene regulation in the development of wheat grains.
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Affiliation(s)
- Meng Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Lu Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Shuanghong Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Junli Zhang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Zhe Fu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Panpan Wu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Anqi Yang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Dexiang Wu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
| | - Genlou Sun
- Biology Department, Saint Mary’s University, Halifax, NS B3H 3C3, Canada
| | - Chengyu Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China (A.Y.); (C.W.)
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6
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Wang Z, Zhang X, Yang X, Tang H, Feng L, Yin Y, Li J. Evolution of the SPX gene family and its role in the response mechanism to low phosphorus stress in self-rooted apple stock. BMC Genomics 2024; 25:488. [PMID: 38755552 PMCID: PMC11108120 DOI: 10.1186/s12864-024-10402-2] [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: 11/02/2023] [Accepted: 05/09/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Phosphorus plays a key role in plant adaptation to adversity and plays a positive role in the yield and quality formation of apples. Genes of the SPX domain-containing family are widely involved in the regulation of phosphorus signalling networks. However, the mechanisms controlling phosphorus deficiency are not completely understood in self-rooted apple stock. RESULTS In this study, 26 members of the apple SPX gene family were identified by genome-wide analysis, and further divided into four subfamilies (SPX, SPX-MFS, SPX-EXS, and SPX-RING) based on their structural features. The chromosome distribution and gene duplications of MdSPXs were also examined. The promoter regions of MdSPXs were enriched for multiple biotic/abiotic stresses, hormone responses and typical P1BS-related elements. Analysis of the expression levels of 26 MdSPXs showed that some members were remarkably induced when subjected to low phosphate (Pi) stress, and in particular MdSPX2, MdSPX3, and MdPHO1.5 exhibited an intense response to low Pi stress. MdSPX2 and MdSPX3 showed significantly divergent expression levels in low Pi sensitive and insensitive apple species. Protein interaction networks were predicted for 26 MdSPX proteins. The interaction of MdPHR1 with MdSPX2, MdSPX3, MdSPX4, and MdSPX6 was demonstrated by yeast two-hybrid assay, suggesting that these proteins might be involved in the Pi-signaling pathway by interacting with MdPHR1. CONCLUSION This research improved the understanding of the apple SPX gene family and contribute to future biological studies of MdSPX genes in self-rooted apple stock.
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Affiliation(s)
- Zenghui Wang
- Shandong Institute of Pomology, Tai'an, 271000, Shandong, China
| | - Xiaowen Zhang
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Xuemei Yang
- Shandong Institute of Pomology, Tai'an, 271000, Shandong, China
| | - Haixia Tang
- Shandong Institute of Pomology, Tai'an, 271000, Shandong, China
| | - Lijuan Feng
- Shandong Institute of Pomology, Tai'an, 271000, Shandong, China
| | - Yanlei Yin
- Shandong Institute of Pomology, Tai'an, 271000, Shandong, China.
| | - Jialin Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China.
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7
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Qi T, Yang W, Hassan MJ, Liu J, Yang Y, Zhou Q, Li H, Peng Y. Genome-wide identification of Aux/IAA gene family in white clover (Trifolium repens L.) and functional verification of TrIAA18 under different abiotic stress. BMC PLANT BIOLOGY 2024; 24:346. [PMID: 38684940 PMCID: PMC11057079 DOI: 10.1186/s12870-024-05034-3] [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: 01/19/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND White clover (Trifolium repens L.) is an excellent leguminous cool-season forage with a high protein content and strong nitrogen-fixing ability. Despite these advantages, its growth and development are markedly sensitive to environmental factors. Indole-3-acetic acid (IAA) is the major growth hormone in plants, regulating plant growth, development, and response to adversity. Nevertheless, the specific regulatory functions of Aux/IAA genes in response to abiotic stresses in white clover remain largely unexplored. RESULTS In this study, we identified 47 Aux/IAA genes in the white clover genome, which were categorized into five groups based on phylogenetic analysis. The TrIAAs promoter region co-existed with different cis-regulatory elements involved in developmental and hormonal regulation, and stress responses, which may be closely related to their diverse regulatory roles. Collinearity analysis showed that the amplification of the TrIAA gene family was mainly carried out by segmental duplication. White clover Aux/IAA genes showed different expression patterns in different tissues and under different stress treatments. In addition, we performed a yeast two-hybrid analysis to investigate the interaction between white clover Aux/IAA and ARF proteins. Heterologous expression indicated that TrIAA18 could enhance stress tolerance in both yeast and transgenic Arabidopsis thaliana. CONCLUSION These findings provide new scientific insights into the molecular mechanisms of growth hormone signaling in white clover and its functional characteristics in response to environmental stress.
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Affiliation(s)
- Tiangang Qi
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Weiqiang Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Muhammad Jawad Hassan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiefang Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yujiao Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qinyu Zhou
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hang Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yan Peng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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8
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Madison I, Gillan L, Peace J, Gabrieli F, Van den Broeck L, Jones JL, Sozzani R. Phosphate starvation: response mechanisms and solutions. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6417-6430. [PMID: 37611151 DOI: 10.1093/jxb/erad326] [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: 12/23/2022] [Accepted: 08/21/2023] [Indexed: 08/25/2023]
Abstract
Phosphorus is essential to plant growth and agricultural crop yields, yet the challenges associated with phosphorus fertilization in agriculture, such as aquatic runoff pollution and poor phosphorus bioavailability, are increasingly difficult to manage. Comprehensively understanding the dynamics of phosphorus uptake and signaling mechanisms will inform the development of strategies to address these issues. This review describes regulatory mechanisms used by specific tissues in the root apical meristem to sense and take up phosphate from the rhizosphere. The major regulatory mechanisms and related hormone crosstalk underpinning phosphate starvation responses, cellular phosphate homeostasis, and plant adaptations to phosphate starvation are also discussed, along with an overview of the major mechanism of plant systemic phosphate starvation responses. Finally, this review discusses recent promising genetic engineering strategies for improving crop phosphorus use and computational approaches that may help further design strategies for improved plant phosphate acquisition. The mechanisms and approaches presented include a wide variety of species including not only Arabidopsis but also crop species such as Oryza sativa (rice), Glycine max (soybean), and Triticum aestivum (wheat) to address both general and species-specific mechanisms and strategies. The aspects of phosphorus deficiency responses and recently employed strategies of improving phosphate acquisition that are detailed in this review may provide insights into the mechanisms or phenotypes that may be targeted in efforts to improve crop phosphorus content and plant growth in low phosphorus soils.
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Affiliation(s)
- Imani Madison
- Plant and Microbial Biology Department and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27695, USA
| | - Lydia Gillan
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Jasmine Peace
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Flavio Gabrieli
- Dipartimento di Ingegneria Industriale (DII), Università degli studi di Padova, Padova, Italy
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali (DSA3), Università degli Studi di Perugia, Perugia, Italy
| | - Lisa Van den Broeck
- Plant and Microbial Biology Department and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27695, USA
| | - Jacob L Jones
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Rosangela Sozzani
- Plant and Microbial Biology Department and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27695, USA
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9
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Liang J, Lu L, Zhang W, Chi M, Shen M, An C, Chen S, Wang X, Liu R, Qin Y, Zheng P. Comprehensive characterization and expression analysis of enzymatic antioxidant gene families in passion fruit ( Passiflora edulis). iScience 2023; 26:108329. [PMID: 38026217 PMCID: PMC10656276 DOI: 10.1016/j.isci.2023.108329] [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: 07/25/2023] [Revised: 09/15/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Passion fruit, a valuable tropical fruit, faces climate-related growth challenges. Antioxidant enzymes are vital for both stress protection and growth regulation in plants. We first provided systemic analysis of enzymatic antioxidant gene families in passion fruit, identifying 90 members including 11 PeSODs, 45 PeAPXs, 8 PeCATs, 7 PeGPXs, 6 PeMDHARs, 8 PeDHARs, and 5 PeGRs. Gene members in each gene family with same subcellular localization showed closer phylogenetic relationship. Many antioxidant genes exhibited tissue- or developmental stage-specific expression patterns during floral and fruit development, with some widely expressed. Their co-expressed genes were linked to photosynthesis and energy metabolism, suggesting roles in protecting highly proliferating tissues from oxidative damage. Potential genes for enhancing temperature stress resistance were identified. The involvement of diverse regulatory factors including miRNAs, transcription factors, and CREs might contribute to the complex roles of antioxidant genes. This study informs future research on antioxidant genes and passion fruit breeding.
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Affiliation(s)
- Jianxiang Liang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lin Lu
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenbin Zhang
- Xinluo Breeding Center for Excellent Germplasms, Longyan 361000, China
| | - Ming Chi
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mengqian Shen
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chang An
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shengzhen Chen
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaomei Wang
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning Investigation Station of South Subtropical Fruit Trees, Ministry of Agriculture, Nanning 530004, China
| | - Ruoyu Liu
- Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan Qin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ping Zheng
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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10
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Chen J, Han X, Liu L, Yang B, Zhuo R, Yao X. Genome-Wide Detection of SPX Family and Profiling of CoSPX-MFS3 in Regulating Low-Phosphate Stress in Tea-Oil Camellia. Int J Mol Sci 2023; 24:11552. [PMID: 37511309 PMCID: PMC10380294 DOI: 10.3390/ijms241411552] [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: 07/01/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Camellia oleifera a member of the family Theaceae, is a phosphorus (P) tolerator native to southern China. The SPX gene family critically regulates plant growth and development and maintains phosphate (Pi) homeostasis. However, the involvement of SPX genes in Pi signaling in Tea-Oil Camellia remains unknown. In this work, 20 SPX genes were identified and categorized into four subgroups. Conserved domains, motifs, gene structure, chromosomal location and gene duplication events were also investigated in the SPX gene family. Defense and stress responsiveness cis-elements were identified in the SPX gene promoters, which participated in low-Pi stress responses. Based on transcriptome data and qRT-PCR results, nine CoSPX genes had similar expression patterns and eight genes (except CoPHO1H3) were up-regulated at 30 days after exposure to low-Pi stress. CoSPX-MFS3 was selected as a key candidate gene by WGCNA analysis. CoSPX-MFS3 was a tonoplast protein. Overexpression of CoSPX-MFS3 in Arabidopsis promoted the accumulation of total P content and decreased the anthocyanin content. Overexpression of CoSPX-MFS3 could enhance low-Pi tolerance by increased biomass and organic acid contents in transgenic Arabidopsis lines. Furthermore, the expression patterns of seven phosphate starvation genes were higher in transgenic Arabidopsis than those in the wild type. These results highlight novel physiological roles of the SPX family genes in C. oleifera under low-Pi stress, and lays the foundation for a deeper knowledge of the response mechanism of C. oleifera to low-Pi stress.
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Affiliation(s)
- Juanjuan Chen
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
- Forestry Faculty, Nanjing Forestry University, Nanjing 210037, China
| | - Xiaojiao Han
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Linxiu Liu
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Bingbing Yang
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Renying Zhuo
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Xiaohua Yao
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
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11
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Mishra DC, Majumdar SG, Kumar A, Bhati J, Chaturvedi KK, Kumar RR, Goswami S, Rai A, Budhlakoti N. Regulatory Networks of lncRNAs, miRNAs, and mRNAs in Response to Heat Stress in Wheat (Triticum Aestivum L.): An Integrated Analysis. Int J Genomics 2023; 2023:1774764. [PMID: 37033711 PMCID: PMC10079388 DOI: 10.1155/2023/1774764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/25/2022] [Accepted: 09/03/2022] [Indexed: 04/03/2023] Open
Abstract
Climate change has become a major source of concern, particularly in agriculture, because it has a significant impact on the production of economically important crops such as wheat, rice, and maize. In the present study, an attempt has been made to identify differentially expressed heat stress-responsive long non-coding RNAs (lncRNAs) in the wheat genome using publicly available wheat transcriptome data (24 SRAs) representing two conditions, namely, control and heat-stressed. A total of 10,965 lncRNAs have been identified and, among them, 153, 143, and 211 differentially expressed transcripts have been found under 0 DAT, 1 DAT, and 4 DAT heat-stress conditions, respectively. Target prediction analysis revealed that 4098 lncRNAs were targeted by 119 different miRNA responses to a plethora of environmental stresses, including heat stress. A total of 171 hub genes had 204 SSRs (simple sequence repeats), and a set of target sequences had SNP potential as well. Furthermore, gene ontology analysis revealed that the majority of the discovered lncRNAs are engaged in a variety of cellular and biological processes related to heat stress responses. Furthermore, the modeled three-dimensional (3D) structures of hub genes encoding proteins, which had an appropriate range of similarity with solved structures, provided information on their structural roles. The current study reveals many elements of gene expression regulation in wheat under heat stress, paving the way for the development of improved climate-resilient wheat cultivars.
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12
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Luo J, Liu Z, Yan J, Shi W, Ying Y. Genome-Wide Identification of SPX Family Genes and Functional Characterization of PeSPX6 and PeSPX-MFS2 in Response to Low Phosphorus in Phyllostachys edulis. PLANTS (BASEL, SWITZERLAND) 2023; 12:1496. [PMID: 37050121 PMCID: PMC10096891 DOI: 10.3390/plants12071496] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/10/2023] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
Moso bamboo (Phyllostachys edulis) is the most widely distributed bamboo species in the subtropical regions of China. Due to the fast-growing characteristics of P. edulis, its growth requires high nutrients, including phosphorus. Previous studies have shown that SPX proteins play key roles in phosphorus signaling and homeostasis. However, the systematic identification, molecular characterization, and functional characterization of the SPX gene family have rarely been reported in P. edulis. In this study, 23 SPXs were identified and phylogenetic analysis showed that they were classified into three groups and distributed on 13 chromosomes. The analysis of conserved domains indicated that there was a high similarity between PeSPXs among SPX proteins in other species. RNA sequencing and qRT-PCR analysis indicated that PeSPX6 and PeSPX-MFS2, which were highly expressed in roots, were clearly upregulated under low phosphorus. Co-expression network analysis and a dual luciferase experiment in tobacco showed that PeWRKY6 positively regulated the PeSPX6 expression, while PeCIGR1-2, PeMYB20, PeWRKY6, and PeWRKY53 positively regulated the PeSPX-MFS2 expression. Overall, these results provide a basis for the identification of SPX genes in P. edulis and further exploration of their functions in mediating low phosphorus responses.
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Liang J, Fang Y, An C, Yao Y, Wang X, Zhang W, Liu R, Wang L, Aslam M, Cheng Y, Qin Y, Zheng P. Genome-wide identification and expression analysis of the bHLH gene family in passion fruit (Passiflora edulis) and its response to abiotic stress. Int J Biol Macromol 2023; 225:389-403. [PMID: 36400210 DOI: 10.1016/j.ijbiomac.2022.11.076] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/23/2022] [Accepted: 11/01/2022] [Indexed: 11/17/2022]
Abstract
Passion fruit is a tropical fruit crop with significant agricultural, economic and ornamental values. The growth and development of passion fruit are greatly affected by climatic conditions. In plants, the basic helix-loop-helix (bHLH) gene family plays essential roles in the floral organ and fruit development, as well as stress response. However, the characteristics and functions of the bHLH genes of passion fruit remain unclear. Here, 138 passion fruit bHLH members were identified and classified into 20 subfamilies. The structural analysis illustrated that PebHLH proteins of the specific subfamily are relatively conserved. Collinearity analysis indicated that the expansion of the PebHLH gene family mainly took place by segmental duplication, and the structural diversity of duplicated genes might contribute to their functional diversity. PebHLHs, which potentially regulate different floral organ and fruit development, were further screened out, and many of these genes were differentially expressed under various stress treatments. The co-presence of different cis-regulatory elements involved in developmental regulation, hormone and stress responses in the promoter regions of PebHLHs might be closely related to their diverse regulatory roles. Overall, this study will be helpful for further functional investigation of PebHLHs and provides clues for improvement of the passion fruit breeding.
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Affiliation(s)
- Jianxiang Liang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yunying Fang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chang An
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Yuanbin Yao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaomei Wang
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning Investigation Station of South Subtropical Fruit Trees, Ministry of Agriculture, Nanning 530004, China
| | - Wenbin Zhang
- Xinluo Breeding Center for Excellent Germplasms, Longyan 361000, China
| | - Ruoyu Liu
- Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lulu Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Mohammad Aslam
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yan Cheng
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan Qin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China; Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Ping Zheng
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Hou H, Kong X, Zhou Y, Yin C, Jiang Y, Qu H, Li T. Genome-wide identification and characterization of bZIP transcription factors in relation to litchi (Litchi chinensis Sonn.) fruit ripening and postharvest storage. Int J Biol Macromol 2022; 222:2176-2189. [DOI: 10.1016/j.ijbiomac.2022.09.292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/24/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022]
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15
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Tyagi S, Jha SK, Kumar A, Saripalli G, Bhurta R, Hurali DT, Sathee L, Mallick N, Mir RR, Chinnusamy V. Genome-wide characterization and identification of cyclophilin genes associated with leaf rust resistance in bread wheat (Triticum aestivum L.). Front Genet 2022; 13:972474. [PMID: 36246582 PMCID: PMC9561851 DOI: 10.3389/fgene.2022.972474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Cyclophilins (CYPs) are a group of highly conserved proteins involved in host-pathogen interactions in diverse plant species. However, the role of CYPs during disease resistance in wheat remains largely elusive. In the present study, the systematic genome-wide survey revealed a set of 81 TaCYP genes from three subfamilies (GI, GII, and GIII) distributed on all 21 wheat chromosomes. The gene structures of TaCYP members were found to be highly variable, with 1–14 exons/introns and 15 conserved motifs. A network of miRNA targets with TaCYPs demonstrated that TaCYPs were targeted by multiple miRNAs and vice versa. Expression profiling was done in leaf rust susceptible Chinese spring (CS) and the CS-Ae. Umbellulata derived resistant IL “Transfer (TR). Three homoeologous TaCYP genes (TaCYP24, TaCYP31, and TaCYP36) showed high expression and three homoeologous TaCYP genes (TaCYP44, TaCYP49, and TaCYP54) showed low expression in TR relative to Chinese Spring. Most of the other TaCYPs showed comparable expression changes (down- or upregulation) in both contrasting TR and CS. Expression of 16 TaCYPs showed significant association (p < 0.05) with superoxide radical and hydrogen peroxide abundance, suggesting the role of TaCYPs in downstream signaling processes during wheat-leaf rust interaction. The differentially expressing TaCYPs may be potential targets for future validation using transgenic (overexpression, RNAi or CRISPR-CAS) approaches and for the development of leaf rust-resistant wheat genotypes.
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Affiliation(s)
- Sandhya Tyagi
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shailendra Kumar Jha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Shailendra Kumar Jha, ; Vinod,
| | - Anuj Kumar
- Centre for Agricultural Bioinformatics (CABin), Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Gautam Saripalli
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, United States
| | - Ramesh Bhurta
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Deepak T. Hurali
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Lekshmy Sathee
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Niharika Mallick
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), Wadura Campus, Srinagar, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Ou K, He X, Cai K, Zhao W, Jiang X, Ai W, Ding Y, Cao Y. Phosphate-Solubilizing Pseudomonas sp. Strain WS32 Rhizosphere Colonization-Induced Expression Changes in Wheat Roots. Front Microbiol 2022; 13:927889. [PMID: 35847091 PMCID: PMC9279123 DOI: 10.3389/fmicb.2022.927889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Rhizosphere colonization is a pre-requisite for the favorable application of plant growth-promoting rhizobacteria (PGPR). Exchange and mutual recognition of signaling molecules occur frequently between plants and microbes. Here, the luciferase luxAB gene was electrotransformed into the phosphate-solubilizing strain Pseudomonas sp. WS32, a type of plant growth-promoting rhizobacterium with specific affinity for wheat. A labeled WS32 strain (WS32-L) was applied to determine the temporal and spatial traits of colonization within the wheat rhizosphere using rhizoboxes experimentation under natural condition. The effects of colonization on wheat root development and seedling growth were evaluated, and RNA sequencing (RNA-seq) was performed to explore the transcriptional changes that occur in wheat roots under WS32 colonization. The results showed that WS32-L could survive in the wheat rhizosphere for long periods and could expand into new zones following wheat root extension. Significant increases in seedling fresh and dry weight, root fresh and dry weight, root surface area, number of root tips, and phosphorus accumulation in the wheat leaves occurred in response to WS32 rhizosphere colonization. RNA-seq analysis showed that a total of 1485 genes in wheat roots were differentially expressed between the inoculated conditions and the uninoculated conditions. Most of the transcriptional changes occurred for genes annotated to the following functional categories: "phosphorus and other nutrient transport," "hormone metabolism and organic acid secretion," "flavonoid signal recognition," "membrane transport," and "transcription factor regulation." These results are therefore valuable to future studies focused on the molecular mechanisms underlying the growth-promoting activities of PGPR on their host plants.
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Affiliation(s)
- Kangmiao Ou
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiangyi He
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Ke Cai
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Weirong Zhao
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiaoxun Jiang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Wenfeng Ai
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yue Ding
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yuanyuan Cao
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, Anhui Agricultural University, Hefei, China
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17
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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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18
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Hao Y, Hao M, Cui Y, Kong L, Wang H. Genome-wide survey of the dehydrin genes in bread wheat (Triticum aestivum L.) and its relatives: identification, evolution and expression profiling under various abiotic stresses. BMC Genomics 2022; 23:73. [PMID: 35065618 PMCID: PMC8784006 DOI: 10.1186/s12864-022-08317-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 01/13/2022] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Bread wheat (Triticum aestivum) is an important staple cereal grain worldwide. The ever-increasing environmental stress makes it very important to mine stress-resistant genes for wheat breeding programs. Therefore, dehydrin (DHN) genes can be considered primary candidates for such programs, since they respond to multiple stressors. RESULTS In this study, we performed a genome-wide analysis of the DHN gene family in the genomes of wheat and its three relatives. We found 55 DHN genes in T. aestivum, 31 in T. dicoccoides, 15 in T. urartu, and 16 in Aegilops tauschii. The phylogenetic, synteny, and sequence analyses showed we can divide the DHN genes into five groups. Genes in the same group shared similar conserved motifs and potential function. The tandem TaDHN genes responded strongly to drought, cold, and high salinity stresses, while the non-tandem genes respond poorly to all stress conditions. According to the interaction network analysis, the cooperation of multiple DHN proteins was vital for plants in combating abiotic stress. CONCLUSIONS Conserved, duplicated DHN genes may be important for wheat being adaptable to a different stress conditions, thus contributing to its worldwide distribution as a staple food. This study not only highlights the role of DHN genes help the Triticeae species against abiotic stresses, but also provides vital information for the future functional studies in these crops.
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Affiliation(s)
- Yongchao Hao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018, China
| | - Ming Hao
- College of Forestry, Shandong Agricultural University, Taian, 271018, China
| | - Yingjie Cui
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018, China
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018, China
| | - Hongwei Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018, China.
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Nezamivand-Chegini M, Ebrahimie E, Tahmasebi A, Moghadam A, Eshghi S, Mohammadi-Dehchesmeh M, Kopriva S, Niazi A. New insights into the evolution of SPX gene family from algae to legumes; a focus on soybean. BMC Genomics 2021; 22:915. [PMID: 34969367 PMCID: PMC8717665 DOI: 10.1186/s12864-021-08242-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/09/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND SPX-containing proteins have been known as key players in phosphate signaling and homeostasis. In Arabidopsis and rice, functions of some SPXs have been characterized, but little is known about their function in other plants, especially in the legumes. RESULTS We analyzed SPX gene family evolution in legumes and in a number of key species from algae to angiosperms. We found that SPX harboring proteins showed fluctuations in domain fusions from algae to the angiosperms with, finally, four classes appearing and being retained in the land plants. Despite these fluctuations, Lysine Surface Cluster (KSC), and the third residue of Phosphate Binding Sites (PBS) showed complete conservation in almost all of SPXs except few proteins in Selaginella moellendorffii and Papaver sumniferum, suggesting they might have different ligand preferences. In addition, we found that the WGD/segmentally or dispersed duplication types were the most frequent contributors to the SPX expansion, and that there is a positive correlation between the amount of WGD contribution to the SPX expansion in individual species and its number of EXS genes. We could also reveal that except SPX class genes, other classes lost the collinearity relationships among Arabidopsis and legume genomes. The sub- or neo-functionalization of the duplicated genes in the legumes makes it difficult to find the functional orthologous genes. Therefore, we used two different methods to identify functional orthologs in soybean and Medicago. High variance in the dynamic and spatial expression pattern of GmSPXs proved the new or sub-functionalization in the paralogs. CONCLUSION This comprehensive analysis revealed how SPX gene family evolved from algae to legumes and also discovered several new domains fused to SPX domain in algae. In addition, we hypothesized that there different phosphate sensing mechanisms might occur in S. moellendorffii and P. sumniferum. Finally, we predicted putative functional orthologs of AtSPXs in the legumes, especially, orthologs of AtPHO1, involved in long-distance Pi transportation. These findings help to understand evolution of phosphate signaling and might underpin development of new legume varieties with improved phosphate use efficiency.
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Affiliation(s)
| | - Esmaeil Ebrahimie
- Institute of biotechnology, Shiraz university, Shiraz, Iran
- La Trobe Genomics Research Platform, School of Life Sciences, College of Science, Health and Engineering, La Trobe University, Melbourne, VIC, 3086, Australia
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, SA, 5371, Australia
| | | | - Ali Moghadam
- Institute of biotechnology, Shiraz university, Shiraz, Iran
| | - Saeid Eshghi
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz, Iran
| | | | - Stanislav Kopriva
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
| | - Ali Niazi
- Institute of biotechnology, Shiraz university, Shiraz, Iran.
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20
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Xiao J, Xie X, Li C, Xing G, Cheng K, Li H, Liu N, Tan J, Zheng W. Identification of SPX family genes in the maize genome and their expression under different phosphate regimes. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 168:211-220. [PMID: 34649024 DOI: 10.1016/j.plaphy.2021.09.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 08/31/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
Many studies have revealed that SPX (SYG1/Pho81/XPR1) family genes play a key role in signal transduction related to phosphorus (P) deficiency in plants. Here, we identified 33 SPX gene family members in maize through genome-wide analysis and classified them into 4 subfamilies according to SPX structural characteristics (SPX, SPX-MFS, SPX-EXS and SPX-RING). The promoter regions of ZmSPXs are rich in biotic/abiotic-related stress elements. The quantitative real-time PCR analysis of 33 ZmSPXs revealed that all members except for ZmSPX3 of the SPX subfamily were significantly induced under P-deficient conditions, especially ZmSPX4.1 and ZmSPX4.2, which showed strong responses to low P stress and exhibited remarkably different expression patterns in low Pi sensitive and insensitive cultivars of maize. These results suggested that the SPX subfamily might play pivotal roles in P stress sensing and response. Experimental observations of subcellular localization in maize protoplasts indicated the following results, implying multiple roles in cell metabolism: ZmSPX2, ZmSPX5 and ZmSPX6 localized in the nucleus; ZmSPX1 and ZmSPX3 localized in the nucleus and cytoplasm; and ZmSPX4.2 localized in the chloroplast. A Y2H assay suggested that ZmPHR1 could interact with ZmSPX3, ZmSPX4.2, ZmSPX5, and ZmSPX6, indicating the involvement of these proteins in the P stress response in a ZmPHR1-mediated manner.
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Affiliation(s)
- Jibin Xiao
- Collaborative Innovation Center of Henan Grain Crops / State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Xuanmin Xie
- Collaborative Innovation Center of Henan Grain Crops / State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Chuang Li
- Collaborative Innovation Center of Henan Grain Crops / State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Guozhen Xing
- Collaborative Innovation Center of Henan Grain Crops / State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Kun Cheng
- Collaborative Innovation Center of Henan Grain Crops / State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Hui Li
- College of Resource and Environment, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Na Liu
- Collaborative Innovation Center of Henan Grain Crops / State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Jinfang Tan
- College of Resource and Environment, Henan Agricultural University, Zhengzhou, 450002, China; School of Agriculture, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Wenming Zheng
- Collaborative Innovation Center of Henan Grain Crops / State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China.
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21
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Exploration of wheat yellow mosaic virus-responsive miRNAs and their targets in wheat by miRNA and degradome sequencing. J Biosci 2021. [DOI: 10.1007/s12038-021-00207-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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22
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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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Xu X, Zhang L, Zhao W, Fu L, Han Y, Wang K, Yan L, Li Y, Zhang XH, Min DH. Genome-wide analysis of the serine carboxypeptidase-like protein family in Triticum aestivum reveals TaSCPL184-6D is involved in abiotic stress response. BMC Genomics 2021; 22:350. [PMID: 33992092 PMCID: PMC8126144 DOI: 10.1186/s12864-021-07647-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/21/2021] [Indexed: 12/17/2022] Open
Abstract
Background The serine carboxypeptidase-like protein (SCPL) family plays a vital role in stress response, growth, development and pathogen defense. However, the identification and functional analysis of SCPL gene family members have not yet been performed in wheat. Results In this study, we identified a total of 210 candidate genes encoding SCPL proteins in wheat. According to their structural characteristics, it is possible to divide these members into three subfamilies: CPI, CPII and CPIII. We uncovered a total of 209 TaSCPL genes unevenly distributed across 21 wheat chromosomes, of which 65.7% are present in triads. Gene duplication analysis showed that ~ 10.5% and ~ 64.8% of the TaSCPL genes are derived from tandem and segmental duplication events, respectively. Moreover, the Ka/Ks ratios between duplicated TaSCPL gene pairs were lower than 0.6, which suggests the action of strong purifying selection. Gene structure analysis showed that most of the TaSCPL genes contain multiple introns and that the motifs present in each subfamily are relatively conserved. Our analysis on cis-acting elements showed that the promoter sequences of TaSCPL genes are enriched in drought-, ABA- and MeJA-responsive elements. In addition, we studied the expression profiles of TaSCPL genes in different tissues at different developmental stages. We then evaluated the expression levels of four TaSCPL genes by qRT-PCR, and selected TaSCPL184-6D for further downstream analysis. The results showed an enhanced drought and salt tolerance among TaSCPL184-6D transgenic Arabidopsis plants, and that the overexpression of the gene increased proline and decreased malondialdehyde levels, which might help plants adapting to adverse environments. Our results provide comprehensive analyses of wheat SCPL genes that might work as a reference for future studies aimed at improving drought and salt tolerance in wheat. Conclusions We conducte a comprehensive bioinformatic analysis of the TaSCPL gene family in wheat, which revealing the potential roles of TaSCPL genes in abiotic stress. Our analysis also provides useful resources for improving the resistance of wheat. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07647-6.
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Affiliation(s)
- Xiaomin Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Lili Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Wan Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Liang Fu
- Xinxiang Academy of Agricultural Sciences of He'nan Province, Xinxiang, China
| | - Yuxuan Han
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Keke Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Luyu Yan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Ye Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiao-Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
| | - Dong-Hong Min
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.
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Singh G, Tiwari A, Choudhir G, P H, Kumar A, Sharma S. Unraveling the potential role of bioactive molecules produced by Trichoderma spp. as inhibitors of tomatinase enzyme having an important role in wilting disease: an in-silico approach. J Biomol Struct Dyn 2021; 40:7535-7544. [PMID: 33719892 DOI: 10.1080/07391102.2021.1898476] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Tomatinase; a saponin detoxification enzyme produced by Fusarium oxysporumf.sp. lycopersici is reported as a causative agent for wilting disease in tomato crops. The disease is instigated by inhibiting the activity of α-tomatine. Trichoderma spp. widely used as biocontrol agent play an essential role in plant growth and pathogen control. In the current study, an in-silico approach using substrate docking, molecular dynamics and MM/PBSA analysis was used to evaluate the potential role of bioactive metabolites produced by Trichoderma spp. The study aims to establish the efficacy of catalytic tendency of the bioactive metabolites to combat the effect of tomatinase enzyme employing α-tomatine as the substrate. By means of the integrated molecular modeling approach; novel bioactive metabolites namely, Trichodermamide B, Trichosetin and Virone were found to be the potential inhibitors against tomatinase enzyme secreted by Fusarium oxysporum f.sp. lycopersici. Molecular dynamic (MD) simulations displayed that the screened ligands bound tomatinase during 150 ns of MD simulations. Furthermore, the (MM-PBSA) free energy calculations depicted that screened molecules possess stable and favorable energies for Trichodermamide B (-7.1 kcal/mol), Trichosetin (-7.4 kcal/mol) and Virone (-7.9 kcal/mol) thereby instigating robust binding with the enzyme's binding site. The results attained in this study, reflects that these bioactive metabolites may serve as potential substrates to control and inhibit the tomatinase enzyme; playing an integral role in combating the wilt disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Garima Singh
- Centre for Rural Development & Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Abhay Tiwari
- Centre for Rural Development & Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Gourav Choudhir
- Centre for Rural Development & Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Hariprasad P
- Centre for Rural Development & Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Anuj Kumar
- Uttarakhand Council for Biotechnology, Dehradun, Uttarakhand, India
| | - Satyawati Sharma
- Centre for Rural Development & Technology, Indian Institute of Technology Delhi, New Delhi, India
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Development and use of miRNA-derived SSR markers for the study of genetic diversity, population structure, and characterization of genotypes for breeding heat tolerant wheat varieties. PLoS One 2021; 16:e0231063. [PMID: 33539339 PMCID: PMC7861453 DOI: 10.1371/journal.pone.0231063] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 01/13/2021] [Indexed: 12/12/2022] Open
Abstract
Heat stress is an important abiotic factor that limits wheat production globally, including south-east Asia. The importance of micro (mi) RNAs in gene expression under various biotic and abiotic stresses is well documented. Molecular markers, specifically simple sequence repeats (SSRs), play an important role in the wheat improvement breeding programs. Given the role of miRNAs in heat stress-induced transcriptional regulation and acclimatization, the development of miRNA-derived SSRs would prove useful in studying the allelic diversity at the heat-responsive miRNA-genes in wheat. In the present study, efforts have been made to identify SSRs from 96 wheat heat-responsive miRNA-genes and their characterization using a panel of wheat genotypes with contrasting reactions (tolerance/susceptible) to heat stress. A set of 13 miRNA-derived SSR markers were successfully developed as an outcome. These miRNA-SSRs are located on 11 different common wheat chromosomes (2A, 3A, 3B, 3D, 4D, 5A, 5B, 5D, 6A, 6D, and 7A). Among 13 miRNA-SSRs, seven were polymorphic on a set of 37 selected wheat genotypes. Within these polymorphic SSRs, three makers, namely HT-169j, HT-160a, and HT-160b, were found promising as they could discriminate heat-tolerant and heat-susceptible genotypes. This is the first report of miRNA-SSR development in wheat and their deployment in genetic diversity and population structure studies and characterization of trait-specific germplasm. The study suggests that this new class of molecular makers has great potential in the marker-assisted breeding (MAB) programs targeted at improving heat tolerance and other adaptability or developmental traits in wheat and other crops.
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26
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Li T, Li M, Jiang Y, Duan X. Genome-wide identification, characterization and expression profile of glutaredoxin gene family in relation to fruit ripening and response to abiotic and biotic stresses in banana (Musa acuminata). Int J Biol Macromol 2020; 170:636-651. [PMID: 33385451 DOI: 10.1016/j.ijbiomac.2020.12.167] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 11/30/2022]
Abstract
Glutaredoxins (GRXs) are disulfide oxidoreductases that are involved in various biological processes. However, little information on the role of GRXs in the regulation of fruit ripening and the response to stress is available. In this study, we isolated 64 GRX genes from banana genome. Their encoded GRX proteins could be classified into four classes: CC, CGFS, CPYC and GRL types. The distribution and synteny of these GRXs on chromosomes, the gene structures, the promoter sequences, and the possible protein subcellular localizations were characterized. Molecular interaction network analysis suggested that MaGRX might interact with glutathione reductase (GR), sulfiredoxin, peroxiredoxin (Prx), and NADPH-dependent thioredoxin reductase C (NTRC), contributing to the antioxidative defense of banana fruit. MicroRNA prediction showed that MaGRX genes might be targeted by different miRNAs. Transcriptome analysis characterized the expression profiles of different MaGRX genes during banana fruit ripening, and in response to different storage stresses. The results suggested that CC-type, CPYC-type and GRL-type MaGRXs might be more active than CGFS-type MaGRXs during banana fruit ripening and the response to stress. Moreover, MaGRX6/7/9/11/17/23/28 and MaGRL3/16/19 might play important roles in regulating fruit ripening or in response to low and high temperature, or Fusarium proliferatum infection.
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Affiliation(s)
- Taotao Li
- Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture/Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Mingzhi Li
- Independent Researcher, Guangzhou, 510650, China
| | - Yueming Jiang
- Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture/Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xuewu Duan
- Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture/Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China.
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QTL detection and putative candidate gene prediction for leaf rolling under moisture stress condition in wheat. Sci Rep 2020; 10:18696. [PMID: 33122772 PMCID: PMC7596552 DOI: 10.1038/s41598-020-75703-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/15/2020] [Indexed: 12/20/2022] Open
Abstract
Leaf rolling is an important mechanism to mitigate the effects of moisture stress in several plant species. In the present study, a set of 92 wheat recombinant inbred lines derived from the cross between NI5439 × HD2012 were used to identify QTLs associated with leaf rolling under moisture stress condition. Linkage map was constructed using Axiom 35 K Breeder’s SNP Array and microsatellite (SSR) markers. A linkage map with 3661 markers comprising 3589 SNP and 72 SSR markers spanning 22,275.01 cM in length across 21 wheat chromosomes was constructed. QTL analysis for leaf rolling trait under moisture stress condition revealed 12 QTLs on chromosomes 1B, 2A, 2B, 2D, 3A, 4A, 4B, 5D, and 6B. A stable QTL Qlr.nhv-5D.2 was identified on 5D chromosome flanked by SNP marker interval AX-94892575–AX-95124447 (5D:338665301–5D:410952987). Genetic and physical map integration in the confidence intervals of Qlr.nhv-5D.2 revealed 14 putative candidate genes for drought tolerance which was narrowed down to six genes based on in-silico analysis. Comparative study of leaf rolling genes in rice viz., NRL1, OsZHD1, Roc5, and OsHB3 on wheat genome revealed five genes on chromosome 5D. Out of the identified genes, TraesCS5D02G253100 falls exactly in the QTL Qlr.nhv-5D.2 interval and showed 96.9% identity with OsZHD1. Two genes similar to OsHB3 viz. TraesCS5D02G052300 and TraesCS5D02G385300 exhibiting 85.6% and 91.8% identity; one gene TraesCS5D02G320600 having 83.9% identity with Roc5 gene; and one gene TraesCS5D02G102600 showing 100% identity with NRL1 gene were also identified, however, these genes are located outside Qlr.nhv-5D.2 interval. Hence, TraesCS5D02G253100 could be the best potential candidate gene for leaf rolling and can be utilized for improving drought tolerance in wheat.
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Kumar A, Sharma M, Chaubey SN, Kumar A. Homology modeling and molecular dynamics based insights into Chalcone synthase and Chalcone isomerase in Phyllanthus emblica L. 3 Biotech 2020; 10:373. [PMID: 32832333 DOI: 10.1007/s13205-020-02367-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 07/27/2020] [Indexed: 02/07/2023] Open
Abstract
Chalcone synthase (CHS) and chalcone isomerase (CHI) plays a major role in the biosynthesis of flavonoid in plants. In this study, we made extensive bioinformatics analysis to gain functional and structural insight into PeCHS and PeCHI proteins. The phylogenetic distribution of PeCHS and PeCHI genes encoding proteins demonstrated the close evolutionary relationship with different CHS and CHI proteins of other dicot plants. MicroRNA target analysis showed miR169n and 3p miR5053 targeting PeCHS gene while miR169c-3p and miR4248 are targeting PeCHI gene, respectively. Three-dimensional structural models of PeCHS and PeCHI proteins were elucidated by homology modeling with Ramachandran plots showing the excellent geometry of the proteins structure. Molecular docking revealed that cinnamoyl-coa and naringenin chalcone substrates are strongly bound to PeCHS and PeCHI proteins, respectively. Finally, molecular dynamics (MD) simulation for 30 ns, further yielded stability checks of ligands in the binding pocket and behavior of protein complexes. Thus MD simulation and interaction fraction analysis showed the stable conformation of PeCHS and PeCHI proteins with their respective substrates during theee simulation. Our study provides first-hand structural prospective of PeCHS and PeCHI proteins towards understanding the mechanism of flavonoid biosynthetic pathway in P. emblica.
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Affiliation(s)
- Anuj Kumar
- Advance Centre for Computational and Applied Biotechnology, Uttarakhand Council for Biotechnology (UCB), Dehradun, 248007 India
| | - Mansi Sharma
- Bioclues.Org, Kukatpally, Hyderabad, 500072 India
| | - Swaroopa Nand Chaubey
- Department of Bioinformatics, Biotech Park, Sector G, Jankipuram, Lucknow, UP 226021 India
| | - Avneesh Kumar
- Department of Botany, Akal University, Talwandi Sabo, Bathinda, 151302 India
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