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de Oliveira KKP, de Oliveira RR, Chalfun-Junior A. Small RNAs: Promising Molecules to Tackle Climate Change Impacts in Coffee Production. PLANTS (BASEL, SWITZERLAND) 2023; 12:3531. [PMID: 37895993 PMCID: PMC10610182 DOI: 10.3390/plants12203531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/28/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023]
Abstract
Over the centuries, human society has evolved based on the ability to select and use more adapted species for food supply, which means making plant species tastier and more productive in particular environmental conditions. However, nowadays, this scenario is highly threatened by climate change, especially by the changes in temperature and greenhouse gasses that directly affect photosynthesis, which highlights the need for strategic studies aiming at crop breeding and guaranteeing food security. This is especially worrying for crops with complex phenology, genomes with low variability, and the ones that support a large production chain, such as Coffea sp. L. In this context, recent advances shed some light on the genome function and transcriptional control, revealing small RNAs (sRNAs) that are responsible for environmental cues and could provide variability through gene expression regulation. Basically, sRNAs are responsive to environmental changes and act on the transcriptional and post-transcriptional gene silencing pathways that regulate gene expression and, consequently, biological processes. Here, we first discuss the predicted impact of climate changes on coffee plants and coffee chain production and then the role of sRNAs in response to environmental changes, especially temperature, in different species, together with their potential as tools for genetic improvement. Very few studies in coffee explored the relationship between sRNAs and environmental cues; thus, this review contributes to understanding coffee development in the face of climate change and towards new strategies of crop breeding.
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Affiliation(s)
| | | | - Antonio Chalfun-Junior
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Institute of Biology, Federal University of Lavras, Lavras 3037, Brazil; (K.K.P.d.O.); (R.R.d.O.)
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2
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Samynathan R, Venkidasamy B, Shanmugam A, Ramalingam S, Thiruvengadam M. Functional role of microRNA in the regulation of biotic and abiotic stress in agronomic plants. Front Genet 2023; 14:1272446. [PMID: 37886688 PMCID: PMC10597799 DOI: 10.3389/fgene.2023.1272446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
The increasing demand for food is the result of an increasing population. It is crucial to enhance crop yield for sustainable production. Recently, microRNAs (miRNAs) have gained importance because of their involvement in crop productivity by regulating gene transcription in numerous biological processes, such as growth, development and abiotic and biotic stresses. miRNAs are small, non-coding RNA involved in numerous other biological functions in a plant that range from genomic integrity, metabolism, growth, and development to environmental stress response, which collectively influence the agronomic traits of the crop species. Additionally, miRNA families associated with various agronomic properties are conserved across diverse plant species. The miRNA adaptive responses enhance the plants to survive environmental stresses, such as drought, salinity, cold, and heat conditions, as well as biotic stresses, such as pathogens and insect pests. Thus, understanding the detailed mechanism of the potential response of miRNAs during stress response is necessary to promote the agronomic traits of crops. In this review, we updated the details of the functional aspects of miRNAs as potential regulators of various stress-related responses in agronomic plants.
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Affiliation(s)
- Ramkumar Samynathan
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Baskar Venkidasamy
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Ashokraj Shanmugam
- Plant Physiology and Biotechnology Division, UPASI Tea Research Foundation, Coimbatore, Tamil Nadu, India
| | - Sathishkumar Ramalingam
- Plant Genetic Engineering Lab, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Muthu Thiruvengadam
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul, Republic of Korea
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3
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Role of Bioinformatics in MicroRNA Analysis. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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4
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Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora. Noncoding RNA 2020; 6:ncrna6030039. [PMID: 32932872 PMCID: PMC7549347 DOI: 10.3390/ncrna6030039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/02/2020] [Accepted: 09/08/2020] [Indexed: 12/25/2022] Open
Abstract
Coffea canephora grains are highly traded commodities worldwide. Non-coding RNAs (ncRNAs) are transcriptional products involved in genome regulation, environmental responses, and plant development. There is not an extensive genome-wide analysis that uncovers the ncRNA portion of the C. canephora genome. This study aimed to provide a curated characterization of six ncRNA classes in the Coffea canephora genome. For this purpose, we employed a combination of similarity-based and structural-based computational approaches with stringent curation. Candidate ncRNA loci had expression evidence analyzed using sRNA-seq libraries. We identified 7455 ncRNA loci (6976 with transcriptional evidence) in the C. canephora genome. This comprised of total 115 snRNAs, 1031 snoRNAs, 92 miRNA precursors, 602 tRNAs, 72 rRNAs, and 5064 lncRNAs. For miRNAs, we identified 159 putative high-confidence targets. This study was the most extensive genomic catalog of curated ncRNAs in the Coffea genus. This data might help elaborating more robust hypotheses in future comparative genomic studies as well as gene regulation and genome dynamics, helping to understand the molecular basis of domestication, environmental adaptation, resistance to pests and diseases, and coffee productivity.
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5
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Dos Santos TB, Soares JDM, Lima JE, Silva JC, Ivamoto ST, Baba VY, Souza SGH, Lorenzetti APR, Paschoal AR, Meda AR, Nishiyama Júnior MY, de Oliveira ÚC, Mokochinski JB, Guyot R, Junqueira-de-Azevedo ILM, Figueira AVO, Mazzafera P, Júnior OR, Vieira LGE, Pereira LFP, Domingues DS. An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses. Funct Integr Genomics 2018; 19:151-169. [PMID: 30196429 DOI: 10.1007/s10142-018-0634-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 08/21/2018] [Accepted: 08/28/2018] [Indexed: 01/09/2023]
Abstract
Coffea arabica L. is an important agricultural commodity, accounting for 60% of traded coffee worldwide. Nitrogen (N) is a macronutrient that is usually limiting to plant yield; however, molecular mechanisms of plant acclimation to N limitation remain largely unknown in tropical woody crops. In this study, we investigated the transcriptome of coffee roots under N starvation, analyzing poly-A+ libraries and small RNAs. We also evaluated the concentration of selected amino acids and N-source preferences in roots. Ammonium was preferentially taken up over nitrate, and asparagine and glutamate were the most abundant amino acids observed in coffee roots. We obtained 34,654 assembled contigs by mRNA sequencing, and validated the transcriptional profile of 12 genes by RT-qPCR. Illumina small RNA sequencing yielded 8,524,332 non-redundant reads, resulting in the identification of 86 microRNA families targeting 253 genes. The transcriptional pattern of eight miRNA families was also validated. To our knowledge, this is the first catalog of differentially regulated amino acids, N sources, mRNAs, and sRNAs in Arabica coffee roots.
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Affiliation(s)
- Tiago Benedito Dos Santos
- Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, Londrina, 86047-902, Brazil. .,Universidade do Oeste Paulista, Rodovia Raposo Tavares Km 572, Presidente Prudente, 19067-175, Brazil.
| | - João D M Soares
- Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, Londrina, 86047-902, Brazil
| | - Joni E Lima
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, 13400-970, Brazil.,Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Juliana C Silva
- Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, Londrina, 86047-902, Brazil.,Programa de pós-graduação em Bioinformática, Universidade Tecnológica Federal do Paraná, Cornélio Procópio, 86300-000, Brazil
| | - Suzana T Ivamoto
- Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, Londrina, 86047-902, Brazil.,Departamento de Botânica, Instituto de Biociências de Rio Claro, Universidade Estadual Paulista, Rio Claro, 13506-900, Brazil
| | - Viviane Y Baba
- Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, Londrina, 86047-902, Brazil
| | - Silvia G H Souza
- Laboratório de Biologia Molecular, Universidade Paranaense, Umuarama, 87502-210, Brazil
| | - Alan P R Lorenzetti
- Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina, Londrina, 86057-970, Brazil
| | - Alexandre R Paschoal
- Programa de pós-graduação em Bioinformática, Universidade Tecnológica Federal do Paraná, Cornélio Procópio, 86300-000, Brazil
| | - Anderson R Meda
- Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, Londrina, 86047-902, Brazil
| | | | - Úrsula C de Oliveira
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, 05503-900, Brazil
| | - João B Mokochinski
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, 13083-970, Brazil
| | - Romain Guyot
- IRD, UMR IPME, COFFEEADAPT, BP 64501, 34394, Montpellier Cedex 5, France
| | | | - Antônio V O Figueira
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, 13400-970, Brazil
| | - Paulo Mazzafera
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, 13083-970, Brazil
| | - Osvaldo R Júnior
- Life Sciences Core Facility (LaCTAD), Universidade Estadual de Campinas, Campinas, 13083-886, Brazil
| | - Luiz G E Vieira
- Universidade do Oeste Paulista, Rodovia Raposo Tavares Km 572, Presidente Prudente, 19067-175, Brazil
| | - Luiz F P Pereira
- Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, Londrina, 86047-902, Brazil.,Embrapa Café, Brasília, 70770-901, Brazil
| | - Douglas S Domingues
- Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, Londrina, 86047-902, Brazil.,Departamento de Botânica, Instituto de Biociências de Rio Claro, Universidade Estadual Paulista, Rio Claro, 13506-900, Brazil
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6
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Noronha Fernandes-Brum C, Marinho Rezende P, Cherubino Ribeiro TH, Ricon de Oliveira R, Cunha de Sousa Cardoso T, Rodrigues do Amaral L, de Souza Gomes M, Chalfun-Junior A. A genome-wide analysis of the RNA-guided silencing pathway in coffee reveals insights into its regulatory mechanisms. PLoS One 2017; 12:e0176333. [PMID: 28448529 PMCID: PMC5407642 DOI: 10.1371/journal.pone.0176333] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 04/10/2017] [Indexed: 11/28/2022] Open
Abstract
microRNAs (miRNAs) are derived from self-complementary hairpin structures, while small-interfering RNAs (siRNAs) are derived from double-stranded RNA (dsRNA) or hairpin precursors. The core mechanism of sRNA production involves DICER-like (DCL) in processing the smallRNAs (sRNAs) and ARGONAUTE (AGO) as effectors of silencing, and siRNA biogenesis also involves action of RNA-Dependent RNA Polymerase (RDR), Pol IV and Pol V in biogenesis. Several other proteins interact with the core proteins to guide sRNA biogenesis, action, and turnover. We aimed to unravel the components and functions of the RNA-guided silencing pathway in a non-model plant species of worldwide economic relevance. The sRNA-guided silencing complex members have been identified in the Coffea canephora genome, and they have been characterized at the structural, functional, and evolutionary levels by computational analyses. Eleven AGO proteins, nine DCL proteins (which include a DCL1-like protein that was not previously annotated), and eight RDR proteins were identified. Another 48 proteins implicated in smallRNA (sRNA) pathways were also identified. Furthermore, we identified 235 miRNA precursors and 317 mature miRNAs from 113 MIR families, and we characterized ccp-MIR156, ccp-MIR172, and ccp-MIR390. Target prediction and gene ontology analyses of 2239 putative targets showed that significant pathways in coffee are targeted by miRNAs. We provide evidence of the expansion of the loci related to sRNA pathways, insights into the activities of these proteins by domain and catalytic site analyses, and gene expression analysis. The number of MIR loci and their targeted pathways highlight the importance of miRNAs in coffee. We identified several roles of sRNAs in C. canephora, which offers substantial insight into better understanding the transcriptional and post-transcriptional regulation of this major crop.
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Affiliation(s)
- Christiane Noronha Fernandes-Brum
- Department of Biology, Section of Plant Physiology, Laboratory of Plant Molecular Physiology (LFMP), Federal University of Lavras (UFLA), Lavras, Minas Gerais, Brazil
| | - Pâmela Marinho Rezende
- Department of Biology, Section of Plant Physiology, Laboratory of Plant Molecular Physiology (LFMP), Federal University of Lavras (UFLA), Lavras, Minas Gerais, Brazil
| | - Thales Henrique Cherubino Ribeiro
- Department of Biology, Section of Plant Physiology, Laboratory of Plant Molecular Physiology (LFMP), Federal University of Lavras (UFLA), Lavras, Minas Gerais, Brazil
| | | | - Thaís Cunha de Sousa Cardoso
- Institute of Genetics and Biochemistry (INGEB),Laboratory of Bioinformatics and Molecular Analysis (LBAM), Federal University of Uberlândia (UFU)- Campus Patos de Minas, Patos de Minas, Minas Gerais, Brasil
| | - Laurence Rodrigues do Amaral
- Institute of Genetics and Biochemistry (INGEB),Laboratory of Bioinformatics and Molecular Analysis (LBAM), Federal University of Uberlândia (UFU)- Campus Patos de Minas, Patos de Minas, Minas Gerais, Brasil
| | - Matheus de Souza Gomes
- Institute of Genetics and Biochemistry (INGEB),Laboratory of Bioinformatics and Molecular Analysis (LBAM), Federal University of Uberlândia (UFU)- Campus Patos de Minas, Patos de Minas, Minas Gerais, Brasil
| | - Antonio Chalfun-Junior
- Department of Biology, Section of Plant Physiology, Laboratory of Plant Molecular Physiology (LFMP), Federal University of Lavras (UFLA), Lavras, Minas Gerais, Brazil
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7
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Djami-Tchatchou AT, Sanan-Mishra N, Ntushelo K, Dubery IA. Functional Roles of microRNAs in Agronomically Important Plants-Potential as Targets for Crop Improvement and Protection. FRONTIERS IN PLANT SCIENCE 2017; 8:378. [PMID: 28382044 PMCID: PMC5360763 DOI: 10.3389/fpls.2017.00378] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/06/2017] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs that have recently emerged as important regulators of gene expression, mainly through cleavage and/or translation inhibition of the target mRNAs during or after transcription. miRNAs play important roles by regulating a multitude of biological processes in plants which include maintenance of genome integrity, development, metabolism, and adaptive responses toward environmental stresses. The increasing population of the world and their food demands requires focused efforts for the improvement of crop plants to ensure sustainable food production. Manipulation of mRNA transcript abundance via miRNA control provides a unique strategy for modulating differential plant gene expression and miRNAs are thus emerging as the next generation targets for genetic engineering for improvement of the agronomic properties of crops. However, a deeper understanding of its potential and the mechanisms involved will facilitate the design of suitable strategies to obtain the desirable traits with minimum trade-offs in the modified crops. In this regard, this review highlights the diverse roles of conserved and newly identified miRNAs in various food and industrial crops and recent advances made in the uses of miRNAs to improve plants of agronomically importance so as to significantly enhance crop yields and increase tolerance to various environmental stress agents of biotic-or abiotic origin.
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Affiliation(s)
- Arnaud T. Djami-Tchatchou
- Department of Agriculture and Animal Health, University of South Africa (Florida Campus)Pretoria, South Africa
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and BiotechnologyNew Delhi, India
| | - Khayalethu Ntushelo
- Department of Agriculture and Animal Health, University of South Africa (Florida Campus)Pretoria, South Africa
| | - Ian A. Dubery
- Department of Biochemistry, University of Johannesburg (Auckland Park Kingsway Campus)Johannesburg, South Africa
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8
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Chaves SS, Fernandes-Brum CN, Silva GFF, Ferrara-Barbosa BC, Paiva LV, Nogueira FTS, Cardoso TCS, Amaral LR, de Souza Gomes M, Chalfun-Junior A. New Insights on Coffea miRNAs: Features and Evolutionary Conservation. Appl Biochem Biotechnol 2015; 177:879-908. [PMID: 26277190 DOI: 10.1007/s12010-015-1785-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 07/27/2015] [Indexed: 12/31/2022]
Abstract
Small RNAs influence the gene expression at the post-transcriptional level by guiding messenger RNA (mRNA) cleavage, translational repression, and chromatin modifications. In addition to model plants, the microRNAs (miRNAs) have been identified in different crop species. In this work, we developed a specific pipeline to search for coffee miRNA homologs on expressed sequence tags (ESTs) and genome survey sequences (GSS) databases. As a result, 36 microRNAs were identified and a total of 616 and 362 potential targets for Coffea arabica and Coffea canephora, respectively. The evolutionary analyses of these molecules were performed by comparing the primary and secondary structures of precursors and mature miRNAs with their orthologs. Moreover, using a stem-loop RT-PCR assay, we evaluated the accumulation of mature miRNAs in genomes with different ploidy levels, detecting an increase in the miRNAs accumulation according to the ploidy raising. Finally, a 5' RACE (Rapid Amplification of cDNA Ends) assay was performed to verify the regulation of auxin responsive factor 8 (ARF8) by MIR167 in coffee plants. The great variety of target genes indicates the functional plasticity of these molecules and reinforces the importance of understanding the RNAi-dependent regulatory mechanisms. Our results expand the study of miRNAs and their target genes in this crop, providing new challenges to understand the biology of these species.
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Affiliation(s)
- S S Chaves
- Plant Molecular Physiology Laboratory, Biology Department, Federal University of Lavras (UFLA), s/n - Cx., Lavras, Minas Gerais, P 3037, Brazil
| | - C N Fernandes-Brum
- Plant Molecular Physiology Laboratory, Biology Department, Federal University of Lavras (UFLA), s/n - Cx., Lavras, Minas Gerais, P 3037, Brazil
| | - G F F Silva
- Agricultural Biotechnology Center, Agriculture College "Luiz de Queiroz" (ESALQ)/USP, Piracicaba, SP, Brazil
| | - B C Ferrara-Barbosa
- Plant Molecular Physiology Laboratory, Biology Department, Federal University of Lavras (UFLA), s/n - Cx., Lavras, Minas Gerais, P 3037, Brazil
| | - L V Paiva
- Central Laboratory of Molecular Biology (LCBM), Chemistry Department, Federal University of Lavras (UFLA), Lavras, Minas Gerais, Brazil
| | - F T S Nogueira
- Agricultural Biotechnology Center, Agriculture College "Luiz de Queiroz" (ESALQ)/USP, Piracicaba, SP, Brazil
| | - T C S Cardoso
- Laboratory of Bioinformatics and Molecular Analysis-INGEB/FACOM, Federal University of Uberlandia, Campus Patos de Minas, Patos de Minas, MG, Brazil
| | - L R Amaral
- Laboratory of Bioinformatics and Molecular Analysis-INGEB/FACOM, Federal University of Uberlandia, Campus Patos de Minas, Patos de Minas, MG, Brazil
| | - M de Souza Gomes
- Laboratory of Bioinformatics and Molecular Analysis-INGEB/FACOM, Federal University of Uberlandia, Campus Patos de Minas, Patos de Minas, MG, Brazil
| | - A Chalfun-Junior
- Plant Molecular Physiology Laboratory, Biology Department, Federal University of Lavras (UFLA), s/n - Cx., Lavras, Minas Gerais, P 3037, Brazil.
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9
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Transcriptome-Wide Identification of miRNA Targets under Nitrogen Deficiency in Populus tomentosa Using Degradome Sequencing. Int J Mol Sci 2015; 16:13937-58. [PMID: 26096002 PMCID: PMC4490532 DOI: 10.3390/ijms160613937] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 05/21/2015] [Accepted: 06/01/2015] [Indexed: 12/02/2022] Open
Abstract
miRNAs are endogenous non-coding small RNAs with important regulatory roles in stress responses. Nitrogen (N) is an indispensable macronutrient required for plant growth and development. Previous studies have identified a variety of known and novel miRNAs responsive to low N stress in plants, including Populus. However, miRNAs involved in the cleavage of target genes and the corresponding regulatory networks in response to N stress in Populus remain largely unknown. Consequently, degradome sequencing was employed for global detection and validation of N-responsive miRNAs and their targets. A total of 60 unique miRNAs (39 conserved, 13 non-conserved, and eight novel) were experimentally identified to target 64 mRNA transcripts and 21 precursors. Among them, we further verified the cleavage of 11 N-responsive miRNAs identified previously and provided empirical evidence for the cleavage mode of these miRNAs on their target mRNAs. Furthermore, five miRNA stars (miRNA*s) were shown to have cleavage function. The specificity and diversity of cleavage sites on the targets and miRNA precursors in P. tomentosa were further detected. Identification and annotation of miRNA-mediated cleavage of target genes in Populus can increase our understanding of miRNA-mediated molecular mechanisms of woody plants adapted to low N environments.
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