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Amelioration in traditional farming system by exploring the different plant growth-promoting attributes of endophytes for sustainable agriculture. Arch Microbiol 2022; 204:151. [DOI: 10.1007/s00203-021-02637-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 11/23/2021] [Accepted: 12/06/2021] [Indexed: 11/25/2022]
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2
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Chand Jha U, Nayyar H, Mantri N, Siddique KHM. Non-Coding RNAs in Legumes: Their Emerging Roles in Regulating Biotic/Abiotic Stress Responses and Plant Growth and Development. Cells 2021; 10:cells10071674. [PMID: 34359842 PMCID: PMC8306516 DOI: 10.3390/cells10071674] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 12/28/2022] Open
Abstract
Noncoding RNAs, including microRNAs (miRNAs), small interference RNAs (siRNAs), circular RNA (circRNA), and long noncoding RNAs (lncRNAs), control gene expression at the transcription, post-transcription, and translation levels. Apart from protein-coding genes, accumulating evidence supports ncRNAs playing a critical role in shaping plant growth and development and biotic and abiotic stress responses in various species, including legume crops. Noncoding RNAs (ncRNAs) interact with DNA, RNA, and proteins, modulating their target genes. However, the regulatory mechanisms controlling these cellular processes are not well understood. Here, we discuss the features of various ncRNAs, including their emerging role in contributing to biotic/abiotic stress response and plant growth and development, in addition to the molecular mechanisms involved, focusing on legume crops. Unravelling the underlying molecular mechanisms and functional implications of ncRNAs will enhance our understanding of the coordinated regulation of plant defences against various biotic and abiotic stresses and for key growth and development processes to better design various legume crops for global food security.
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MESH Headings
- Fabaceae/genetics
- Fabaceae/growth & development
- Fabaceae/metabolism
- Food Security
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Plant
- Humans
- MicroRNAs/classification
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Organ Specificity
- Protein Biosynthesis
- RNA, Circular/classification
- RNA, Circular/genetics
- RNA, Circular/metabolism
- RNA, Long Noncoding/classification
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Plant/classification
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Small Interfering/classification
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Species Specificity
- Stress, Physiological/genetics
- Transcription, Genetic
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Affiliation(s)
- Uday Chand Jha
- ICAR—Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
- Correspondence: (U.C.J.); (K.H.M.S.)
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh 160014, India;
| | - Nitin Mantri
- School of Science, RMIT University, Melbourne 3083, Australia;
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth 6001, Australia
- Correspondence: (U.C.J.); (K.H.M.S.)
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3
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Cadavid IC, da Fonseca GC, Margis R. HDAC inhibitor affects soybean miRNA482bd expression under salt and osmotic stress. JOURNAL OF PLANT PHYSIOLOGY 2020; 253:153261. [PMID: 32947244 DOI: 10.1016/j.jplph.2020.153261] [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: 03/21/2020] [Revised: 08/07/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding molecules that modulate gene expression through targeting mRNA by specific-sequence cleavage, translation inhibition, or transcriptional regulation. miRNAs are key molecules in regulatory networks in abiotic stresses such as salt stress and water deficit in plants. Throughout the world, soybean is a critical crop, the production of which is affected by environmental stress conditions. In this study, RNA-Seq libraries from leaves of soybean under salt treatment were analyzed. 17 miRNAs and 31 putative target genes were identified with inverse differential expression patterns, indicating miRNA-target interaction. The differential expression of six miRNAs, including miR482bd-5p, and their potential targets, were confirmed by RT-qPCR. The miR482bd-5p expression was repressed, while its potential HEC1 and BAK1 targets were increased. Polyethylene glycol experiment was used to simulate drought stress, and miR482bd-5p, HEC1, and BAK1 presented a similar expression pattern, as found in salt stress. Histone modifications occur in response to abiotic stress, where histone deacetylases (HDACs) can lead to gene repression and silencing. The miR482bd-5p epigenetic regulation by histone deacetylation was evaluated by using the SAHA-HDAC inhibitor. The miR482bd-5p was up-regulated, and HEC1 was down-regulated under SAHA-salt treatment. It suggests an epigenetic regulation, where the miRNA gene is repressed by HDAC under salt stress, reducing its transcription, with an associated increase in the HEC1 target expression.
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Affiliation(s)
- Isabel Cristina Cadavid
- Programa de Pós-graduação em Biologia Celular e Molecular (PPGBCM), Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Rogerio Margis
- Programa de Pós-graduação em Biologia Celular e Molecular (PPGBCM), Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Departamento de Biofisica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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4
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Fadiji AE, Babalola OO. Metagenomics methods for the study of plant-associated microbial communities: A review. J Microbiol Methods 2020; 170:105860. [PMID: 32027927 DOI: 10.1016/j.mimet.2020.105860] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/31/2020] [Accepted: 02/02/2020] [Indexed: 12/20/2022]
Abstract
Plant microbiota have different effects on the plant which can be beneficial or pathogenic. In this study, we concentrated on beneficial microbes associated with plants using endophytic microbes as a case study. Detailed knowledge of the microbial diversity, abundance, composition, functional genes patterns, and metabolic pathways at genome level could assist in understanding the contributions of microbial community towards plant growth and health. Recently, the study of microbial community has improved greatly with the discovery of next-generation sequencing and bioinformatics technologies. Analysis of next generation sequencing data and a proper computational method plays a key role in examining microbial metagenome. This review presents the general metagenomics and computational methods used in processing plant associated metagenomes with concentration on endophytes. This includes 1) introduction of plant-associated microbiota and the factors driving their diversity. 2) plant metagenome focusing on DNA extraction, verification and quality control. 3) metagenomics methods used in community analysis of endophytes focusing on maize plant and, 4) computational methods used in the study of endophytic microbiomes. Limitations and future prospects of metagenomics and computational methods for the analysis of plant-associated metagenome (endophytic metagenome) were also discussed with the aim of fostering its development. We conclude that there is need to adopt advanced genomic features such as k-mers of random size, which do not depend on annotation and can represent other sequence alternatives.
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Affiliation(s)
- Ayomide Emmanuel Fadiji
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, South Africa.
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5
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Metatranscriptomics and Metaproteomics for Microbial Communities Profiling. UNRAVELLING THE SOIL MICROBIOME 2020. [DOI: 10.1007/978-3-030-15516-2_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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6
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7
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Sheridan C, Depuydt P, De Ro M, Petit C, Van Gysegem E, Delaere P, Dixon M, Stasiak M, Aciksöz SB, Frossard E, Paradiso R, De Pascale S, Ventorino V, De Meyer T, Sas B, Geelen D. Microbial Community Dynamics and Response to Plant Growth-Promoting Microorganisms in the Rhizosphere of Four Common Food Crops Cultivated in Hydroponics. MICROBIAL ECOLOGY 2017; 73:378-393. [PMID: 27645138 DOI: 10.1007/s00248-016-0855-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/05/2016] [Indexed: 05/25/2023]
Abstract
Plant growth promoting microorganisms (PGPMs) of the plant root zone microbiome have received limited attention in hydroponic cultivation systems. In the framework of a project aimed at the development of a biological life support system for manned missions in space, we investigated the effects of PGPMs on four common food crops (durum and bread wheat, potato and soybean) cultivated in recirculating hydroponic systems for a whole life cycle. Each crop was inoculated with a commercial PGPM mixture and the composition of the microbial communities associated with their root rhizosphere, rhizoplane/endosphere and with the recirculating nutrient solution was characterised through 16S- and ITS-targeted Illumina MiSeq sequencing. PGPM addition was shown to induce changes in the composition of these communities, though these changes varied both between crops and over time. Microbial communities of PGPM-treated plants were shown to be more stable over time. Though additional development is required, this study highlights the potential benefits that PGPMs may confer to plants grown in hydroponic systems, particularly when cultivated in extreme environments such as space.
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Affiliation(s)
- C Sheridan
- In Vitro Biology and Horticulture, Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, 653 Coupure Links, 9000, Ghent, Belgium
| | - P Depuydt
- In Vitro Biology and Horticulture, Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, 653 Coupure Links, 9000, Ghent, Belgium
| | - M De Ro
- In Vitro Biology and Horticulture, Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, 653 Coupure Links, 9000, Ghent, Belgium
| | - C Petit
- In Vitro Biology and Horticulture, Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, 653 Coupure Links, 9000, Ghent, Belgium
| | - E Van Gysegem
- In Vitro Biology and Horticulture, Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, 653 Coupure Links, 9000, Ghent, Belgium
| | - P Delaere
- In Vitro Biology and Horticulture, Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, 653 Coupure Links, 9000, Ghent, Belgium
| | - M Dixon
- Controlled Environment Systems Research Facility, School of Environmental Sciences, University of Guelph, Guelph, ON, NIG 2W1, Canada
| | - M Stasiak
- Controlled Environment Systems Research Facility, School of Environmental Sciences, University of Guelph, Guelph, ON, NIG 2W1, Canada
| | - S B Aciksöz
- Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - E Frossard
- Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - R Paradiso
- Division of Plant Biology and Crop Science, Department of Agricultural Sciences, University of Naples Federico II Naples, Via Università, 100 80055, Portici, Naples, Italy
| | - S De Pascale
- Division of Plant Biology and Crop Science, Department of Agricultural Sciences, University of Naples Federico II Naples, Via Università, 100 80055, Portici, Naples, Italy
| | - V Ventorino
- Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico II Naples, Via Università, 100 80055, Portici, Naples, Italy
| | - T De Meyer
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - B Sas
- Department of Food Quality and Food Safety, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
| | - D Geelen
- In Vitro Biology and Horticulture, Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, 653 Coupure Links, 9000, Ghent, Belgium.
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8
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Pfeilmeier S, Caly DL, Malone JG. Bacterial pathogenesis of plants: future challenges from a microbial perspective: Challenges in Bacterial Molecular Plant Pathology. MOLECULAR PLANT PATHOLOGY 2016; 17:1298-313. [PMID: 27170435 PMCID: PMC6638335 DOI: 10.1111/mpp.12427] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 05/08/2016] [Accepted: 05/10/2016] [Indexed: 05/03/2023]
Abstract
Plant infection is a complicated process. On encountering a plant, pathogenic microorganisms must first adapt to life on the epiphytic surface, and survive long enough to initiate an infection. Responsiveness to the environment is critical throughout infection, with intracellular and community-level signal transduction pathways integrating environmental signals and triggering appropriate responses in the bacterial population. Ultimately, phytopathogens must migrate from the epiphytic surface into the plant tissue using motility and chemotaxis pathways. This migration is coupled with overcoming the physical and chemical barriers to entry into the plant apoplast. Once inside the plant, bacteria use an array of secretion systems to release phytotoxins and protein effectors that fulfil diverse pathogenic functions (Fig. ) (Melotto and Kunkel, ; Phan Tran et al., ). As our understanding of the pathways and mechanisms underpinning plant pathogenicity increases, a number of central research challenges are emerging that will profoundly shape the direction of research in the future. We need to understand the bacterial phenotypes that promote epiphytic survival and surface adaptation in pathogenic bacteria. How do these pathways function in the context of the plant-associated microbiome, and what impact does this complex microbial community have on the onset and severity of plant infections? The huge importance of bacterial signal transduction to every stage of plant infection is becoming increasingly clear. However, there is a great deal to learn about how these signalling pathways function in phytopathogenic bacteria, and the contribution they make to various aspects of plant pathogenicity. We are increasingly able to explore the structural and functional diversity of small-molecule natural products from plant pathogens. We need to acquire a much better understanding of the production, deployment, functional redundancy and physiological roles of these molecules. Type III secretion systems (T3SSs) are important and well-studied contributors to bacterial disease. Several key unanswered questions will shape future investigations of these systems. We need to define the mechanism of hierarchical and temporal control of effector secretion. For successful infection, effectors need to interact with host components to exert their function. Advanced biochemical, proteomic and cell biological techniques will enable us to study the function of effectors inside the host cell in more detail and on a broader scale. Population genomics analyses provide insight into evolutionary adaptation processes of phytopathogens. The determination of the diversity and distribution of type III effectors (T3Es) and other virulence genes within and across pathogenic species, pathovars and strains will allow us to understand how pathogens adapt to specific hosts, the evolutionary pathways available to them, and the possible future directions of the evolutionary arms race between effectors and molecular plant targets. Although pathogenic bacteria employ a host of different virulence and proliferation strategies, as a result of the space constraints, this review focuses mainly on the hemibiotrophic pathogens. We discuss the process of plant infection from the perspective of these important phytopathogens, and highlight new approaches to address the outstanding challenges in this important and fast-moving field.
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Affiliation(s)
- Sebastian Pfeilmeier
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Delphine L Caly
- Université de Lille, EA 7394, ICV - Institut Charles Viollette, Lille, F-59000, France
| | - Jacob G Malone
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
- University of East Anglia, Norwich, NR4 7TJ, UK.
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9
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da Fonseca GC, de Oliveira LFV, de Morais GL, Abdelnor RV, Nepomuceno AL, Waterhouse PM, Farinelli L, Margis R. Unusual RNA plant virus integration in the soybean genome leads to the production of small RNAs. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 246:62-69. [PMID: 26993236 DOI: 10.1016/j.plantsci.2016.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/15/2015] [Accepted: 01/29/2016] [Indexed: 05/07/2023]
Abstract
Horizontal gene transfer (HGT) is known to be a major force in genome evolution. The acquisition of genes from viruses by eukaryotic genomes is a well-studied example of HGT, including rare cases of non-retroviral RNA virus integration. The present study describes the integration of cucumber mosaic virus RNA-1 into soybean genome. After an initial metatranscriptomic analysis of small RNAs derived from soybean, the de novo assembly resulted a 3029-nt contig homologous to RNA-1. The integration of this sequence in the soybean genome was confirmed by DNA deep sequencing. The locus where the integration occurred harbors the full RNA-1 sequence followed by the partial sequence of an endogenous mRNA and another sequence of RNA-1 as an inverted repeat and allowing the formation of a hairpin structure. This region recombined into a retrotransposon located inside an exon of a soybean gene. The nucleotide similarity of the integrated sequence compared to other Cucumber mosaic virus sequences indicates that the integration event occurred recently. We described a rare event of non-retroviral RNA virus integration in soybean that leads to the production of a double-stranded RNA in a similar fashion to virus resistance RNAi plants.
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Affiliation(s)
- Guilherme Cordenonsi da Fonseca
- Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil.
| | - Luiz Felipe Valter de Oliveira
- Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil
| | | | | | | | - Peter M Waterhouse
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland, Australia
| | | | - Rogerio Margis
- Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil; Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil.
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10
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Kulcheski FR, Molina LG, da Fonseca GC, de Morais GL, de Oliveira LFV, Margis R. Novel and conserved microRNAs in soybean floral whorls. Gene 2016; 575:213-23. [PMID: 26341053 DOI: 10.1016/j.gene.2015.08.061] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 07/23/2015] [Accepted: 08/28/2015] [Indexed: 11/20/2022]
Abstract
MicroRNAs (miRNAs) correspond to a class of endogenous small non-coding RNAs (19-24 nt) that regulates the gene expression, through mRNA target cleavage or translation inhibition. In plants, miRNAs have been shown to play pivotal roles in a wide variety of metabolic and biological processes like plant growth, development, and response to biotic and abiotic stress. Soybean is one of the most important crops worldwide, due to the production of oil and its high protein content. The reproductive phase is considered the most important for soybean yield, which is mainly intended to produce the grains. The identification of miRNAs is not yet saturated in soybean, and there are no studies linking them to the different floral organs. In this study, three different mature soybean floral whorls were used in the construction of sRNA libraries. The sequencing of petal, carpel and stamen libraries generated a total of 10,165,661 sequences. Subsequent analyses identified 200 miRNAs sequences, among which, 41 were novel miRNAs, 80 were conserved soybean miRNAs, 31 were new antisense conserved soybean miRNAs and 46 were soybean miRNAs isoforms. We also found a new miRNA conserved in other plant species, and finally one miRNA-sibling of a soybean conserved miRNA. Conserved and novel miRNAs were evaluated by RT-qPCR. We observed a differential expression across the three whorls for six miRNAs. Computational predicted targets for miRNAs analyzed by RT-qPCR were identified and present functions related to reproductive process in plants. In summary, the increased accumulation of specific and novel miRNAs in different whorls indicates that miRNAs are an important part of the regulatory network in soybean flower.
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Affiliation(s)
- F R Kulcheski
- PPGBCM, Centro de Biotecnologia, Laboratório de Genomas e Populações de Plantas, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil; Departamento de Biofísica, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - L G Molina
- PPGBCM, Centro de Biotecnologia, Laboratório de Genomas e Populações de Plantas, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil; PPGGBM, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - G C da Fonseca
- PPGBCM, Centro de Biotecnologia, Laboratório de Genomas e Populações de Plantas, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - G L de Morais
- PPGBCM, Centro de Biotecnologia, Laboratório de Genomas e Populações de Plantas, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil; LNCC, Laboratorio Nacional de Ciência da Computação, Petrópolis, RJ, Brazil
| | - L F V de Oliveira
- PPGBCM, Centro de Biotecnologia, Laboratório de Genomas e Populações de Plantas, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil; PPGGBM, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - R Margis
- PPGBCM, Centro de Biotecnologia, Laboratório de Genomas e Populações de Plantas, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil; Departamento de Biofísica, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil; PPGGBM, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil.
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11
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Kaul S, Sharma T, K. Dhar M. "Omics" Tools for Better Understanding the Plant-Endophyte Interactions. FRONTIERS IN PLANT SCIENCE 2016; 7:955. [PMID: 27446181 PMCID: PMC4925718 DOI: 10.3389/fpls.2016.00955] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 06/15/2016] [Indexed: 05/20/2023]
Abstract
Endophytes, which mostly include bacteria, fungi and actinomycetes, are the endosymbionts that reside asymptomatically in plants for at least a part of their life cycle. They have emerged as a valuable source of novel metabolites, industrially important enzymes and as stress relievers of host plant, but still many aspects of endophytic biology are unknown. Functions of individual endophytes are the result of their continuous and complex interactions with the host plant as well as other members of the host microbiome. Understanding plant microbiomes as a system allows analysis and integration of these complex interactions. Modern genomic studies involving metaomics and comparative studies can prove to be helpful in unraveling the gray areas of endophytism. A deeper knowledge of the mechanism of host infestation and role of endophytes could be exploited to improve the agricultural management in terms of plant growth promotion, biocontrol and bioremediation. Genome sequencing, comparative genomics, microarray, next gen sequencing, metagenomics, metatranscriptomics are some of the techniques that are being used or can be used to unravel plant-endophyte relationship. The modern techniques and approaches need to be explored to study endophytes and their putative role in host plant ecology. This review highlights "omics" tools that can be explored for understanding the role of endophytes in the plant microbiome.
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12
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Holt DB, Gupta V, Meyer D, Abel NB, Andersen SU, Stougaard J, Markmann K. micro RNA 172 (miR172) signals epidermal infection and is expressed in cells primed for bacterial invasion in Lotus japonicus roots and nodules. THE NEW PHYTOLOGIST 2015; 208:241-56. [PMID: 25967282 DOI: 10.1111/nph.13445] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/26/2015] [Indexed: 05/13/2023]
Abstract
Legumes interact with rhizobial bacteria to form nitrogen-fixing root nodules. Host signalling following mutual recognition ensures a specific response, but is only partially understood. Focusing on the stage of epidermal infection with Mesorhizobium loti, we analysed endogenous small RNAs (sRNAs) of the model legume Lotus japonicus to investigate their involvement in host response regulation. We used Illumina sequencing to annotate the L. japonicus sRNA-ome and isolate infection-responsive sRNAs, followed by candidate-based functional characterization. Sequences from four libraries revealed 219 novel L. japonicus micro RNAs (miRNAs) from 114 newly assigned families, and 76 infection-responsive sRNAs. Unlike infection-associated coding genes such as NODULE INCEPTION (NIN), a micro RNA 172 (miR172) isoform showed strong accumulation in dependency of both Nodulation (Nod) factor and compatible rhizobia. The genetics of miR172 induction support the existence of distinct epidermal and cortical signalling events. MIR172a promoter activity followed a previously unseen pattern preceding infection thread progression in epidermal and cortical cells. Nodule-associated miR172a expression was infection-independent, representing the second of two genetically separable activity waves. The combined data provide a valuable resource for further study, and identify miR172 as an sRNA marking successful epidermal infection. We show that miR172 acts upstream of several APETALA2-type (AP2) transcription factors, and suggest that it has a role in fine-tuning AP2 levels during bacterial symbiosis.
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Affiliation(s)
- Dennis B Holt
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling (CARB), Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Vikas Gupta
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling (CARB), Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Dörte Meyer
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling (CARB), Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Nikolaj B Abel
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling (CARB), Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling (CARB), Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling (CARB), Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Katharina Markmann
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling (CARB), Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
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13
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Vivas M, Kemler M, Slippers B. Maternal effects on tree phenotypes: considering the microbiome. TRENDS IN PLANT SCIENCE 2015; 20:541-544. [PMID: 26124001 DOI: 10.1016/j.tplants.2015.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 06/03/2015] [Accepted: 06/07/2015] [Indexed: 06/04/2023]
Abstract
The biotic and abiotic environmental experience of plants can influence the offspring without any changes in DNA sequence. These effects can modulate the development of the progeny and their interaction with microorganisms. This interaction includes fungal endophytic communities which have significant effects on trees and their associated ecosystems. In this opinion article, we highlight potential maternal mechanisms through which endophytes could influence the progeny. We argue that a better understanding of these interactions might help to predict the response of trees to stress conditions and enhance the efficiency of tree breeding programs.
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Affiliation(s)
- Maria Vivas
- Department of Genetics, Forestry, and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa.
| | - Martin Kemler
- Department of Genetics, Forestry, and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa
| | - Bernard Slippers
- Department of Genetics, Forestry, and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa
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14
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Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench). J Microbiol Methods 2015; 112:104-17. [DOI: 10.1016/j.mimet.2015.03.012] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 03/12/2015] [Accepted: 03/12/2015] [Indexed: 01/08/2023]
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15
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Barah P, Bones AM. Multidimensional approaches for studying plant defence against insects: from ecology to omics and synthetic biology. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:479-93. [PMID: 25538257 DOI: 10.1093/jxb/eru489] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The biggest challenge for modern biology is to integrate multidisciplinary approaches towards understanding the organizational and functional complexity of biological systems at different hierarchies, starting from the subcellular molecular mechanisms (microscopic) to the functional interactions of ecological communities (macroscopic). The plant-insect interaction is a good model for this purpose with the availability of an enormous amount of information at the molecular and the ecosystem levels. Changing global climatic conditions are abruptly resetting plant-insect interactions. Integration of discretely located heterogeneous information from the ecosystem to genes and pathways will be an advantage to understand the complexity of plant-insect interactions. This review will present the recent developments in omics-based high-throughput experimental approaches, with particular emphasis on studying plant defence responses against insect attack. The review highlights the importance of using integrative systems approaches to study plant-insect interactions from the macroscopic to the microscopic level. We analyse the current efforts in generating, integrating and modelling multiomics data to understand plant-insect interaction at a systems level. As a future prospect, we highlight the growing interest in utilizing the synthetic biology platform for engineering insect-resistant plants.
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Affiliation(s)
- Pankaj Barah
- Cell Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology (NTNU), N 7491 Trondheim, Norway
| | - Atle M Bones
- Cell Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology (NTNU), N 7491 Trondheim, Norway
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16
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Wu Q, Ding SW, Zhang Y, Zhu S. Identification of viruses and viroids by next-generation sequencing and homology-dependent and homology-independent algorithms. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:425-44. [PMID: 26047558 DOI: 10.1146/annurev-phyto-080614-120030] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A fast, accurate, and full indexing of viruses and viroids in a sample for the inspection and quarantine services and disease management is desirable but was unrealistic until recently. This article reviews the rapid and exciting recent progress in the use of next-generation sequencing (NGS) technologies for the identification of viruses and viroids in plants. A total of four viroids/viroid-like RNAs and 49 new plant RNA and DNA viruses from 18 known or unassigned virus families have been identified from plants since 2009. A comparison of enrichment strategies reveals that full indexing of RNA and DNA viruses as well as viroids in a plant sample at single-nucleotide resolution is made possible by one NGS run of total small RNAs, followed by data mining with homology-dependent and homology-independent computational algorithms. Major challenges in the application of NGS technologies to pathogen discovery are discussed.
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Affiliation(s)
- Qingfa Wu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 China;
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17
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Galli V, Guzman F, de Oliveira LFV, Loss-Morais G, Körbes AP, Silva SDA, Margis-Pinheiro MMAN, Margis R. Identifying microRNAs and transcript targets in Jatropha seeds. PLoS One 2014; 9:e83727. [PMID: 24551031 PMCID: PMC3923737 DOI: 10.1371/journal.pone.0083727] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Accepted: 11/06/2013] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs, or miRNAs, are endogenously encoded small RNAs that play a key role in diverse plant biological processes. Jatropha curcas L. has received significant attention as a potential oilseed crop for the production of renewable oil. Here, a sRNA library of mature seeds and three mRNA libraries from three different seed development stages were generated by deep sequencing to identify and characterize the miRNAs and pre-miRNAs of J. curcas. Computational analysis was used for the identification of 180 conserved miRNAs and 41 precursors (pre-miRNAs) as well as 16 novel pre-miRNAs. The predicted miRNA target genes are involved in a broad range of physiological functions, including cellular structure, nuclear function, translation, transport, hormone synthesis, defense, and lipid metabolism. Some pre-miRNA and miRNA targets vary in abundance between the three stages of seed development. A search for sequences that produce siRNA was performed, and the results indicated that J. curcas siRNAs play a role in nuclear functions, transport, catalytic processes and disease resistance. This study presents the first large scale identification of J. curcas miRNAs and their targets in mature seeds based on deep sequencing, and it contributes to a functional understanding of these miRNAs.
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Affiliation(s)
- Vanessa Galli
- Center of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Populations, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
- Brazilian Agricultural Research – EMBRAPA, Pelotas, RS, Brazil
| | - Frank Guzman
- PPGGBM at Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Luiz F. V. de Oliveira
- Center of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Populations, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Guilherme Loss-Morais
- Center of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Populations, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Ana P. Körbes
- PPGGBM at Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | | | | | - Rogério Margis
- Center of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Populations, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
- PPGGBM at Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
- * E-mail:
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18
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Galli V, Guzman F, de Oliveira LFV, Loss-Morais G, Körbes AP, Silva SDA, Margis-Pinheiro MMAN, Margis R. Identifying microRNAs and transcript targets in Jatropha seeds. PLoS One 2014. [PMID: 24551031 DOI: 10.1371/journal.pone.008372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
MicroRNAs, or miRNAs, are endogenously encoded small RNAs that play a key role in diverse plant biological processes. Jatropha curcas L. has received significant attention as a potential oilseed crop for the production of renewable oil. Here, a sRNA library of mature seeds and three mRNA libraries from three different seed development stages were generated by deep sequencing to identify and characterize the miRNAs and pre-miRNAs of J. curcas. Computational analysis was used for the identification of 180 conserved miRNAs and 41 precursors (pre-miRNAs) as well as 16 novel pre-miRNAs. The predicted miRNA target genes are involved in a broad range of physiological functions, including cellular structure, nuclear function, translation, transport, hormone synthesis, defense, and lipid metabolism. Some pre-miRNA and miRNA targets vary in abundance between the three stages of seed development. A search for sequences that produce siRNA was performed, and the results indicated that J. curcas siRNAs play a role in nuclear functions, transport, catalytic processes and disease resistance. This study presents the first large scale identification of J. curcas miRNAs and their targets in mature seeds based on deep sequencing, and it contributes to a functional understanding of these miRNAs.
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Affiliation(s)
- Vanessa Galli
- Center of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Populations, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil ; Brazilian Agricultural Research - EMBRAPA, Pelotas, RS, Brazil
| | - Frank Guzman
- PPGGBM at Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Luiz F V de Oliveira
- Center of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Populations, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Guilherme Loss-Morais
- Center of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Populations, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Ana P Körbes
- PPGGBM at Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | | | | | - Rogério Margis
- Center of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Populations, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil ; PPGGBM at Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
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do Nascimento LC, Costa GGL, Binneck E, Pereira GAG, Carazzolle MF. A web-based bioinformatics interface applied to the GENOSOJA Project: Databases and pipelines. Genet Mol Biol 2012; 35:203-11. [PMID: 22802706 PMCID: PMC3392873 DOI: 10.1590/s1415-47572012000200002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Genosoja consortium is an initiative to integrate different omics research approaches carried out in Brazil. Basically, the aim of the project is to improve the plant by identifying genes involved in responses against stresses that affect domestic production, like drought stress and Asian Rust fungal disease. To do so, the project generated several types of sequence data using different methodologies, most of them sequenced by next generation sequencers. The initial stage of the project is highly dependent on bioinformatics analysis, providing suitable tools and integrated databases. In this work, we describe the main features of the Genosoja web database, including the pipelines to analyze some kinds of data (ESTs, SuperSAGE, microRNAs, subtractive cDNA libraries), as well as web interfaces to access information about soybean gene annotation and expression.
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Affiliation(s)
- Leandro Costa do Nascimento
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Gustavo Gilson Lacerda Costa
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Eliseu Binneck
- Empresa Brasileira de Pesquisa Agropecuária, Londrina, PR, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Marcelo Falsarella Carazzolle
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
- Centro Nacional de Processamento de Alto Desempenho em São Paulo, Universidade Estadual de Campinas, Campinas, SP, Brazil
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