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Killiny N, Nehela Y, Hijaz F, Gonzalez-Blanco P, Hajeri S, Gowda S. Knock-down of δ-aminolevulinic acid dehydratase via virus-induced gene silencing alters the microRNA biogenesis and causes stress-related reactions in citrus plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 299:110622. [PMID: 32900450 DOI: 10.1016/j.plantsci.2020.110622] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 06/11/2023]
Abstract
The δ-aminolevulinic acid (δ-ALA) is an intermediate in the biosynthetic pathway of tetrapyrroles. Tetrapyrroles play vital roles in many biological processes such as photosynthesis, respiration, and light-sensing. ALA-dehydratase (ALAD) combines two molecules of δ-ALA to form porphobilinogen. In citrus, the silencing of ALAD caused discrete yellow spots and necrosis in leaves and stems. Additionally, it caused rapid death in developing new shoots. Herein, we hypothesize that the accumulation of δ-ALA results in severe stress and reduced meristem development. For that reason, we investigated the dynamic changes in the expression profiles of 23 microRNA (miRNA) identified through small RNA sequencing, from CTV-tALAD plants in comparison with healthy C. macrophylla and C. macrophylla infiltrated with CTV-wt. Furthermore, we reported the effect of ALAD silencing on the total phenolics, H2O2, and reactive oxygen species (ROS) levels, to examine the possibilities of miRNAs involving the regulation of these pathways. Our results showed that the total phenolics content, H2O2, and O2- levels were increased in CTV-tALAD plants. Moreover, 63 conserved miRNA members belonging to 23 different miRNA families were differentially expressed in CTV-tALAD plants compared to controls. The identified miRNAs are implicated in auxin biosynthesis and signaling, axillary shoot meristem formation and leaf morphology, starch metabolism, and oxidative stress. Collectively, our findings suggested that ALAD silencing initiates stress on citrus plants. As a result, CTV-tALAD plants exhibit reduced metabolic rate, growth, and development in order to cope with the stress that resulted from the accumulation of δ-ALA. This cascade of events led to leaf, stem, and meristem necrosis and failure of new shoot development.
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Affiliation(s)
- Nabil Killiny
- Department of Plant Pathology, Citrus Research and Education Center, IFAS, University of Florida, 700 Experiment Station Road, Lake Alfred, FL, 33850, USA.
| | - Yasser Nehela
- Department of Plant Pathology, Citrus Research and Education Center, IFAS, University of Florida, 700 Experiment Station Road, Lake Alfred, FL, 33850, USA
| | - Faraj Hijaz
- Department of Plant Pathology, Citrus Research and Education Center, IFAS, University of Florida, 700 Experiment Station Road, Lake Alfred, FL, 33850, USA
| | - Pedro Gonzalez-Blanco
- Department of Plant Pathology, Citrus Research and Education Center, IFAS, University of Florida, 700 Experiment Station Road, Lake Alfred, FL, 33850, USA
| | - Subhas Hajeri
- Department of Plant Pathology, Citrus Research and Education Center, IFAS, University of Florida, 700 Experiment Station Road, Lake Alfred, FL, 33850, USA
| | - Siddarame Gowda
- Department of Plant Pathology, Citrus Research and Education Center, IFAS, University of Florida, 700 Experiment Station Road, Lake Alfred, FL, 33850, USA
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153
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Yang W, Choi MH, Noh B, Noh YS. De Novo Shoot Regeneration Controlled by HEN1 and TCP3/4 in Arabidopsis. PLANT & CELL PHYSIOLOGY 2020; 61:1600-1613. [PMID: 32579181 DOI: 10.1093/pcp/pcaa083] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/14/2020] [Indexed: 05/24/2023]
Abstract
Plants have the ability to regenerate whole plant body parts, including shoots and roots, in vitro from callus derived from a variety of tissues. However, the underlying mechanisms for this de novo organogenesis, which is based on the totipotency of callus cells, are poorly understood. Here, we report that a microRNA (miRNA)-mediated posttranscriptional regulation plays an important role in de novo shoot regeneration. We found that mutations in HUA ENHANCER 1 (HEN1), a gene encoding a small RNA methyltransferase, cause cytokinin-related defects in de novo shoot regeneration. A hen1 mutation caused a large reduction in the miRNA319 (miR319) level and a subsequent increase in its known target (TCP3 and TCP4) transcript levels. TCP transcription factors redundantly inhibited shoot regeneration and directly activated the expression of a negative regulator of cytokinin response ARABIDOPSIS THALIANA RESPONSE REGULATOR 16 (ARR16). A tcp4 mutation at least partly rescued the shoot-regeneration defect and derepression of ARR16 in hen1. These findings demonstrate that the miR319-TCP3/4-ARR16 axis controls de novo shoot regeneration by modulating cytokinin responses.
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Affiliation(s)
- Woorim Yang
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Myung-Hwan Choi
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Bosl Noh
- Research Institute of Basic Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Yoo-Sun Noh
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
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154
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Shen E, Chen T, Zhu X, Fan L, Sun J, Llewellyn DJ, Wilson I, Zhu QH. Expansion of MIR482/2118 by a class-II transposable element in cotton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:2084-2099. [PMID: 32578284 DOI: 10.1111/tpj.14885] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 05/28/2020] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
Some plant microRNA (miRNA) families contain multiple members generating identical or highly similar mature miRNA variants. Mechanisms underlying the expansion of miRNA families remain elusive, although tandem and/or segmental duplications have been proposed. In this study of two tetraploid cottons, Gossypium hirsutum and Gossypium barbadense, and their extant diploid progenitors, Gossypium arboreum and Gossypium raimondii, we investigated the gain and loss of members of the miR482/2118 superfamily, which modulates the expression of nucleotide-binding site leucine-rich repeat (NBS-LRR) disease resistance genes. We found significant expansion of MIR482/2118d in G. barbadense, G. hirsutum and G. raimondii, but not in G. arboreum. Several newly expanded MIR482/2118d loci have mutated to produce different miR482/2118 variants with altered target-gene specificity. Based on detailed analysis of sequences flanking these MIR482/2118 loci, we found that this expansion of MIR482/2118d and its derivatives resulted from an initial capture of an MIR482/2118d by a class-II DNA transposable element (TE) in G. raimondii prior to the tetraploidization event, followed by transposition to new genomic locations in G. barbadense, G. hirsutum and G. raimondii. The 'GosTE' involved in the capture and proliferation of MIR482/2118d and its derivatives belongs to the PIF/Harbinger superfamily, generating a 3-bp target site duplication upon insertion at new locations. All orthologous MIR482/2118 loci in the two diploids were retained in the two tetraploids, but mutation(s) in miR482/2118 were observed across all four species as well as in different cultivars of both G. barbadense and G. hirsutum, suggesting a dynamic co-evolution of miR482/2118 and its NBS-LRR targets. Our results provide fresh insights into the mechanisms contributing to MIRNA proliferation and enrich our knowledge on TEs.
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Affiliation(s)
- Enhui Shen
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- New Rural Development Institute, Zhejiang University, Hangzhou, 310058, China
| | - Tianzi Chen
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Xintian Zhu
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Longjiang Fan
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jie Sun
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, 832000, China
| | - Danny J Llewellyn
- Black Mountain Laboratories, CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Iain Wilson
- Black Mountain Laboratories, CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Qian-Hao Zhu
- Black Mountain Laboratories, CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
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155
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Zhang H, Chen F, Liang Z, Wu Y, Pi J, Wang L, Du J, Shen J, Pan A, Pu Y. Analysis of miRNAs and their target genes associated with mucosal damage caused by transport stress in the mallard duck intestine. PLoS One 2020; 15:e0237699. [PMID: 32810175 PMCID: PMC7437463 DOI: 10.1371/journal.pone.0237699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 07/31/2020] [Indexed: 12/12/2022] Open
Abstract
Bowel health is an important factor for duck rearing that has been linked to feed uptake and growth and death rates. Because the regulatory networks associated with acute stress-mediated injury in the duck gastrointestinal tract have not clearly elucidated, we aimed to explore potential miRNA-mRNA pairs and their regulatory roles in oxidative stress injury caused by transport stress. Here, 1-day-old mallard ducklings from the same breeder flock were collected and transported for 8 h, whereas the control group was not being transported. Various parameters reflecting oxidative stress and the tissue appearance of the intestine were assessed. The data showed that the plasma T-AOC and SOD concentrations were decreased in the transported ducklings. The intestine of the transported ducklings also displayed significant damage. High-throughput sequencing of the intestine revealed 44 differentially expressed miRNAs and 75 differentially expressed genes, which constituted 344 miRNA-mRNA pairs. KEGG pathway analysis revealed that the metabolic, FoxO signaling, influenza A and TGF-β signaling pathways were mainly involved in the mechanism underlying the induction of intestinal damage induced by simulated transport stress in ducks. A miRNA-mRNA pair, miR-217-5p/CHRDL1, was selected to validate the miRNA-mRNA negative relationship, and the results showed that miR-217-5p could influence CHRDL1 expression. This study provides new useful information for future research on the regulatory network associated with mucosal damage in the duck intestine.
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Affiliation(s)
- Hao Zhang
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, PR China
| | - Fang Chen
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, PR China
| | - Zhenhua Liang
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, PR China
| | - Yan Wu
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, PR China
| | - Jinsong Pi
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, PR China
| | - Lixia Wang
- Institute of Animal Husbandry and Veterinary Sciences, Wuhan Academy of Agricultural Sciences, Wuhan, PR China
| | - Jinping Du
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, PR China
| | - Jie Shen
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, PR China
| | - Ailuan Pan
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, PR China
| | - Yuejin Pu
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, PR China
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156
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Dolata J, Zielezinski A, Stepien A, Kruszka K, Bielewicz D, Pacak A, Jarmolowski A, Karlowski W, Szweykowska-Kulinska Z. Quantitative Analysis of Plant miRNA Primary Transcripts. Methods Mol Biol 2020; 2170:53-77. [PMID: 32797451 DOI: 10.1007/978-1-0716-0743-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
MicroRNAs control plant development and are key regulators of plant responses to biotic and abiotic stresses. Thus, their expression must be carefully controlled since both excess and deficiency of a given microRNA may be deleterious to plant cell. MicroRNA expression regulation can occur at several stages of their biogenesis pathway. One of the most important of these regulatory checkpoints is transcription efficiency. mirEX database is a tool for exploration and visualization of plant pri-miRNA expression profiles. It includes results obtained using high-throughput RT-qPCR platform designed to monitor pri-miRNA expression in different miRNA biogenesis mutants and developmental stages of Arabidopsis, barley, and Pellia plants. A step-by-step instruction for browsing the database and detailed protocol for high-throughput RT-qPCR experiments, including list of primers designed for the amplification of pri-miRNAs, are presented.
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Affiliation(s)
- Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poznań, Poland
| | - Andrzej Zielezinski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poznań, Poland
| | - Agata Stepien
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poznań, Poland
| | - Katarzyna Kruszka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poznań, Poland
| | - Dawid Bielewicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poznań, Poland
| | - Andrzej Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poznań, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poznań, Poland
| | - Wojciech Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poznań, Poland.
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poznań, Poland.
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157
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Chen C, Liu C, Jiang A, Zhao Q, Zhang Y, Hu W. miRNA and Degradome Sequencing Identify miRNAs and Their Target Genes Involved in the Browning Inhibition of Fresh-Cut Apples by Hydrogen Sulfide. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:8462-8470. [PMID: 32697084 DOI: 10.1021/acs.jafc.0c02473] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Surface browning is the major limit for the shelf life of fresh-cut apples, and hydrogen sulfide (H2S) treatment can effectively inhibit the browning. However, the molecular mechanism on how fresh-cut apples respond to H2S was poorly understood. MicroRNAs (miRNAs) are a class of endogenous small noncoding RNAs, which regulate multiple crucial biological processes in almost all aspects of the life cycle. Herein, 12 small RNA libraries and one mixed degradome library were constructed from control and H2S-treated fresh-cut apples immediately after treatment (C0 and S0) and 6 d of storage (C6 and S6) at 4 °C. The results identified nine (three upregulated and six downregulated) and 10 (two upregulated and eight downregulated) differentially expressed miRNAs (DEmiRNAs) in S0 versus C0 and S6 versus C6, respectively. The target genes of DEmiRNAs were transcription factors and functional proteins. The miR156 targeting SPL, miR164 targeting NAC, miR319 targeting TCP4, GAMYB, and acyl-CoA-binding protein 4, and miR6478 targeting patatin-like protein 2 might play important roles in the browning inhibition of fresh-cut apples by H2S via regulating the ROS, phenylpropanoid, and lipid metabolism. The results give valuable information for further studying the role of miRNA in regulating browning processes and the underlying molecular mechanism of H2S treatment on browning inhibition.
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Affiliation(s)
- Chen Chen
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Chenghui Liu
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Aili Jiang
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Qiqi Zhao
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Yanhui Zhang
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Wenzhong Hu
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
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158
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Repression of microRNA 160 results in retarded seed integument growth and smaller final seed size in cotton. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.cj.2019.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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159
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High-Throughput Sequencing and Expression Analysis Suggest the Involvement of Pseudomonas putida RA-Responsive microRNAs in Growth and Development of Arabidopsis. Int J Mol Sci 2020; 21:ijms21155468. [PMID: 32751751 PMCID: PMC7432263 DOI: 10.3390/ijms21155468] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/18/2020] [Accepted: 07/21/2020] [Indexed: 01/11/2023] Open
Abstract
Beneficial soil microorganisms largely comprise of plant growth-promoting rhizobacteria (PGPR), which adhere to plant roots and facilitate their growth and development. Pseudomonas putida (RA) strain MTCC5279 is one such PGPR that exhibits several characteristics of plant growth promotion, such as P-solubilization, and siderophores and IAA production. Plant–PGPR interactions are very complex phenomena, and essentially modulate the expression of numerous genes, consequently leading to changes in the physiological, biochemical, cellular and molecular responses of plants. Therefore, in order to understand the molecular bases of plant–PGPR interactions, we carried out the identification of microRNAs from the roots of Arabidopsis upon P. putida RA-inoculation, and analyses of their expression. MicroRNAs (miRNAs) are 20- to 24-nt non-coding small RNAs known to regulate the expression of their target genes. Small RNA sequencing led to the identification of 293 known and 67 putative novel miRNAs, from the control and RA-inoculated libraries. Among these, 15 known miRNAs showed differential expression upon RA-inoculation in comparison to the control, and their expressions were corroborated by stem-loop quantitative real-time PCR. Overall, 28,746 and 6931 mRNAs were expected to be the targets of the known and putative novel miRNAs, respectively, which take part in numerous biological, cellular and molecular processes. An inverse correlation between the expression of RA-responsive miRNAs and their target genes also strengthened the crucial role of RA in developmental regulation. Our results offer insights into the understanding of the RA-mediated modulation of miRNAs and their targets in Arabidopsis, and pave the way for the further exploitation and characterization of candidate RA-responsive miRNA(s) for various crop improvement strategies directed towards plant sustainable growth and development.
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160
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Ali E, Raza MA, Cai M, Hussain N, Shahzad AN, Hussain M, Ali M, Bukhari SAH, Sun P. Calmodulin-binding transcription activator (CAMTA) genes family: Genome-wide survey and phylogenetic analysis in flax (Linum usitatissimum). PLoS One 2020; 15:e0236454. [PMID: 32702710 PMCID: PMC7377914 DOI: 10.1371/journal.pone.0236454] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 07/05/2020] [Indexed: 12/21/2022] Open
Abstract
Flax (Linum usitatissimum) is a member of family linaceae with annual growth habit. It is included among those crops which were domesticated very early and has been used in development related studies as a model plant. In plants, Calmodulin-binding transcription activators (CAMTAs) comprise a unique set of Calmodulin-binding proteins. To elucidate the transport mechanism of secondary metabolites in flax, a genome-based study on these transporters was performed. The current investigation identified nine CAMTAs proteins, classified into three categories during phylogenetic analysis. Each group had significant evolutionary role as illustrated by the conservation of gene structures, protein domains and motif organizations over the distinctive phylogenetic classes. GO annotation suggested a link to sequence-specific DNA and protein binding, response to low temperature and transcription regulation by RNA polymerase II. The existence of different hormonal and stress responsive cis-regulatory elements in promotor region may directly correlate with the variation of their transcripts. MicroRNA target analysis revealed that various groups of miRNA families targeted the LuCAMTAs genes. Identification of CAMTA genes, miRNA studies and phylogenetic analysis may open avenues to uncover the underlying functional mechanism of this important family of genes in flax.
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Affiliation(s)
- Essa Ali
- Department of Food Science and Technology, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Mohammad Ammar Raza
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China
| | - Ming Cai
- Department of Food Science and Technology, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Nazim Hussain
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | | | - Mubshar Hussain
- Department of Agronomy, Bahauddin Zakariya University, Multan, Pakistan
| | - Murtaza Ali
- Department of Basic Science & Humanities, University of Engineering and Technology, Mardan, Pakistan
| | | | - Peilong Sun
- Department of Food Science and Technology, Zhejiang University of Technology, Hangzhou, Zhejiang, China
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161
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Luan W, Dai Y, Li XY, Wang Y, Tao X, Li CX, Mao P, Ma XR. Identification of tRFs and phasiRNAs in tomato (Solanum lycopersicum) and their responses to exogenous abscisic acid. BMC PLANT BIOLOGY 2020; 20:320. [PMID: 32635887 PMCID: PMC7339384 DOI: 10.1186/s12870-020-02528-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 06/26/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND The non-coding small RNA tRFs (tRNA-derived fragments) and phasiRNAs (plant-specific) exert important roles in plant growth, development and stress resistances. However, whether the tRFs and phasiRNAs respond to the plant important stress hormone abscisic acid (ABA) remain enigma. RESULTS Here, the RNA-sequencing was implemented to decipher the landscape of tRFs and phasiRNAs in tomato (Solanum lycopersicum) leaves and their responses when foliar spraying exogenous ABA after 24 h. In total, 733 tRFs and 137 phasiRNAs were detected. The tRFs were mainly derived from the tRNAAla transporting alanine, which tended to be cleaved at the 5'terminal guanine site and D loop uracil site to produce tRFAla with length of 20 nt. Most of phasiRNAs originated from NBS-LRR resistance genes. Expression analysis revealed that 156 tRFs and 68 phasiRNAs expressed differentially, respectively. Generally, exogenous ABA mainly inhibited the expression of tRFs and phasiRNAs. Furthermore, integrating analysis of target gene prediction and transcriptome data presented that ABA significantly downregulated the abundance of phsaiRNAs associated with biological and abiotic resistances. Correspondingly, their target genes such as AP2/ERF, WRKY and NBS-LRR, STK and RLK, were mainly up-regulated. CONCLUSIONS Combined with the previous analysis of ABA-response miRNAs, it was speculated that ABA can improve the plant resistances to various stresses by regulating the expression and interaction of small RNAs (such as miRNAs, tRFs, phasiRNAs) and their target genes. This study enriches the plant tRFs and phasiRNAs, providing a vital basis for further investigating ABA response-tRFs and phasiRNAs and their functions in biotic and abiotic stresses.
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Affiliation(s)
- Wei Luan
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ya Dai
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Yu Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Xiang Tao
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Cai-Xia Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Ping Mao
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Xin-Rong Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China.
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162
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Pandey AK, Gedda MR, Verma AK. Effect of Arsenic Stress on Expression Pattern of a Rice Specific miR156j at Various Developmental Stages and Their Allied Co-expression Target Networks. FRONTIERS IN PLANT SCIENCE 2020; 11:752. [PMID: 32612618 PMCID: PMC7308582 DOI: 10.3389/fpls.2020.00752] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 05/12/2020] [Indexed: 05/28/2023]
Abstract
In plants, arsenic (As) stress modulates metabolic cascades at various developmental stages by influencing the pattern of gene expressions mediated by small non-coding RNAs, especially Micro-RNAs, involved in the moderation of a myriad of cellular processes needed for plant adaptation upon oxidative stress. miR156j of miR156 gene family, involved mainly in the regulation of growth and development in plants. This study was designed to find out the role of arsenic toxicity on Osa-miR156j expression in all physiological growth stages. To better understand the functional role of Osa-miR156j in rice, we observed the expression in different developmental stages (seedlings, tillering and flowering) and various tissues of leaf, stem and root tissues (at 0, 24, 48, and 72 h) under 25 μM arsenite [As (III)] exposure. Additionally, using bioinformatic tools to target genes of Osa-miR156j and the potential co-expressed genes were explored at different development stages in the various tissues of rice under stress conditions. The expression of Osa-miR156j showed its temporal downregulation in various tissues in different developmental stages. Of note, the downregulation was more pronounced in root tissues at seedlings, tillering, and flowering stages during 0-72 h under arsenite exposure as compared to other tissues. Overall, the As stress altered the gene expression more prominently at seedlings developmental stage followed by flowering and tillering. Additionally, through the In silico approach, the target functions and presence of oxidative stress-responsive cis-acting regulatory elements/motifs also confirmed Osa-miR156j involvement in the regulation of arsenic stress in rice. The findings of this study demonstrate the prominent role of Osa-miR156j in rice under arsenite stress, which was found to modulate the metabolic activities in rice plants at different developmental stages, and thus it might be useful for the development of arsenic tolerant varieties.
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Affiliation(s)
- Akhilesh Kumar Pandey
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Mallikarjuna Rao Gedda
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Ashok K. Verma
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
- Biotechnology Laboratory, U.P. Council of Sugarcane Research, Shahjahanpur, India
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163
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Jeyaraj A, Elango T, Li X, Guo G. Utilization of microRNAs and their regulatory functions for improving biotic stress tolerance in tea plant [ Camellia sinensis (L.) O. Kuntze]. RNA Biol 2020; 17:1365-1382. [PMID: 32478595 DOI: 10.1080/15476286.2020.1774987] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs play a central role in responses to biotic stressors through their interactions with their target mRNAs. Tea plant (Camellia sinensis L.), an important beverage crop, is vulnerable to tea geometrid and anthracnose disease that causes considerable crop loss and tea production worldwide. Sustainable production of tea in the current scenario to biotic factors is major challenges. To overcome the problem of biotic stresses, high-throughput sequencing (HTS) with bioinformatics analyses has been used as an effective approach for the identification of stress-responsive miRNAs and their regulatory functions in tea plant. These stress-responsive miRNAs can be utilized for miRNA-mediated gene silencing to enhance stress tolerance in tea plant. Therefore, this review summarizes the current understanding of miRNAs regulatory functions in tea plant responding to Ectropis oblique and Colletotrichum gloeosporioides attacks for future miRNA research. Also, it highlights the utilization of miRNA-mediated gene silencing strategies for developing biotic stress-tolerant tea plant.
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Affiliation(s)
- Anburaj Jeyaraj
- Tea Research Institute, Nanjing Agricultural University , Nanjing, China.,Department of Biotechnology, Karpagam Academy of Higher Education , Tamilnadu, India
| | - Tamilselvi Elango
- Tea Research Institute, Nanjing Agricultural University , Nanjing, China
| | - Xinghui Li
- Tea Research Institute, Nanjing Agricultural University , Nanjing, China
| | - Guiyi Guo
- Henan Key Laboratory of Tea Plant Comprehensive Utilization in South Henan, Xinyang Agriculture and Forestry University , Xinyang, P.R. China
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164
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Guo Z, Kuang Z, Wang Y, Zhao Y, Tao Y, Cheng C, Yang J, Lu X, Hao C, Wang T, Cao X, Wei J, Li L, Yang X. PmiREN: a comprehensive encyclopedia of plant miRNAs. Nucleic Acids Res 2020; 48:D1114-D1121. [PMID: 31602478 PMCID: PMC6943064 DOI: 10.1093/nar/gkz894] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/29/2019] [Accepted: 10/09/2019] [Indexed: 01/09/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules that function as diverse endogenous gene regulators at the post-transcriptional level. In the past two decades, as research effort on miRNA identification, function and evolution has soared, so has the demand for miRNA databases. However, the current plant miRNA databases suffer from several typical drawbacks, including a lack of entries for many important species, uneven annotation standards across different species, abundant questionable entries, and limited annotation. To address these issues, we developed a knowledge-based database called Plant miRNA Encyclopedia (PmiREN, http://www.pmiren.com/), which was based on uniform processing of sequenced small RNA libraries using miRDeep-P2, followed by manual curation using newly updated plant miRNA identification criteria, and comprehensive annotation. PmiREN currently contains 16,422 high confidence novel miRNA loci in 88 plant species and 3,966 retrieved from miRBase. For every miRNA entry, information on precursor sequence, precursor secondary structure, expression pattern, clusters and synteny in the genome, potential targets supported by Parallel Analysis of RNA Ends (PARE) sequencing, and references is attached whenever possible. PmiREN is hierarchically accessible and has eight built-in search engines. We believe PmiREN is useful for plant miRNA cataloguing and data mining, therefore a resource for data-driven miRNA research in plants.
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Affiliation(s)
- Zhonglong Guo
- Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P. R. China.,State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, P. R. China
| | - Zheng Kuang
- Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P. R. China.,State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, P. R. China
| | - Ying Wang
- Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P. R. China.,State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, P. R. China
| | - Yongxin Zhao
- Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P. R. China
| | - Yihan Tao
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, P. R. China
| | - Chen Cheng
- Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P. R. China
| | - Jing Yang
- Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P. R. China.,National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an 710062, P. R. China
| | - Xiayang Lu
- Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P. R. China.,National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an 710062, P. R. China
| | - Chen Hao
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, P. R. China
| | - Tianxin Wang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, P. R. China
| | - Xiaoyan Cao
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an 710062, P. R. China
| | - Jianhua Wei
- Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P. R. China
| | - Lei Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, P. R. China
| | - Xiaozeng Yang
- Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P. R. China
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165
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Small RNA sequencing revealed various microRNAs involved in ethylene-triggered flowering process in Aechmea fasciata. Sci Rep 2020; 10:7348. [PMID: 32355186 PMCID: PMC7193560 DOI: 10.1038/s41598-020-63597-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 04/02/2020] [Indexed: 12/20/2022] Open
Abstract
Ethylene-triggered flowering is a common phenomenon in plants of the family Bromeliaceae, but its molecular mechanism remains unclear. As a classical group of small RNAs, microRNAs play an essential role in the regulation of flowering. In this study, we found that various miRNAs participate in the ethylene-triggered flowering process in Aechmea fasciata via small RNA sequencing using juvenile and adult plants treated with ethylene for 24 hours. Finally, 63 known miRNAs, 52 novel miRNAs and 1721 target genes were identified or predicted. Expression changes of specific miRNAs were validated by qRT-PCR and northern blotting. Some predicted targets, including SPL, GAMYB and ARF, were verified in RLM-RACE experiments. Gene Ontology (GO) and KEGG analysis showed that numerous developmental and RNA-related processes were enriched. Integrated analysis of the transcriptomic data with small RNA sequencing revealed that numerous miRNAs and targets involved in ethylene-triggered flowering in A. fasciata. Our study is helpful for illuminating the molecular basis of the ethylene-triggered flowering phenomenon in Bromeliaceae.
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166
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Ding Y, Shi Y, Yang S. Molecular Regulation of Plant Responses to Environmental Temperatures. MOLECULAR PLANT 2020; 13:544-564. [PMID: 32068158 DOI: 10.1016/j.molp.2020.02.004] [Citation(s) in RCA: 268] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 05/19/2023]
Abstract
Temperature is a key factor governing the growth and development, distribution, and seasonal behavior of plants. The entire plant life cycle is affected by environmental temperatures. Plants grow rapidly and exhibit specific changes in morphology under mild average temperature conditions, a response termed thermomorphogenesis. When exposed to chilling or moist chilling low temperatures, flowering or seed germination is accelerated in some plant species; these processes are known as vernalization and cold stratification, respectively. Interestingly, once many temperate plants are exposed to chilling temperatures for some time, they can acquire the ability to resist freezing stress, a process termed cold acclimation. In the face of global climate change, heat stress has emerged as a frequent challenge, which adversely affects plant growth and development. In this review, we summarize and discuss recent progress in dissecting the molecular mechanisms regulating plant thermomorphogenesis, vernalization, and responses to extreme temperatures. We also discuss the remaining issues that are crucial for understanding the interactions between plants and temperature.
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Affiliation(s)
- Yanglin Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yiting Shi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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167
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Goswami K, Mittal D, Gautam B, Sopory SK, Sanan-Mishra N. Mapping the Salt Stress-Induced Changes in the Root miRNome in Pokkali Rice. Biomolecules 2020; 10:E498. [PMID: 32218214 PMCID: PMC7226372 DOI: 10.3390/biom10040498] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 12/29/2022] Open
Abstract
A plant's response to stress conditions is governed by intricately coordinated gene expression. The microRNAs (miRs) have emerged as relatively new players in the genetic network, regulating gene expression at the transcriptional and post-transcriptional level. In this study, we performed comprehensive profiling of miRs in roots of the naturally salt-tolerant Pokkali rice variety to understand their role in regulating plant physiology in the presence of salt. For comparisons, root miR profiles of the salt-sensitive rice variety Pusa Basmati were generated. It was seen that the expression levels of 65 miRs were similar for roots of Pokkali grown in the absence of salt (PKNR) and Pusa Basmati grown in the presence of salt (PBSR). The salt-induced dis-regulations in expression profiles of miRs showed controlled changes in the roots of Pokkali (PKSR) as compared to larger variations seen in the roots of Pusa Basmati. Target analysis of salt-deregulated miRs identified key transcription factors, ion-transporters, and signaling molecules that act to maintain cellular Ca2+ homeostasis and limit ROS production. These miR:mRNA nodes were mapped to the Quantitative trait loci (QTLs) to identify the correlated root traits for understanding their significance in plant physiology. The results obtained indicate that the adaptability of Pokkali to excess salt may be due to the genetic regulation of different cellular components by a variety of miRs.
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Affiliation(s)
- Kavita Goswami
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India (S.K.S.)
- Department of Computational Biology and Bioinformatics, Jacob School of Biotechnology and Bioengineering, Sam Higginbottom university of Agriculture, Technology and Sciences, Prayagraj (Formally Allahabad) 211007, India
| | - Deepti Mittal
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India (S.K.S.)
| | - Budhayash Gautam
- Department of Computational Biology and Bioinformatics, Jacob School of Biotechnology and Bioengineering, Sam Higginbottom university of Agriculture, Technology and Sciences, Prayagraj (Formally Allahabad) 211007, India
| | - Sudhir K. Sopory
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India (S.K.S.)
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India (S.K.S.)
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168
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Wani SH, Kumar V, Khare T, Guddimalli R, Parveda M, Solymosi K, Suprasanna P, Kavi Kishor PB. Engineering salinity tolerance in plants: progress and prospects. PLANTA 2020; 251:76. [PMID: 32152761 DOI: 10.1007/s00425-020-03366-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 02/24/2020] [Indexed: 05/20/2023]
Abstract
There is a need to integrate conceptual framework based on the current understanding of salt stress responses with different approaches for manipulating and improving salt tolerance in crop plants. Soil salinity exerts significant constraints on global crop production, posing a serious challenge for plant breeders and biotechnologists. The classical transgenic approach for enhancing salinity tolerance in plants revolves by boosting endogenous defence mechanisms, often via a single-gene approach, and usually involves the enhanced synthesis of compatible osmolytes, antioxidants, polyamines, maintenance of hormone homeostasis, modification of transporters and/or regulatory proteins, including transcription factors and alternative splicing events. Occasionally, genetic manipulation of regulatory proteins or phytohormone levels confers salinity tolerance, but all these may cause undesired reduction in plant growth and/or yields. In this review, we present and evaluate novel and cutting-edge approaches for engineering salt tolerance in crop plants. First, we cover recent findings regarding the importance of regulatory proteins and transporters, and how they can be used to enhance salt tolerance in crop plants. We also evaluate the importance of halobiomes as a reservoir of genes that can be used for engineering salt tolerance in glycophytic crops. Additionally, the role of microRNAs as critical post-transcriptional regulators in plant adaptive responses to salt stress is reviewed and their use for engineering salt-tolerant crop plants is critically assessed. The potentials of alternative splicing mechanisms and targeted gene-editing technologies in understanding plant salt stress responses and developing salt-tolerant crop plants are also discussed.
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Affiliation(s)
- Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani, Anantnag, Jammu and Kashmir, 192 101, India.
| | - Vinay Kumar
- Department of Biotechnology, Modern College, Savitribai Phule Pune University, Ganeshkhind, Pune, 411 016, India
- Department of Environmental Science, Savitribai Phule Pune University, Ganeshkhind, Pune, 411 016, India
| | - Tushar Khare
- Department of Biotechnology, Modern College, Savitribai Phule Pune University, Ganeshkhind, Pune, 411 016, India
| | | | | | - Katalin Solymosi
- Department of Plant Anatomy, Institute of Biology, ELTE-Eötvös Loránd University, Budapest, 1053, Hungary
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India
| | - P B Kavi Kishor
- Department of Biotechnology, Vignan's Foundation for Science Technology and Research, Vadlamudi, Guntur, 522 213, India
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169
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Fu L, Ding Z, Tan D, Han B, Sun X, Zhang J. Genome-wide discovery and functional prediction of salt-responsive lncRNAs in duckweed. BMC Genomics 2020; 21:212. [PMID: 32138656 PMCID: PMC7059339 DOI: 10.1186/s12864-020-6633-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 02/28/2020] [Indexed: 02/06/2023] Open
Abstract
Background Salt significantly depresses the growth and development of the greater duckweed, Spirodela polyrhiza, a model species of floating aquatic plants. Physiological responses of this plant to salt stress have been characterized, however, the roles of long noncoding RNAs (lncRNAs) remain unknown. Results In this work, totally 2815 novel lncRNAs were discovered in S. polyrhiza by strand-specific RNA sequencing, of which 185 (6.6%) were expressed differentially under salinity condition. Co-expression analysis indicated that the trans-acting lncRNAs regulated their co-expressed genes functioning in amino acid metabolism, cell- and cell wall-related metabolism, hormone metabolism, photosynthesis, RNA transcription, secondary metabolism, and transport. In total, 42 lncRNA-mRNA pairs that might participate in cis-acting regulation were found, and these adjacent genes were involved in cell wall, cell cycle, carbon metabolism, ROS regulation, hormone metabolism, and transcription factor. In addition, the lncRNAs probably functioning as miRNA targets were also investigated. Specifically, TCONS_00033722, TCONS_00044328, and TCONS_00059333 were targeted by a few well-studied salt-responsive miRNAs, supporting the involvement of miRNA and lncRNA interactions in the regulation of salt stress responses. Finally, a representative network of lncRNA-miRNA-mRNA was proposed and discussed to participate in duckweed salt stress via auxin signaling. Conclusions This study is the first report on salt-responsive lncRNAs in duckweed, and the findings will provide a solid foundation for in-depth functional characterization of duckweed lncRNAs in response to salt stress.
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Affiliation(s)
- Lili Fu
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China.,Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China
| | - Zehong Ding
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China. .,Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China.
| | - Deguan Tan
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China.,Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China
| | - Bingying Han
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China.,Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China
| | - Xuepiao Sun
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China.,Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China
| | - Jiaming Zhang
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China. .,Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China.
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170
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Choi SW, Ryu MY, Viczián A, Jung HJ, Kim GM, Arce AL, Achkar NP, Manavella P, Dolde U, Wenkel S, Molnár A, Nagy F, Cho SK, Yang SW. Light Triggers the miRNA-Biogenetic Inconsistency for De-etiolated Seedling Survivability in Arabidopsis thaliana. MOLECULAR PLANT 2020; 13:431-445. [PMID: 31678531 DOI: 10.1016/j.molp.2019.10.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/17/2019] [Accepted: 10/21/2019] [Indexed: 06/10/2023]
Abstract
The shift of dark-grown seedlings into light causes enormous transcriptome changes followed by a dramatic developmental transition. Here, we show that microRNA (miRNA) biogenesis also undergoes regulatory changes during de-etiolation. Etiolated seedlings maintain low levels of primary miRNAs (pri-miRNAs) and miRNA processing core proteins, such as Dicer-like 1, SERRATE, and HYPONASTIC LEAVES 1, whereas during de-etiolation both pri-miRNAs and the processing components accumulate to high levels. However, the levels of most miRNAs do not notably increase in response to light. To reconcile this inconsistency, we demonstrated that an unknown suppressor decreases miRNA-processing activity and light-induced SMALL RNA DEGRADING NUCLEASE 1 shortens the half-life of several miRNAs in de-etiolated seedlings. Taken together, these data suggest a novel mechanism, miRNA-biogenetic inconsistency, which accounts for the intricacy of miRNA biogenesis during de-etiolation. This mechanism is essential for the survival of de-etiolated seedlings after long-term skotomorphogenesis and their optimal adaptation to ever-changing light conditions.
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Affiliation(s)
- Suk Won Choi
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Moon Young Ryu
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - András Viczián
- Institute of Plant Biology, Biological Research Centre (BRC), Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - Hyun Ju Jung
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Gu Min Kim
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Agustin L Arce
- Instituto de Agrobiotecnología del Litoral (IAL) Centro Científico Tecnológico Santa Fe (CCT), Santa Fe, Argentina
| | - Natalia P Achkar
- Instituto de Agrobiotecnología del Litoral (IAL) Centro Científico Tecnológico Santa Fe (CCT), Santa Fe, Argentina
| | - Pablo Manavella
- Instituto de Agrobiotecnología del Litoral (IAL) Centro Científico Tecnológico Santa Fe (CCT), Santa Fe, Argentina
| | - Ulla Dolde
- Laboratoire de Recherche en Sciences Végétales, 24, chemin de Borde-Rouge, BP 42617 Auzeville, Castanet-Tolosan 31326, France
| | - Stephan Wenkel
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, Copenhagen 1871, Denmark
| | - Attila Molnár
- Institute of Molecular Plant Sciences, School of Biological Sciences, The King's Buildings, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Ferenc Nagy
- Institute of Plant Biology, Biological Research Centre (BRC), Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - Seok Keun Cho
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea.
| | - Seong Wook Yang
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea; Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, Copenhagen 1871, Denmark.
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171
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Yu X, Gong H, Cao L, Hou Y, Qu S. MicroRNA397b negatively regulates resistance of Malus hupehensis to Botryosphaeria dothidea by modulating MhLAC7 involved in lignin biosynthesis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 292:110390. [PMID: 32005395 DOI: 10.1016/j.plantsci.2019.110390] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/20/2019] [Accepted: 12/23/2019] [Indexed: 05/23/2023]
Abstract
MicroRNA (miRNA)-mediated post-transcriptional regulation plays a vital role in the response of plants to pathogens. Although the microRNA397 family has been implicated in physiological processes as an important regulator, little is known about its function in the resistance of plants to pathogens. Here, Malus hupehensis miR397, which was induced by Botryosphaeria dothidea infection, was identified to directly target M. hupehensis Laccase7 (MhLAC7). The expression analysis of mature Mh-miR397 and MhLAC7 revealed their partly opposite expression patterns. The coexpression of Mh-miR397b in MhLAC7 overexpressing Nicotiana benthamiana suppressed the accumulation of exogenous MhLAC7 and endogenous NbLAC7, which led to decreased lignin content and reduced plant resistance to Botrytis cinerea. As reflected by increasing disease severity and pathogen growth, overexpression of miR397b in both the resistant M. hupehensis and susceptible M. domestica 'Gala' resulted in an increased sensitivity to B. dothidea infection, owing to reduced LAC7 expression and lignin content; however, the inhibition of miR397 had opposite effects. MicroRNA397 functions as a negative regulator in the resistance of Malus to B. dothidea by modulating the LAC7 expression and lignin biosynthesis.
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Affiliation(s)
- Xinyi Yu
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, PR China
| | - Hongyong Gong
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Lifang Cao
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Yingjun Hou
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Shenchun Qu
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
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172
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Li J, Shen Y, Zhu J, Liu S, Zeng N, Zhan X. miR398 is involved in the relief of phenanthrene-induced oxidative toxicity in wheat roots. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 258:113701. [PMID: 31818619 DOI: 10.1016/j.envpol.2019.113701] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/30/2019] [Accepted: 11/29/2019] [Indexed: 05/28/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental pollutants and could produce oxidative toxicity to plants. Our previous study has shown that miR398 is involved in response to phenanthrene treatment by targeting CSD1 and CSD2. However, it is not clear which is essential for CSD1 and CSD2 and how miR398 changes. In this study, we performed discontinuous PAGE to separate superoxide dismutase (SOD) isozymes and found that two bands of the cytosolic Cu/Zn-SOD are induced by phenanthrene at day 5 and 7. Low expression of pri-miR398 and high expression of pre-miR398 indicate that the conversion process from pri-miR398 to pre-miR398 is impeded, which causes decrease in mature miR398. The relative expression of CSD1 is entirely up-regulated, further confirming the important role of CSD1 in response to phenanthrene exposure. Besides, the overexpression of WRKY implies its potential function in answering the call from phenanthrene stress. Therefore, it is concluded that the gene silencing of CSD1 recedes due to the biosynthesis inhibition of miR398, causing the increase of SOD activity in response to phenanthrene exposure in wheat roots. Our results are useful not only for better understanding miRNAs regulation in detoxication of reactive oxygen species, but also for alleviating the toxicity to crops caused by PAHs.
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Affiliation(s)
- Jinfeng Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, People's Republic of China
| | - Yu Shen
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, People's Republic of China
| | - Jiahui Zhu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, People's Republic of China
| | - Shiqi Liu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, People's Republic of China
| | - Nengde Zeng
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, People's Republic of China
| | - Xinhua Zhan
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, People's Republic of China.
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173
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Singh S, Kumar A, Panda D, Modi MK, Sen P. Identification and characterization of drought responsive miRNAs from a drought tolerant rice genotype of Assam. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.plgene.2019.100213] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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174
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Ahmed W, Li R, Xia Y, Bai G, Siddique KHM, Zhang H, Zheng Y, Yang X, Guo P. Comparative Analysis of miRNA Expression Profiles Between Heat-Tolerant and Heat-Sensitive Genotypes of Flowering Chinese Cabbage Under Heat Stress Using High-Throughput Sequencing. Genes (Basel) 2020; 11:E264. [PMID: 32121287 PMCID: PMC7140848 DOI: 10.3390/genes11030264] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/19/2020] [Accepted: 02/19/2020] [Indexed: 12/19/2022] Open
Abstract
Heat stress disturbs cellular homeostasis, thus usually impairs yield of flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee). MicroRNAs (miRNAs) play a significant role in plant responses to different stresses by modulating gene expression at the post-transcriptional level. However, the roles that miRNAs and their target genes may play in heat tolerance of flowering Chinese cabbage remain poorly characterized. The current study sequenced six small RNA libraries generated from leaf tissues of flowering Chinese cabbage collected at 0, 6, and 12 h after 38 °C heat treatment, and identified 49 putative novel miRNAs and 43 known miRNAs that differentially expressed between heat-tolerant and heat-sensitive flowering Chinese cabbage. Among them, 14 novel and nine known miRNAs differentially expressed only in the heat-tolerant genotype under heat-stress, therefore, their target genes including disease resistance protein TAO1-like, RPS6, reticuline oxidase-like protein, etc. might play important roles in enhancing heat-tolerance. Gene Ontology (GO) analysis revealed that targets of these differentially expressed miRNAs may play key roles in responses to temperature stimulus, cell part, cellular process, cell, membrane, biological regulation, binding, and catalytic activities. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified their important functions in signal transduction, environmental adaptation, global and overview maps, as well as in stress adaptation and in MAPK signaling pathways such as cell death. These findings provide insight into the functions of the miRNAs in heat stress tolerance of flowering Chinese cabbage.
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Affiliation(s)
- Waqas Ahmed
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Ronghua Li
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Yanshi Xia
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Guihua Bai
- United States Department of Agriculture - Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas 66506, United States of America
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture & Environment, The University of Western Australia, LB 5005, Perth WA 6001, Australia
| | - Hua Zhang
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510308, China
| | - Yansong Zheng
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510308, China
| | - Xinquan Yang
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Peiguo Guo
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou 510006, China
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175
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Asefpour Vakilian K. Machine learning improves our knowledge about miRNA functions towards plant abiotic stresses. Sci Rep 2020; 10:3041. [PMID: 32080299 PMCID: PMC7033123 DOI: 10.1038/s41598-020-59981-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/06/2020] [Indexed: 12/03/2022] Open
Abstract
During the last two decades, human has increased his knowledge about the role of miRNAs and their target genes in plant stress response. Biotic and abiotic stresses result in simultaneous tissue-specific up/down-regulation of several miRNAs. In this study, for the first time, feature selection algorithms have been used to investigate the contribution of individual plant miRNAs in Arabidopsis thaliana response towards different levels of several abiotic stresses including drought, salinity, cold, and heat. Results of information theory-based feature selection revealed that miRNA-169, miRNA-159, miRNA-396, and miRNA-393 had the highest contributions to plant response towards drought, salinity, cold, and heat, respectively. Furthermore, regression models, i.e., decision tree (DT), support vector machines (SVMs), and Naïve Bayes (NB) were used to predict the plant stress by having the plant miRNAs' concentration. SVM with Gaussian kernel was capable of predicting plant stress (R2 = 0.96) considering miRNA concentrations as input features. Findings of this study prove the performance of machine learning as a promising tool to investigate some aspects of miRNAs' contribution to plant stress responses that have been undiscovered until today.
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Affiliation(s)
- Keyvan Asefpour Vakilian
- Department of Agrotechnology, College of Abouraihan, University of Tehran, Tehran, Iran.
- Private Laboratory of Biosensor Applications, Hamadan, Iran.
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176
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Abd-Hamid NA, Ahmad-Fauzi MI, Zainal Z, Ismail I. Diverse and dynamic roles of F-box proteins in plant biology. PLANTA 2020; 251:68. [PMID: 32072251 DOI: 10.1007/s00425-020-03356-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 02/05/2020] [Indexed: 05/23/2023]
Abstract
The SCF complex is a widely studied multi-subunit ring E3 ubiquitin ligase that tags targeted proteins with ubiquitin for protein degradation by the ubiquitin 26S-proteasome system (UPS). The UPS is an important system that generally keeps cellular events tightly regulated by purging misfolded or damaged proteins and selectively degrading important regulatory proteins. The specificity of this post-translational regulation is controlled by F-box proteins (FBPs) via selective recognition of a protein-protein interaction motif at the C-terminal domain. Hence, FBPs are pivotal proteins in determining the plant response in multiple scenarios. It is not surprising that the FBP family is one of the largest protein families in the plant kingdom. In this review, the roles of FBPs, specifically in plants, are compiled to provide insights into their involvement in secondary metabolites, plant stresses, phytohormone signalling, plant developmental processes and miRNA biogenesis.
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Affiliation(s)
- Nur-Athirah Abd-Hamid
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Muhammad-Izzat Ahmad-Fauzi
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Zamri Zainal
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ismanizan Ismail
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
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177
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Kouhi F, Sorkheh K, Ercisli S. MicroRNA expression patterns unveil differential expression of conserved miRNAs and target genes against abiotic stress in safflower. PLoS One 2020; 15:e0228850. [PMID: 32069300 PMCID: PMC7028267 DOI: 10.1371/journal.pone.0228850] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 01/25/2020] [Indexed: 01/08/2023] Open
Abstract
Environmental stresses influence the growth and development of plants by influencing patterns of gene expression. Different regulators control gene expression, including transcription factors (TFs) and microRNAs. MicroRNAs (miRNAs: ~21 nucleotides long) are encoded by miRNA genes transcribed by RNA polymerase II (RNP-II) and play key roles in plant development and physiology. There is little knowledge currently available on miRNAs and their function in response to environmental stresses in safflower. To obtain more information on safflower miRNAs, we initially used a comparative genomics approach and succeeded in identifying 126 miRNAs belonging to 29 conserved families, along with their target genes. In this study, we investigated the expression profiles of seven conserved miRNAs related to drought, salinity, heat, and Cd stress in the leaf and root organs using qRT-PCR, for the first time. Gene Ontology (GO) analysis found that target genes of miRNAs are often TFs such as AP2/ERF and HD-ZIP as well as NAC domain-containing proteins. Expression analyses confirmed that miRNAs can play a vital role in keeping safflower stress-tolerant. Differential expression of miR156, miR162, miR164, miR166, miR172, miR398, and miR408 regulate the expression of their respective target genes. These genes activate several pathways leading to physiological and biochemical responses to abiotic stresses. Some conserved miRNAs were regulated by abiotic stresses. Our finding provides valuable information to understand miRNAs in relation to different abiotic stresses in safflower.
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Affiliation(s)
- Farshid Kouhi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Karim Sorkheh
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
- * E-mail: (SE); , (KS)
| | - Sezai Ercisli
- Department of Horticulture, Agricultural Faculty, Ataturk University, Erzurum, Turkey
- * E-mail: (SE); , (KS)
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178
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Yang Z, Zhu P, Kang H, Liu L, Cao Q, Sun J, Dong T, Zhu M, Li Z, Xu T. High-throughput deep sequencing reveals the important role that microRNAs play in the salt response in sweet potato (Ipomoea batatas L.). BMC Genomics 2020; 21:164. [PMID: 32066373 PMCID: PMC7027035 DOI: 10.1186/s12864-020-6567-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/07/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs), a class of small regulatory RNAs, have been proven to play important roles in plant growth, development and stress responses. Sweet potato (Ipomoea batatas L.) is an important food and industrial crop that ranks seventh in staple food production. However, the regulatory mechanism of miRNA-mediated abiotic stress response in sweet potato remains unclear. RESULTS In this study, we employed deep sequencing to identify both conserved and novel miRNAs from salinity-exposed sweet potato cultivars and its untreated control. Twelve small non-coding RNA libraries from NaCl-free (CK) and NaCl-treated (Na150) sweet potato leaves and roots were constructed for salt-responsive miRNA identification in sweet potatoes. A total of 475 known miRNAs (belonging to 66 miRNA families) and 175 novel miRNAs were identified. Among them, 51 (22 known miRNAs and 29 novel miRNAs) were significantly up-regulated and 76 (61 known miRNAs and 15 novel miRNAs) were significantly down-regulated by salinity stress in sweet potato leaves; 13 (12 known miRNAs and 1 novel miRNAs) were significantly up-regulated and 9 (7 known miRNAs and 2 novel miRNAs) were significantly down-regulated in sweet potato roots. Furthermore, 636 target genes of 314 miRNAs were validated by degradome sequencing. Deep sequencing results confirmed by qRT-PCR experiments indicated that the expression of most miRNAs exhibit a negative correlation with the expression of their targets under salt stress. CONCLUSIONS This study provides insights into the regulatory mechanism of miRNA-mediated salt response and molecular breeding of sweet potatoes though miRNA manipulation.
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Affiliation(s)
- Zhengmei Yang
- 0000 0000 9698 6425grid.411857.eKey Lab of Phylogeny and Comparative Genomics of the Jiangsu Province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 Jiangsu Province China
| | - Panpan Zhu
- 0000 0001 0356 9399grid.14005.30Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 500-757 South Korea
| | - Hunseung Kang
- 0000 0001 0356 9399grid.14005.30Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 500-757 South Korea
| | - Lin Liu
- 0000 0001 0472 9649grid.263488.3Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 Guangdong China
| | - Qinghe Cao
- Xuzhou Academy of Agricultural Sciences/Sweet Potato Research Institute, CAAS, Xuzhou, 221121 Jiangsu China
| | - Jian Sun
- 0000 0000 9698 6425grid.411857.eKey Lab of Phylogeny and Comparative Genomics of the Jiangsu Province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 Jiangsu Province China
| | - Tingting Dong
- 0000 0000 9698 6425grid.411857.eKey Lab of Phylogeny and Comparative Genomics of the Jiangsu Province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 Jiangsu Province China
| | - Mingku Zhu
- 0000 0000 9698 6425grid.411857.eKey Lab of Phylogeny and Comparative Genomics of the Jiangsu Province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 Jiangsu Province China
| | - Zongyun Li
- 0000 0000 9698 6425grid.411857.eKey Lab of Phylogeny and Comparative Genomics of the Jiangsu Province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 Jiangsu Province China
| | - Tao Xu
- 0000 0000 9698 6425grid.411857.eKey Lab of Phylogeny and Comparative Genomics of the Jiangsu Province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 Jiangsu Province China
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179
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Identification of Grafting-Responsive MicroRNAs Associated with Growth Regulation in Pecan [Carya illinoinensis (Wangenh.) K. Koch]. FORESTS 2020. [DOI: 10.3390/f11020196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Pecan [Carya illinoinensis (Wangenh.) K. Koch] is an economically important nut tree and grafting is often used for clonal propagation of cultivars. However, there is a lack of research on the effects of rootstocks on scions, which are meaningful targets for directed breeding of pecan grafts. MicroRNAs (miRNAs) play an important role in many biological processes, but the mechanism underlying the involvement of miRNAs in grafting-conferred physiological changes is unclear. To identify the grafting-responsive miRNAs that may be involved in the regulation of growth in grafted pecan, six small RNA libraries were constructed from the phloem of two groups of grafts with significantly different growth performance on short and tall rootstocks. A total of 441 conserved miRNAs belonging to 42 miRNA families and 603 novel miRNAs were identified. Among the identified miRNAs, 24 (seven conserved and 17 novel) were significantly differentially expressed by the different grafts, implying that they might be responsive to grafting and potentially involved in the regulation of graft growth. Ninety-five target genes were predicted for the differentially expressed miRNAs; gene annotation was available for 33 of these. Analysis of their targets suggested that the miRNAs may regulate auxin transport, cell activity, and inorganic phosphate (Pi) acquisition, and thereby, mediate pecan graft growth. Use of the recently-published pecan genome enabled identification of a substantial population of miRNAs, which are now available for further research. We also identified the grafting-responsive miRNAs and their potential roles in pecan graft growth, providing a basis for research on long-distance regulation in grafted pecan.
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180
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Fan G, Liu Y, Du H, Kuang T, Zhang Y. Identification of drought-responsive miRNAs in Hippophae tibetana using high-throughput sequencing. 3 Biotech 2020; 10:53. [PMID: 32015949 DOI: 10.1007/s13205-019-2045-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 12/30/2019] [Indexed: 10/25/2022] Open
Abstract
MicroRNAs (miRNAs) play an important role in abiotic stress response in plants. However, the total miRNA profiles (miRNome) and drought-responsive miRNAs in H. tibetana have not been identified. In this study, we present the first report on the miRNome profiles of H. tibetana by high-throughput sequencing technology. 116 known and 4 predicted novel miRNAs were all identified in six H. tibetana samples. Moreover, to reveal the drought-responsive miRNAs in H. tibetana, we compared the miRNA profiles of H. tibetana grown under water sufficiency and drought stress. The results showed that 39 known miRNAs were up-regulated, while 34 miRNAs were downregulated under drought stress. Moreover, the expression of two novel miRNAs (novel_mir_24 and novel_mir_87) showed notable changes in response to drought stress. The target genes of these differentially expressed miRNAs were mainly enriched in cellular process, metabolic process, cell part, and response to stimulus. The identified drought-responsive miRNAs might be used for improving drought tolerance in H. tibetana and other plateau plants.
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181
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Manoj SR, Karthik C, Kadirvelu K, Arulselvi PI, Shanmugasundaram T, Bruno B, Rajkumar M. Understanding the molecular mechanisms for the enhanced phytoremediation of heavy metals through plant growth promoting rhizobacteria: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 254:109779. [PMID: 31726280 DOI: 10.1016/j.jenvman.2019.109779] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 09/27/2019] [Accepted: 10/25/2019] [Indexed: 05/22/2023]
Abstract
Rapid industrialization, modern agricultural practices and other anthropogenic activities add a significant quantity of toxic heavy metals into the environment, which induces severe toxic effects on all form of living organisms, alter the soil properties and its biological activity. Remediation of heavy metal contaminated sites has become an urgent necessity. Among the existing strategies, phytoremediation is an eco-friendly and much convincing tool for the remediation of heavy metals. However, the applicability of phytoremediation in contaminated sites is restricted by two prime factors such as i) slow growth rate at higher metal contaminated sites and ii) metal bioavailability. This circumstance could be minimized and accelerate the phytoremediation efficiency by incorporating the potential plant growth promoting rhizobacterial (PGPR) as a combined approach. PGPR inoculation might improve the plant growth through the production of plant growth promoting substances and improve the heavy metal remediation efficiency by the secretion of chelating agents, acidification and redox changes. Moreover, rhizobacterial inoculation consolidates the metal tolerance and uptake by regulating the expression of various metal transporters, tolerant and metal chelator genes. However, the exact underlying molecular mechanism of PGPR mediated plant growth promotion and phytoremediation of heavy metals is poorly understood. Thus, the present review provides clear information about the molecular mechanisms excreted by PGPR strains in plant growth promotion and phytoremediation of heavy metals.
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Affiliation(s)
- Srinivas Ravi Manoj
- Plant and Microbial Biotechnology Laboratory, Department of Biotechnology, School of Biosciences, Periyar University, Salem, 636 011, Tamil Nadu, India
| | - Chinnannan Karthik
- DRDO - BU - Centre for Life Sciences, Bharathiar University Campus, Coimbatore, 641 046, Tamil Nadu, India.
| | - Krishna Kadirvelu
- DRDO - BU - Centre for Life Sciences, Bharathiar University Campus, Coimbatore, 641 046, Tamil Nadu, India.
| | - Padikasan Indra Arulselvi
- Plant and Microbial Biotechnology Laboratory, Department of Biotechnology, School of Biosciences, Periyar University, Salem, 636 011, Tamil Nadu, India
| | - Thangavel Shanmugasundaram
- DRDO - BU - Centre for Life Sciences, Bharathiar University Campus, Coimbatore, 641 046, Tamil Nadu, India
| | - Benedict Bruno
- Department of Environmental Sciences, Bharathiar University, Coimbatore, 641046, Tamil Nadu, India
| | - Mani Rajkumar
- Department of Environmental Sciences, Bharathiar University, Coimbatore, 641046, Tamil Nadu, India
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182
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Zhu H, Chen C, Zeng J, Yun Z, Liu Y, Qu H, Jiang Y, Duan X, Xia R. MicroRNA528, a hub regulator modulating ROS homeostasis via targeting of a diverse set of genes encoding copper-containing proteins in monocots. THE NEW PHYTOLOGIST 2020; 225:385-399. [PMID: 31429090 DOI: 10.1111/nph.16130] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/13/2019] [Indexed: 05/04/2023]
Abstract
Plant microRNAs (miRNAs) regulate vital cellular processes, including responses to extreme temperatures with which reactive oxygen species (ROS) are often closely associated. In the present study, it was found that aberrant temperatures caused extensive changes in abundance to numerous miRNAs in banana fruit, especially the copper (Cu)-associated miRNAs. Among them, miR528 was significantly downregulated under cold stress and it was found to target genes encoding polyphenol oxidase (PPO), different from those identified in rice and maize. Expression of PPO genes was upregulated by > 100-fold in cold conditions, leading to ROS surge and subsequent peel browning of banana fruit. Extensive comparative genomic analyses revealed that the monocot-specific miR528 can potentially target a large collection of genes encoding Cu-containing proteins. Most of them are actively involved in cellular ROS metabolism, including not only ROS generating oxidases, but also ROS scavenging enzymes. It also was demonstrated that miR528 has evolved a distinct preference of target genes in different monocots, with its target site varying in position among/within gene families, implying a highly dynamic process of target gene diversification. Its broad capacity to target genes encoding Cu-containing protein implicates miR528 as a key regulator for modulating the cellular ROS homeostasis in monocots.
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Affiliation(s)
- Hong Zhu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Chengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
- China Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, Guangzhou, 510642, China
| | - Jun Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Ze Yun
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yuanlong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
- China Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, Guangzhou, 510642, China
| | - Hongxia Qu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yueming Jiang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Xuewu Duan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
- China Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, Guangzhou, 510642, China
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183
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Wang R, Lan L, Liu L, Cheng L. Asymmetric polymerase chain reaction and loop-mediated isothermal amplification (AP-LAMP) for ultrasensitive detection of microRNAs. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2019.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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184
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Wu W, Wu Y, Hu D, Zhou Y, Hu Y, Chen Y, Chen M. PncStress: a manually curated database of experimentally validated stress-responsive non-coding RNAs in plants. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5809233. [PMID: 32185394 PMCID: PMC7078067 DOI: 10.1093/database/baaa001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/10/2019] [Accepted: 01/02/2020] [Indexed: 12/14/2022]
Abstract
Non-coding RNAs (ncRNAs) are recognized as key regulatory molecules in many biological processes. Accumulating evidence indicates that ncRNA-related mechanisms play important roles in plant stress responses. Although abundant plant stress-responsive ncRNAs have been identified, these experimentally validated results have not been gathered into a single public domain archive. Therefore, we established PncStress by curating experimentally validated stress-responsive ncRNAs in plants, including microRNAs, long non-coding RNAs and circular RNAs. The current version of PncStress contains 4227 entries from 114 plants covering 48 biotic and 91 abiotic stresses. For each entry, PncStress has biological information and network visualization. Serving as a manually curated database, PncStress will become a valuable resource in support of plant stress response research.
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Affiliation(s)
- Wenyi Wu
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yan Wu
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Dahui Hu
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yincong Zhou
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yanshi Hu
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yujie Chen
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.,College of Life Sciences and Food Engineering, Inner Mongolia University for the Nationalities, Tongliao 028043, China
| | - Ming Chen
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.,College of Life Sciences and Food Engineering, Inner Mongolia University for the Nationalities, Tongliao 028043, China
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185
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Identification, characterization and expression analysis of passion fruit ( Passiflora edulis) microRNAs. 3 Biotech 2020; 10:25. [PMID: 31938684 PMCID: PMC6938847 DOI: 10.1007/s13205-019-2000-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/29/2019] [Indexed: 02/04/2023] Open
Abstract
microRNAs (miRNAs) are highly conserved, short (~ 21-nucleotide), endogenous, non-coding RNA molecules that play major roles in post-transcriptional silencing by guiding target mRNA cleavage or translational inhibition. In this study, applying high-stringent genome-wide computational-based approaches, a total of 28 putative miRNAs belonging to 17 miRNA families were identified from an antioxidant-rich medicinal plant passion fruit (Passiflora edulis). Inter-tissue (leaves and fruits) and inter-varietal (yellow and purple fruit varieties) quantitative study of six putative passion fruit miRNAs (ped-miR160, ped-miR164, ped-miR166, ped-miR393, ped-miR394, and ped-miR398) showed differential expression. Using psRNATarget tool, a total of 25 potential target proteins of the characterized passion fruit miRNAs were also identified. Most of the target proteins identified in this study, including SQUAMOSA promoter binding, Class III HD-Zip, NAC, Scarecrow, APETALA2, Auxin response factor, MYB, and superoxide dismutase, were found to be involved in development, metabolism, and defense/stress response signaling.
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186
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Mishra R, Mohapatra R, Mahanty B, Joshi RK. Analysis of microRNAs and their targets from onion (Allium cepa) using genome survey sequences (GSS) and expressed sequence tags (ESTs). Bioinformation 2019; 15:907-917. [PMID: 32256010 PMCID: PMC7088424 DOI: 10.6026/97320630015907] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 12/30/2019] [Accepted: 12/31/2019] [Indexed: 01/31/2023] Open
Abstract
MicroRNAs are small non-coding RNAs of 21-24 nucleotides in length that acts as important modulators of gene expression related to numerous biological processes including development and defense response in eukaryotes. However, only a limited report on onion (Allium cepa) miRNAs is available and their associated role in growth and development of onion is not yet clear. Therefore, it is of interest to identify miRNAs and their targets in Allium cepa using the genome survey sequences (GSSs) and expressed sequence tags (ESTs) and deduce the functions of the target genes using gene ontology (GO) terms. We report 14 potential miRNAs belonging to 13 different families (miR162, miR168, miR172c, miR172e, miR398, miR400, miR414, miR1134, miR1223, miR6219, miR7725, miR8570, miR8703 and miR8752). BLAST analysis using psRNATarget server predicted 39 potential targets for the identified miRNAs majority of which were transcription factors implicated in plant growth, development, hormone signaling and stress responses. These data forms the basis for further analysis and verification towards understanding the miRNA mediated regulatory mechanism in Allium cepa.
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Affiliation(s)
- Rukmini Mishra
- School of Applied Sciences, Centurion University of Technology and Management, Odisha, India
| | - Rupesh Mohapatra
- Centre for Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751030, Odisha, India
| | - Bijayalaxmi Mahanty
- Dept. of Biotechnology, Rama Devi Women's University, Vidya Vihar, Bhubaneswar-751022, Odisha, India
| | - Raj Kumar Joshi
- Dept. of Biotechnology, Rama Devi Women's University, Vidya Vihar, Bhubaneswar-751022, Odisha, India
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187
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Sanz-Carbonell A, Marques MC, Martinez G, Gomez G. Dynamic architecture and regulatory implications of the miRNA network underlying the response to stress in melon. RNA Biol 2019; 17:292-308. [PMID: 31766933 DOI: 10.1080/15476286.2019.1697487] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
miRNAs are small RNAs that regulate mRNAs at both transcriptional and posttranscriptional level. In plants, miRNAs are involved in the regulation of different processes including development and stress-response. Elucidating how stress-responsive miRNAs are regulated is key to understand the global response to stress but also to develop efficient biotechnological tools that could help to cope with stress. Here, we describe a computational approach based on sRNA sequencing, transcript quantification and degradome data to analyse the accumulation, function and structural organization of melon miRNAs reactivated under seven biotic and abiotic stress conditions at two and four days post-treatment. Our pipeline allowed us to identify fourteen stress-responsive miRNAs (including evolutionary conserved such as miR156, miR166, miR172, miR319, miR398, miR399, miR894 and miR408) at both analysed times. According to our analysis miRNAs were categorized in three groups showing a broad-, intermediate- or narrow- response range. miRNAs reactive to a broad range of environmental cues appear as central components in the stress-response network. The strictly coordinated response of miR398 and miR408 (broad response-range) to the seven stress treatments during the period analysed here reinforces this notion. Although both, the amplitude and diversity of the miRNA-related response to stress changes during the exposition time, the architecture of the miRNA-network is conserved. This organization of miRNA response to stress is also conserved in rice and soybean supporting the conservation of miRNA-network organization in other crops. Overall, our work sheds light into how miRNA networks in plants organize and function during stress.
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Affiliation(s)
- Alejandro Sanz-Carbonell
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat de València (UV), Parc Científic, Paterna, Spain.,Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Maria Carmen Marques
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat de València (UV), Parc Científic, Paterna, Spain.,Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - German Martinez
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat de València (UV), Parc Científic, Paterna, Spain.,Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Gustavo Gomez
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat de València (UV), Parc Científic, Paterna, Spain.,Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
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188
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Identification of miRNA, their targets and miPEPs in peanut (Arachis hypogaea L.). Comput Biol Chem 2019; 83:107100. [DOI: 10.1016/j.compbiolchem.2019.107100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 07/04/2019] [Accepted: 08/06/2019] [Indexed: 01/28/2023]
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189
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Manuweera B, Reynolds G, Kahanda I. Computational methods for the ab initio identification of novel microRNA in plants: a systematic review. PeerJ Comput Sci 2019; 5:e233. [PMID: 33816886 PMCID: PMC7924660 DOI: 10.7717/peerj-cs.233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 10/14/2019] [Indexed: 06/12/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) play a vital role as post-transcriptional regulators in gene expression. Experimental determination of miRNA sequence and structure is both expensive and time consuming. The next-generation sequencing revolution, which facilitated the rapid accumulation of biological data has brought biology into the "big data" domain. As such, developing computational methods to predict miRNAs has become an active area of inter-disciplinary research. OBJECTIVE The objective of this systematic review is to focus on the developments of ab initio plant miRNA identification methods over the last decade. DATA SOURCES Five databases were searched for relevant articles, according to a well-defined review protocol. STUDY SELECTION The search results were further filtered using the selection criteria that only included studies on novel plant miRNA identification using machine learning. DATA EXTRACTION Relevant data from each study were extracted in order to carry out an analysis on their methodologies and findings. RESULTS Results depict that in the last decade, there were 20 articles published on novel miRNA identification methods in plants of which only 11 of them were primarily focused on plant microRNA identification. Our findings suggest a need for more stringent plant-focused miRNA identification studies. CONCLUSION Overall, the study accuracies are of a satisfactory level, although they may generate a considerable number of false negatives. In future, attention must be paid to the biological plausibility of computationally identified miRNAs to prevent further propagation of biologically questionable miRNA sequences.
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Affiliation(s)
- Buwani Manuweera
- Gianforte School of Computing, Montana State University, Bozeman, MT, United States of America
| | - Gillian Reynolds
- Gianforte School of Computing, Montana State University, Bozeman, MT, United States of America
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, United States of America
| | - Indika Kahanda
- Gianforte School of Computing, Montana State University, Bozeman, MT, United States of America
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190
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Eichmeier A, Kiss T, Penazova E, Pecenka J, Berraf-Tebbal A, Baranek M, Pokluda R, Cechova J, Gramaje D, Grzebelus D. MicroRNAs in Vitis vinifera cv. Chardonnay Are Differentially Expressed in Response to Diaporthe Species. Genes (Basel) 2019; 10:E905. [PMID: 31703418 PMCID: PMC6896114 DOI: 10.3390/genes10110905] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/31/2019] [Accepted: 11/05/2019] [Indexed: 01/08/2023] Open
Abstract
Diaporthe species are important pathogens, saprobes, and endophytes on grapevines. Several species are known, either as agents of pre- or post-harvest infections, as causal agents of many relevant diseases, including swelling arm, trunk cankers, leaf spots, root and fruit rots, wilts, and cane bleaching. A growing body of evidence exists that a class of small non-coding endogenous RNAs, known as microRNAs (miRNAs), play an important role in post-transcriptional gene regulation, during plant development and responses to biotic and abiotic stresses. In this study, we explored differentially expressed miRNAs in response to Diaporthe eres and Diaporthe bohemiae infection in Vitis vinifera cv. Chardonnay under in vitro conditions. We used computational methods to predict putative miRNA targets in order to explore the involvement of possible pathogen response pathways. We identified 136 known and 41 new miRNA sequence variants, likely generated through post-transcriptional modifications. In the Diaporthe eres treatment, 61 known and 17 new miRNAs were identified while in the Diaporthe bohemiae treatment, 101 known and 21 new miRNAs were revealed. Our results contribute to further understanding the role miRNAs play during plant pathogenesis, which is possibly crucial in understanding disease symptom development in grapevines infected by D. eres and D. bohemiae.
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Affiliation(s)
- Ales Eichmeier
- Faculty of Horticulture, Mendeleum-Institute of Genetics, Mendel University in Brno, Valticka 334, 69144 Lednice, Czech Republic; (T.K.); (E.P.); (J.P.); (A.B.-T.); (M.B.); (R.P.); (J.C.); (D.G.)
| | - Tomas Kiss
- Faculty of Horticulture, Mendeleum-Institute of Genetics, Mendel University in Brno, Valticka 334, 69144 Lednice, Czech Republic; (T.K.); (E.P.); (J.P.); (A.B.-T.); (M.B.); (R.P.); (J.C.); (D.G.)
| | - Eliska Penazova
- Faculty of Horticulture, Mendeleum-Institute of Genetics, Mendel University in Brno, Valticka 334, 69144 Lednice, Czech Republic; (T.K.); (E.P.); (J.P.); (A.B.-T.); (M.B.); (R.P.); (J.C.); (D.G.)
| | - Jakub Pecenka
- Faculty of Horticulture, Mendeleum-Institute of Genetics, Mendel University in Brno, Valticka 334, 69144 Lednice, Czech Republic; (T.K.); (E.P.); (J.P.); (A.B.-T.); (M.B.); (R.P.); (J.C.); (D.G.)
| | - Akila Berraf-Tebbal
- Faculty of Horticulture, Mendeleum-Institute of Genetics, Mendel University in Brno, Valticka 334, 69144 Lednice, Czech Republic; (T.K.); (E.P.); (J.P.); (A.B.-T.); (M.B.); (R.P.); (J.C.); (D.G.)
| | - Miroslav Baranek
- Faculty of Horticulture, Mendeleum-Institute of Genetics, Mendel University in Brno, Valticka 334, 69144 Lednice, Czech Republic; (T.K.); (E.P.); (J.P.); (A.B.-T.); (M.B.); (R.P.); (J.C.); (D.G.)
| | - Robert Pokluda
- Faculty of Horticulture, Mendeleum-Institute of Genetics, Mendel University in Brno, Valticka 334, 69144 Lednice, Czech Republic; (T.K.); (E.P.); (J.P.); (A.B.-T.); (M.B.); (R.P.); (J.C.); (D.G.)
| | - Jana Cechova
- Faculty of Horticulture, Mendeleum-Institute of Genetics, Mendel University in Brno, Valticka 334, 69144 Lednice, Czech Republic; (T.K.); (E.P.); (J.P.); (A.B.-T.); (M.B.); (R.P.); (J.C.); (D.G.)
| | - David Gramaje
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas—Universidad de la Rioja—Gobierno de La Rioja, Ctra. de Burgos Km. 6, 26007 Logroño, Spain;
| | - Dariusz Grzebelus
- Faculty of Horticulture, Mendeleum-Institute of Genetics, Mendel University in Brno, Valticka 334, 69144 Lednice, Czech Republic; (T.K.); (E.P.); (J.P.); (A.B.-T.); (M.B.); (R.P.); (J.C.); (D.G.)
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, 31425 Krakow, Poland
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191
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Cervera-Seco L, Marques MAC, Sanz-Carbonell A, Marquez-Molins J, Carbonell A, Darï S JA, Gomez G. Identification and Characterization of Stress-Responsive TAS3-Derived TasiRNAs in Melon. PLANT & CELL PHYSIOLOGY 2019; 60:2382-2393. [PMID: 31290971 DOI: 10.1093/pcp/pcz131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 06/27/2019] [Indexed: 05/27/2023]
Abstract
Small interfering RNAs (siRNA) are key regulators of gene expression that play essential roles in diverse biological processes. Trans-acting siRNAs (tasiRNAs) are a class of plant-endogenous siRNAs that lead the cleavage of nonidentical transcripts. TasiRNAs are usually involved in fine-tuning development. However, increasing evidence supports that tasiRNAs may be involved in stress response. Melon is a crop of great economic importance extensively cultivated in semiarid regions frequently exposed to changing environmental conditions that limit its productivity. However, knowledge of the precise role of siRNAs in general, and of tasiRNAs in particular, in regulating the response to adverse environmental conditions is limited. Here, we provide the first comprehensive analysis of computationally inferred melon-tasiRNAs responsive to two biotic (viroid-infection) and abiotic (cold treatment) stress conditions. We identify two TAS3-loci encoding to length (TAS3-L) and short (TAS3-S) transcripts. The TAS candidates predicted from small RNA-sequencing data were characterized according to their chromosome localization and expression pattern in response to stress. The functional activity of cmTAS genes was validated by transcript quantification and degradome assays of the tasiRNA precursors and their predicted targets. Finally, the functionality of a representative cmTAS3-derived tasiRNA (TAS3-S) was confirmed by transient assays showing the cleavage of ARF target transcripts.
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Affiliation(s)
- Luis Cervera-Seco
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Cient�ficas (CSIC)-Universitat de Val�ncia (UV), Parc Cient�fic, Cat. Agust�n Escardino 9, Paterna, Spain
| | - Marï A Carmen Marques
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Cient�ficas (CSIC)-Universitat de Val�ncia (UV), Parc Cient�fic, Cat. Agust�n Escardino 9, Paterna, Spain
| | - Alejandro Sanz-Carbonell
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Cient�ficas (CSIC)-Universitat de Val�ncia (UV), Parc Cient�fic, Cat. Agust�n Escardino 9, Paterna, Spain
| | - Joan Marquez-Molins
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Cient�ficas (CSIC)-Universitat de Val�ncia (UV), Parc Cient�fic, Cat. Agust�n Escardino 9, Paterna, Spain
| | - Alberto Carbonell
- Instituto de Biolog�a Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Cient�ficas (CSIC) Universitat Polit�cnica de Val�ncia, CPI 8E, Av. de los Naranjos s/n, Valencia, Spain
| | - Josï-Antonio Darï S
- Instituto de Biolog�a Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Cient�ficas (CSIC) Universitat Polit�cnica de Val�ncia, CPI 8E, Av. de los Naranjos s/n, Valencia, Spain
| | - Gustavo Gomez
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Cient�ficas (CSIC)-Universitat de Val�ncia (UV), Parc Cient�fic, Cat. Agust�n Escardino 9, Paterna, Spain
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192
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Seeve CM, Sunkar R, Zheng Y, Liu L, Liu Z, McMullen M, Nelson S, Sharp RE, Oliver MJ. Water-deficit responsive microRNAs in the primary root growth zone of maize. BMC PLANT BIOLOGY 2019; 19:447. [PMID: 31651253 PMCID: PMC6814125 DOI: 10.1186/s12870-019-2037-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/12/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND MicroRNA-mediated gene regulatory networks play a significant role in plant growth and development and environmental stress responses. RESULTS We identified 79 microRNAs (miRNAs) and multiple miRNA variants (isomiRs) belonging to 26 miRNA families in the primary root growth zone of maize seedlings grown at one of three water potentials: well-watered (- 0.02 MPa), mild water deficit stress (- 0.3 MPa), and severe water deficit stress (- 1.6 MPa). The abundances of 3 miRNAs (mild stress) and 34 miRNAs representing 17 families (severe stress) were significantly different in water-deficit stressed relative to well-watered controls (FDR < 0.05 and validated by stem loop RT-qPCR). Degradome sequencing revealed 213 miRNA-regulated transcripts and trancriptome profiling revealed that the abundance of 77 (miRNA-regulated) were regulated by water-defecit stress. miR399e,i,j-3p was strongly regulated by water-defcit stress implicating the possibility of nutrient deficiency during stress. CONCLUSIONS We have identified a number of maize miRNAs that respond to specific water deficits applied to the primary root growth zone. We have also identified transcripts that are targets for miRNA regulation in the root growth zone under water-deficit stress. The miR399e,i,j-3p that is known to regulate phosphate uptake in response to nutrient deficiencies responds to water-deficit stress, however, at the seedling stage the seed provides adequate nutrients for root growth thus miR399e,i,j-3p may play a separate role in water-deficit responses. A water-deficit regulated maize transcript, similar to known miR399 target mimics, was identified and we hypothesized that it is another regulatory player, moderating the role of miR399e,i,j-3p, in primary root growth zone water deficit responses.
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Affiliation(s)
- Candace M. Seeve
- USDA-ARS, Plant Genetics Research Unit, Columbia, MO 65211 USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211 USA
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078 USA
| | - Yun Zheng
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, 650500 Yunnan China
| | - Li Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500 Yunnan China
| | - Zhijie Liu
- Huazhong Agricultural University, Wuhan, 430070 Hubei Province China
| | - Michael McMullen
- Division of Plant Sciences, Columbia, University of Missouri, Columbia, MO 65211 USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211 USA
| | - Sven Nelson
- USDA-ARS, Plant Genetics Research Unit, Columbia, MO 65211 USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211 USA
| | - Robert E. Sharp
- Division of Plant Sciences, Columbia, University of Missouri, Columbia, MO 65211 USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211 USA
| | - Melvin J. Oliver
- USDA-ARS, Plant Genetics Research Unit, Columbia, MO 65211 USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211 USA
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193
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Ahmed W, Xia Y, Zhang H, Li R, Bai G, Siddique KHM, Guo P. Identification of conserved and novel miRNAs responsive to heat stress in flowering Chinese cabbage using high-throughput sequencing. Sci Rep 2019; 9:14922. [PMID: 31624298 PMCID: PMC6797766 DOI: 10.1038/s41598-019-51443-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 10/01/2019] [Indexed: 12/12/2022] Open
Abstract
Plant microRNAs (miRNAs) are noncoding and endogenous key regulators that play significant functions in regulating plant responses to stress, and plant growth and development. Heat stress is a critical abiotic stress that reduces the yield and quality of flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee). However, limited information is available on whether miRNAs are involved in the regulation of heat stress in B. campestris. A high-throughput sequencing approach was used to identify novel and conserved heat-responsive miRNAs in four small RNA libraries of flowering Chinese cabbage using leaves collected at 0 h, 1 h, 6 h and 12 h after a 38 °C heat-stress treatment. The analysis identified 41 conserved miRNAs (belonging to 19 MIR families), of which MIR156, MIR159, MIR168, MIR171 and MIR1885 had the most abundant molecules. Prediction and evaluation of novel miRNAs using the unannotated reads resulted in 18 candidate miRNAs. Differential expression analysis showed that most of the identified miRNAs were downregulated in heat-treated groups. To better understand functional importance, bioinformatic analysis predicted 432 unique putative target miRNAs involved in cells, cell parts, catalytic activity, cellular processes and abiotic stress responses. Furthermore, the Kyoto Encyclopedia of Genes and Genomes maps of flowering Chinese cabbage identified the significant role of miRNAs in stress adaptation and stress tolerance, and in several mitogen-activated protein kinases signaling pathways including cell death. This work presents a comprehensive study of the miRNAs for understanding the regulatory mechanisms and their participation in the heat stress of flowering Chinese cabbage.
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Affiliation(s)
- Waqas Ahmed
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Yanshi Xia
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Hua Zhang
- Guangzhou Academy of Agricultural Sciences, Guangzhou, 510308, China
| | - Ronghua Li
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Guihua Bai
- United States Department of Agriculture - Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas, 66506, United States of America
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture & Environment, The University of Western Australia, LB 5005, Perth, WA, 6001, Australia
| | - Peiguo Guo
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, 510006, China.
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194
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Wu S, Tan H, Hao X, Xie Z, Wang X, Li D, Tian L. Profiling miRNA expression in photo-thermo-sensitive male genic sterility line (PTGMS) PA64S under high and low temperature. PLANT SIGNALING & BEHAVIOR 2019; 14:1679015. [PMID: 31610741 PMCID: PMC6866692 DOI: 10.1080/15592324.2019.1679015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/29/2019] [Accepted: 10/07/2019] [Indexed: 06/10/2023]
Abstract
Peiai64S (PA64S) is a photo-thermo-sensitive genic male sterile line (PTGMS), with wide application in hybrid seed production in rice (Oryza sativa L.). Micro-RNAs are 21-24 nt, endogenously expressed small RNAs that have been characterized in various developmental stages of rice, but none have been studied with respect to the regulation of TGMS in rice. Here, we employed high-throughput sequencing to identify expression profiles of miRNAs in the anthers of PA64S at high (PA64S-H) and low temperature (PA64S-L). Two small RNA libraries from PA64S-H and PA64-L anthers were sequenced, and 263 known and 321 novel candidate miRNAs were identified. Based on the number of sequencing reads, a total of 133 known miRNAs were found to be differentially expressed between PA64S-H and PA64S-L. Target prediction showed that the target genes encode MYB and TCP transcription factors, and bHLH proteins. These target genes are related to pollen development and male sterility, suggesting that miRNA/targets may play roles in regulating TGMS in rice. Further, starch and sucrose metabolism pathways, sphingolipid metabolism, arginine and proline metabolism, and plant hormone signal transduction pathways were enriched by KEGG pathway annotation. These findings contribute to our understanding of the role of miRNAs during anther development and TGMS occurrence in rice.
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Affiliation(s)
- Sha Wu
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, P.R. China
| | - Hang Tan
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, P.R. China
| | - Xiaohua Hao
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, P.R. China
| | - Zijing Xie
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, P.R. China
| | - Xiaohui Wang
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, P.R. China
| | - Dongping Li
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, P.R. China
| | - Lianfu Tian
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, P.R. China
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195
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Liu C, Yang X, Yan Z, Fan Y, Feng G, Liu D. Analysis of differential gene expression in cold-tolerant vs. cold-sensitive varieties of snap bean (Phaseolus vulgaris L.) in response to low temperature stress. Genes Genomics 2019; 41:1445-1455. [PMID: 31535316 DOI: 10.1007/s13258-019-00870-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 09/04/2019] [Indexed: 11/24/2022]
Abstract
BACKGROUND Snap bean, Phaseolus vulgaris L., as a warm-season vegetable, low temperature stress seriously affect the yield and quality. At present, little is known about the genes and molecular regulation mechanism in cold response in snap bean exposed to low temperature. OBJECTIVES Our objectives were to identify the low temperature response genes in snap bean and to examine differences in the gene response between cold-tolerant and cold-sensitive genotypes. METHODS We used two highly inbred snap bean lines in this study, the cold-tolerant line '120', and the cold-sensitive line '093'. The plants were grown to the three leaf and one heart stage and exposed to 4 °C low temperature. We used RNA sequencing (RNA-seq) to analyze the differences of gene expression. RESULTS 988 and 874 cold-responsive genes were identified in 'T120 vs CK120' and 'T093 vs CK093' ('T' stands for low temperature treatment, and 'CK' stands for control at room temperature), respectively. Of these, 555 and 442 genes were unique to cold-stressed lines '120' and '093', respectively compared to the control. Our analysis of these differentially expressed genes indicates that Ca2+, ROS, and hormones act as signaling molecules that play important roles in low temperature response in P. vulgaris. Altering the expression of genes in these signaling pathways activates expression of downstream response genes which can interact with other signaling regulatory networks. This may maintained the balance of ROS and hormones, making line '120' more cold-tolerant than line '093'. CONCLUSION Our results provide a preliminarily understanding of the molecular basis of low temperature response in snap bean, and also establish a foundation for the future genetic improvement of cold sensitivity in snap bean by incorporating genes for cold tolerance.
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Affiliation(s)
- Chang Liu
- Horticulture Department, Academy of Crop Science, Heilongjiang University, 74 Xuefu Road, Harbin, 150000, Heilongjiang, China.,Work Station of Science and Technique for Post-doctoral in Sugar Beet Institute Affiliated to Heilongjiang University, 74 Xuefu Road, Harbin, 150000, Heilongjiang, China.,Post-doctoral Research Station Affiliated To Northeast Agricultural University, 59 Mucai Road, Harbin, 150000, Heilongjiang, China
| | - Xiaoxu Yang
- Horticulture Department, Academy of Crop Science, Heilongjiang University, 74 Xuefu Road, Harbin, 150000, Heilongjiang, China.,Work Station of Science and Technique for Post-doctoral in Sugar Beet Institute Affiliated to Heilongjiang University, 74 Xuefu Road, Harbin, 150000, Heilongjiang, China.,Post-doctoral Research Station Affiliated To Northeast Agricultural University, 59 Mucai Road, Harbin, 150000, Heilongjiang, China
| | - Zhishan Yan
- Horticulture Department, Academy of Crop Science, Heilongjiang University, 74 Xuefu Road, Harbin, 150000, Heilongjiang, China
| | - Youjun Fan
- Horticulture Department, Academy of Crop Science, Heilongjiang University, 74 Xuefu Road, Harbin, 150000, Heilongjiang, China
| | - Guojun Feng
- Horticulture Department, Academy of Crop Science, Heilongjiang University, 74 Xuefu Road, Harbin, 150000, Heilongjiang, China.
| | - Dajun Liu
- Horticulture Department, Academy of Crop Science, Heilongjiang University, 74 Xuefu Road, Harbin, 150000, Heilongjiang, China.
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196
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Jeyaraj A, Wang X, Wang S, Liu S, Zhang R, Wu A, Wei C. Identification of Regulatory Networks of MicroRNAs and Their Targets in Response to Colletotrichum gloeosporioides in Tea Plant ( Camellia sinensis L.). FRONTIERS IN PLANT SCIENCE 2019; 10:1096. [PMID: 31572415 PMCID: PMC6751461 DOI: 10.3389/fpls.2019.01096] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/09/2019] [Indexed: 05/21/2023]
Abstract
Anthracnose disease is caused by Colletotrichum gloeosporioides, and is common in leaves of the tea plant (Camellia sinensis). MicroRNAs (miRNAs) have been known as key modulators of gene expression in response to environmental stresses, disease resistance, defense responses, and plant immunity. However, the role of miRNAs in responses to C. gloeosporioides remains unexplored in tea plant. Therefore, in the present study, six miRNA sequencing data sets and two degradome data sets were generated from C. gloeosporioides-inoculated and control tea leaves. A total of 485 conserved and 761 novel miRNAs were identified. Of those, 239 known and 369 novel miRNAs exhibited significantly differential expression under C. gloeosporioides stress. One thousand one hundred thirty-four and 596 mRNAs were identified as targets of 389 conserved and 299 novel miRNAs by degradome analysis, respectively. Based on degradome analysis, most of the predicted targets are negatively correlated with their corresponding conserved and novel miRNAs. The expression levels of 12 miRNAs and their targets were validated by quantitative real-time PCR. A negative correlation between expression profiles of five miRNAs (PC-5p-80764_22, csn-miR160c, csn-miR828a, csn-miR164a, and csn-miR169e) and their targets (WRKY, ARF, MYB75, NAC, and NFY transcription factor) was observed. The predicted targets of five interesting miRNAs were further validated through 5'RLM-RACE. Furthermore, Gene Ontology and metabolism pathway analysis revealed that most of the target genes were involved in the regulation of auxin pathway, ROS scavenging pathway, salicylic acid mediated pathway, receptor kinases, and transcription factors for plant growth and development as well as stress responses in tea plant against C. gloeosporioides stress. This study enriches the resources of stress-responsive miRNAs and their targets in C. sinensis and thus provides novel insights into the miRNA-mediated regulatory mechanisms, which could contribute to the enhanced susceptibility of C. gloeosporioides in tea plant.
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Affiliation(s)
- Anburaj Jeyaraj
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- Department of Biotechnology, Karpagam Academy of Higher Education, Coimbatore, India
| | - Xuewen Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- Department of Genetics, University of Georgia, Athens, United States
| | - Shuangshuang Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Ran Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Ailin Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
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197
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Ahmed W, Xia Y, Li R, Bai G, Siddique KHM, Guo P. Non-coding RNAs: Functional roles in the regulation of stress response in Brassica crops. Genomics 2019; 112:1419-1424. [PMID: 31430515 DOI: 10.1016/j.ygeno.2019.08.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 07/03/2019] [Accepted: 08/16/2019] [Indexed: 12/22/2022]
Abstract
Brassica crops face a combination of different abiotic and biotic stresses in the field that can reduce plant growth and development by affecting biochemical and morpho-physiological processes. Emerging evidence suggests that non-coding RNAs (ncRNAs), especially microRNAs (miRNAs) and long ncRNAs (lncRNAs), play a significant role in the modulation of gene expression in response to plant stresses. Recent advances in computational and experimental approaches are of great interest for identifying and functionally characterizing ncRNAs. While progress in this field is limited, numerous ncRNAs involved in the regulation of gene expression in response to stress have been reported in Brassica. In this review, we summarize the modes of action and functions of stress-related miRNAs and lncRNAs in Brassica as well as the approaches used to identify ncRNAs.
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Affiliation(s)
- Waqas Ahmed
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Yanshi Xia
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Ronghua Li
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Guihua Bai
- United States Department of Agriculture - Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas 66506, United States
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture & Environment, The University of Western Australia, LB 5005, Perth, WA 6001, Australia
| | - Peiguo Guo
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China.
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198
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Zhang L, Zou J, Li S, Wang B, Raboanatahiry N, Li M. Characterization and expression profiles of miRNAs in the triploid hybrids of Brassica napus and Brassica rapa. BMC Genomics 2019; 20:649. [PMID: 31412776 PMCID: PMC6694508 DOI: 10.1186/s12864-019-6001-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 07/26/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Polyploidy provides a means of interspecific genome transfer to incorporate preferable traits from progenitor to progeny. However, few studies on miRNA expression profiles of interspecific hybrids of B. napus (AnAnCnCn) and B. rapa (ArAr) have been reported. RESULTS Here, we apply small RNA sequencing to explore miRNA expression patterns between B. napus, B. rapa and their F1 hybrid. Bioinformatics analysis identified 376, 378, 383 conserved miRNAs and 82, 76, 82 novel miRNAs in B. napus, B. rapa and the F1 hybrid, respectively. Moreover, 213 miRNAs were found to be differentially expressed between B. napus, B. rapa and the F1 hybrid. The present study also shows 211 miRNAs, including 77 upregulated and 134 downregulated miRNAs, to be nonadditively expressed in the F1 hybrid. Furthermore, miRNA synteny analysis revealed high genomic conservation between the genomes of B. napus, B. rapa and their F1 hybrid, with some miRNA loss and gain events in the F1 hybrid. CONCLUSIONS This study not only provides useful resources for exploring global miRNA expression patterns and genome structure but also facilitates genetic research on the roles of miRNAs in genomic interactions of Brassica allopolyploids.
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Affiliation(s)
- Libin Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jun Zou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shisheng Li
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000, China
| | - Baoshan Wang
- College of Life Science, Shandong Normal University, Jinan, 250000, China
| | - Nadia Raboanatahiry
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Maoteng Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China. .,Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000, China.
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199
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Wang J, Deng Y, Zhou Y, Liu D, Yu H, Zhou Y, Lv J, Ou L, Li X, Ma Y, Dai X, Liu F, Zou X, Ouyang B, Li F. Full-length mRNA sequencing and gene expression profiling reveal broad involvement of natural antisense transcript gene pairs in pepper development and response to stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:763-783. [PMID: 31009127 DOI: 10.1111/tpj.14351] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/18/2019] [Accepted: 03/27/2019] [Indexed: 06/09/2023]
Abstract
Pepper is an important vegetable with great economic value and unique biological features. In the past few years, significant development has been made toward understanding the huge complex pepper genome; however, pepper functional genomics has not been well studied. To better understand the pepper gene structure and pepper gene regulation, we conducted full-length mRNA sequencing by PacBio sequencing and obtained 57 862 high-quality full-length mRNA sequences derived from 18 362 previously annotated and 5769 newly detected genes. New gene models were built that combined the full-length mRNA sequences and corrected approximately 500 fragmented gene models from previous annotations. Based on the full-length mRNA, we identified 4114 and 5880 pepper genes forming natural antisense transcript (NAT) genes in-cis and in-trans, respectively. Most of these genes accumulate small RNAs in their overlapping regions. By analyzing these NAT gene expression patterns in our transcriptome data, we identified many NAT pairs responsive to a variety of biological processes in pepper. Pepper formate dehydrogenase 1 (FDH1), which is required for R-gene-mediated disease resistance, may be regulated by nat-siRNAs and participate in a positive feedback loop in salicylic acid biosynthesis during resistance responses. Several cis-NAT pairs and subgroups of trans-NAT genes were responsive to pepper pericarp and placenta development, which may play roles in capsanthin and capsaicin biosynthesis. Using a comparative genomics approach, the evolutionary mechanisms of cis-NATs were investigated, and we found that an increase in intergenic sequences accounted for the loss of most cis-NATs, while transposon insertion contributed to the formation of most new cis-NATs. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at http://bigd.big.ac.cn/gsa Accession number, CRA001412.
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Affiliation(s)
- Jubin Wang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, HB, China
| | - Yingtian Deng
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, HB, China
| | - Yingjia Zhou
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, HB, China
| | - Dan Liu
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, HB, China
| | - Huiyang Yu
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, HB, China
| | - Yuhong Zhou
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, HB, China
| | - Junheng Lv
- Hunan Institute of Vegetable Research, Academy of Agricultural Sciences of Hunan Province, Changsha, HN, China
| | - Lijun Ou
- Hunan Institute of Vegetable Research, Academy of Agricultural Sciences of Hunan Province, Changsha, HN, China
| | - Xuefeng Li
- Hunan Institute of Vegetable Research, Academy of Agricultural Sciences of Hunan Province, Changsha, HN, China
| | - Yanqing Ma
- Hunan Institute of Vegetable Research, Academy of Agricultural Sciences of Hunan Province, Changsha, HN, China
| | - Xiongze Dai
- Hunan Institute of Vegetable Research, Academy of Agricultural Sciences of Hunan Province, Changsha, HN, China
| | - Feng Liu
- Hunan Institute of Vegetable Research, Academy of Agricultural Sciences of Hunan Province, Changsha, HN, China
| | - Xuexiao Zou
- Hunan Institute of Vegetable Research, Academy of Agricultural Sciences of Hunan Province, Changsha, HN, China
| | - Bo Ouyang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, HB, China
| | - Feng Li
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, HB, China
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200
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Hunt M, Banerjee S, Surana P, Liu M, Fuerst G, Mathioni S, Meyers BC, Nettleton D, Wise RP. Small RNA discovery in the interaction between barley and the powdery mildew pathogen. BMC Genomics 2019; 20:610. [PMID: 31345162 PMCID: PMC6657096 DOI: 10.1186/s12864-019-5947-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/30/2019] [Indexed: 01/04/2023] Open
Abstract
Background Plants encounter pathogenic and non-pathogenic microorganisms on a nearly constant basis. Small RNAs such as siRNAs and miRNAs/milRNAs influence pathogen virulence and host defense responses. We exploited the biotrophic interaction between the powdery mildew fungus, Blumeria graminis f. sp. hordei (Bgh), and its diploid host plant, barley (Hordeum vulgare) to explore fungal and plant sRNAs expressed during Bgh infection of barley leaf epidermal cells. Results RNA was isolated from four fast-neutron immune-signaling mutants and their progenitor over a time course representing key stages of Bgh infection, including appressorium formation, penetration of epidermal cells, and development of haustorial feeding structures. The Cereal Introduction (CI) 16151 progenitor carries the resistance allele Mla6, while Bgh isolate 5874 harbors the AVRa6 avirulence effector, resulting in an incompatible interaction. Parallel Analysis of RNA Ends (PARE) was used to verify sRNAs with likely transcript targets in both barley and Bgh. Bgh sRNAs are predicted to regulate effectors, metabolic genes, and translation-related genes. Barley sRNAs are predicted to influence the accumulation of transcripts that encode auxin response factors, NAC transcription factors, homeodomain transcription factors, and several splicing factors. We also identified phasing small interfering RNAs (phasiRNAs) in barley that overlap transcripts that encode receptor-like kinases (RLKs) and nucleotide-binding, leucine-rich domain proteins (NLRs). Conclusions These data suggest that Bgh sRNAs regulate gene expression in metabolism, translation-related, and pathogen effectors. PARE-validated targets of predicted Bgh milRNAs include both EKA (effectors homologous to AVRk1 and AVRa10) and CSEP (candidate secreted effector protein) families. We also identified barley phasiRNAs and miRNAs in response to Bgh infection. These include phasiRNA loci that overlap with a significant proportion of receptor-like kinases, suggesting an additional sRNA control mechanism may be active in barley leaves as opposed to predominant R-gene phasiRNA overlap in many eudicots. In addition, we identified conserved miRNAs, novel miRNA candidates, and barley genome mapped sRNAs that have PARE validated transcript targets in barley. The miRNA target transcripts are enriched in transcription factors, signaling-related proteins, and photosynthesis-related proteins. Together these results suggest both barley and Bgh control metabolism and infection-related responses via the specific accumulation and targeting of genes via sRNAs. Electronic supplementary material The online version of this article (10.1186/s12864-019-5947-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matt Hunt
- Interdepartmental Genetics & Genomics, Iowa State University, Ames, Iowa, 50011, USA.,Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa, 50011, USA
| | - Sagnik Banerjee
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa, 50011, USA.,Interdepartmental Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, 50011, USA
| | - Priyanka Surana
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa, 50011, USA.,Interdepartmental Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, 50011, USA
| | - Meiling Liu
- Interdepartmental Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, 50011, USA.,Department of Statistics, Iowa State University, Ames, Iowa, 50011, USA
| | - Greg Fuerst
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Iowa State University, Ames, Iowa, 50011, USA
| | - Sandra Mathioni
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.,Division of Plant Sciences, University of Missouri - Columbia, 52 Agriculture Lab, Columbia, MO, 65211, USA
| | - Dan Nettleton
- Interdepartmental Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, 50011, USA.,Department of Statistics, Iowa State University, Ames, Iowa, 50011, USA
| | - Roger P Wise
- Interdepartmental Genetics & Genomics, Iowa State University, Ames, Iowa, 50011, USA. .,Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa, 50011, USA. .,Interdepartmental Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, 50011, USA. .,Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Iowa State University, Ames, Iowa, 50011, USA.
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