1
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Wang WQ, Liu XF, Zhu YJ, Zhu JZ, Liu C, Wang ZY, Shen XX, Allan AC, Yin XR. Identification of miRNA858 long-loop precursors in seed plants. THE PLANT CELL 2024; 36:1637-1654. [PMID: 38114096 PMCID: PMC11062470 DOI: 10.1093/plcell/koad315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/20/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
MicroRNAs (miRNAs) are a class of nonprotein-coding short transcripts that provide a layer of post-transcriptional regulation essential to many plant biological processes. MiR858, which targets the transcripts of MYB transcription factors, can affect a range of secondary metabolic processes. Although miR858 and its 187-nt precursor have been well studied in Arabidopsis (Arabidopsis thaliana), a systematic investigation of miR858 precursors and their functions across plant species is lacking due to a problem in identifying the transcripts that generate this subclass. By re-evaluating the transcript of miR858 and relaxing the length cut-off for identifying hairpins, we found in kiwifruit (Actinidia chinensis) that miR858 has long-loop hairpins (1,100 to 2,100 nt), whose intervening sequences between miRNA generating complementary sites were longer than all previously reported miRNA hairpins. Importantly, these precursors of miR858 containing long-loop hairpins (termed MIR858L) are widespread in seed plants including Arabidopsis, varying between 350 and 5,500 nt. Moreover, we showed that MIR858L has a greater impact on proanthocyanidin and flavonol levels in both Arabidopsis and kiwifruit. We suggest that an active MIR858L-MYB regulatory module appeared in the transition of early land plants to large upright flowering plants, making a key contribution to plant secondary metabolism.
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Affiliation(s)
- Wen-qiu Wang
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Xiao-fen Liu
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yong-jing Zhu
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Jia-zhen Zhu
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Chao Liu
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Zhi-ye Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Xing-Xing Shen
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Andrew C Allan
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Xue-ren Yin
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
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2
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Azad MF, Dawar P, Esim N, Rock CD. Role of miRNAs in sucrose stress response, reactive oxygen species, and anthocyanin biosynthesis in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2023; 14:1278320. [PMID: 38023835 PMCID: PMC10656695 DOI: 10.3389/fpls.2023.1278320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023]
Abstract
In plants, sucrose is the main transported disaccharide that is the primary product of photosynthesis and controls a multitude of aspects of the plant life cycle including structure, growth, development, and stress response. Sucrose is a signaling molecule facilitating various stress adaptations by crosstalk with other hormones, but the molecular mechanisms are not well understood. Accumulation of high sucrose concentrations is a hallmark of many abiotic and biotic stresses, resulting in the accumulation of reactive oxygen species and secondary metabolite anthocyanins that have antioxidant properties. Previous studies have shown that several MYeloBlastosis family/MYB transcription factors are positive and negative regulators of sucrose-induced anthocyanin accumulation and subject to microRNA (miRNA)-mediated post-transcriptional silencing, consistent with the notion that miRNAs may be "nodes" in crosstalk signaling by virtue of their sequence-guided targeting of different homologous family members. In this study, we endeavored to uncover by deep sequencing small RNA and mRNA transcriptomes the effects of exogenous high sucrose stress on miRNA abundances and their validated target transcripts in Arabidopsis. We focused on genotype-by-treatment effects of high sucrose stress in Production of Anthocyanin Pigment 1-Dominant/pap1-D, an activation-tagged dominant allele of MYB75 transcription factor, a positive effector of secondary metabolite anthocyanin pathway. In the process, we discovered links to reactive oxygen species signaling through miR158/161/173-targeted Pentatrico Peptide Repeat genes and two novel non-canonical targets of high sucrose-induced miR408 and miR398b*(star), relevant to carbon metabolic fluxes: Flavonoid 3'-Hydroxlase (F3'H), an important enzyme in determining the B-ring hydroxylation pattern of flavonoids, and ORANGE a post-translational regulator of Phytoene Synthase expression, respectively. Taken together, our results contribute to understanding the molecular mechanisms of carbon flux shifts from primary to secondary metabolites in response to high sugar stress.
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Affiliation(s)
- Md. Fakhrul Azad
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Pranav Dawar
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Nevzat Esim
- Department of Molecular Biology and Genetics, Bіngöl University, Bingöl, Türkiye
| | - Christopher D. Rock
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
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3
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Mittal M, Dhingra A, Dawar P, Payton P, Rock CD. The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea). THE PLANT GENOME 2023; 16:e20350. [PMID: 37351954 DOI: 10.1002/tpg2.20350] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 06/24/2023]
Abstract
MicroRNAs (miRNAs) are 21-24 nt small RNAs (sRNAs) that negatively regulate protein-coding genes and/or trigger phased small-interfering RNA (phasiRNA) production. Two thousand nine hundred miRNA families, of which ∼40 are deeply conserved, have been identified in ∼80 different plant species genomes. miRNA functions in response to abiotic stresses is less understood than their roles in development. Only seven peanut MIRNA families are documented in miRBase, yet a reference genome assembly is now published and over 480 plant-like MIRNA loci were predicted in the diploid peanut progenitor Arachis duranensis genome. We explored by computational analysis of a leaf sRNA library and publicly available sRNA, degradome, and transcriptome datasets the miRNA and phasiRNA space associated with drought and heat stresses in peanut. We characterized 33 novel candidate and 33 ancient conserved families of MIRNAs and present degradome evidence for their cleavage activities on mRNA targets, including several noncanonical targets and novel phasiRNA-producing noncoding and mRNA loci with validated novel targets such as miR1509 targeting serine/threonine-protein phosphatase7 and miRc20 and ahy-miR3514 targeting penta-tricopeptide repeats (PPRs), in contradistinction to other claims of miR1509/173/7122 superfamily miRNAs indirectly targeting PPRs via TAS-like noncoding RNA loci. We characterized the inverse correlations of significantly differentially expressed drought- and heat-regulated miRNAs, assayed by sRNA blots or transcriptome datasets, with target mRNA expressions in the same datasets. Meta-analysis of an expression atlas and over representation of miRNA target genes in co-expression networks suggest that miRNAs have functions in unique aspects of peanut gynophore development. Genome-wide MIRNA annotation of the published allopolyploid peanut genome can facilitate molecular breeding of value-added traits.
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Affiliation(s)
- Meenakshi Mittal
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Anuradha Dhingra
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Pranav Dawar
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Paxton Payton
- USDA-ARS Plant Stress and Germplasm Lab, Lubbock, Texas, USA
| | - Christopher D Rock
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
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4
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Umu SU, Paynter VM, Trondsen H, Buschmann T, Rounge TB, Peterson KJ, Fromm B. Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine. CELL GENOMICS 2023; 3:100348. [PMID: 37601971 PMCID: PMC10435380 DOI: 10.1016/j.xgen.2023.100348] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/15/2023] [Accepted: 05/26/2023] [Indexed: 08/22/2023]
Abstract
The annotation of microRNAs depends on the availability of transcriptomics data and expert knowledge. This has led to a gap between the availability of novel genomes and high-quality microRNA complements. Using >16,000 microRNAs from the manually curated microRNA gene database MirGeneDB, we generated trained covariance models for all conserved microRNA families. These models are available in our tool MirMachine, which annotates conserved microRNAs within genomes. We successfully applied MirMachine to a range of animal species, including those with large genomes and genome duplications and extinct species, where small RNA sequencing is hard to achieve. We further describe a microRNA score of expected microRNAs that can be used to assess the completeness of genome assemblies. MirMachine closes a long-persisting gap in the microRNA field by facilitating automated genome annotation pipelines and deeper studies into the evolution of genome regulation, even in extinct organisms.
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Affiliation(s)
- Sinan Uğur Umu
- Department of Pathology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Vanessa M. Paynter
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Håvard Trondsen
- Department of Pathology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Trine B. Rounge
- Department of Research, Cancer Registry of Norway, Oslo, Norway
- Centre for Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Kevin J. Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Bastian Fromm
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, Tromsø, Norway
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5
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Alzahrani S, Applegate C, Swarbreck D, Dalmay T, Folkes L, Moulton V. Degradome Assisted Plant MicroRNA Prediction Under Alternative Annotation Criteria. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:3374-3383. [PMID: 34559659 DOI: 10.1109/tcbb.2021.3115023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Current microRNA (miRNA) prediction methods are generally based on annotation criteria that tend to miss potential functional miRNAs. Recently, new miRNA annotation criteria have been proposed that could lead to improvements in miRNA prediction methods in plants. Here, we investigate the effect of the new criteria on miRNA prediction in Arabidopsis thaliana and present a new degradome assisted functional miRNA prediction approach. We investigated the effect by applying the new criteria, and a more permissive criteria on miRNA prediction using existing miRNA prediction tools. We also developed an approach to miRNA prediction that is assisted by the functional information extracted from the analysis of degradome sequencing. We demonstrate the improved performance of degradome assisted miRNA prediction compared to unassisted prediction and evaluate the approach using miRNA differential expression analysis. We observe how the miRNA predictions fit under the different criteria and show a potential novel miRNA that has been missed within Arabidopsis thaliana. Additionally, we introduce a freely available software 'PAREfirst' that employs the degradome assisted approach. The study shows that some miRNAs could be missed due to the stringency of the former annotation criteria, and combining a degradome assisted approach with more permissive miRNA criteria can expand confident miRNA predictions.
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6
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Yu X, Hou Y, Cao L, Zhou T, Wang S, Hu K, Chen J, Qu S. MicroRNA candidate miRcand137 in apple is induced by Botryosphaeria dothidea for impairing host defense. PLANT PHYSIOLOGY 2022; 189:1814-1832. [PMID: 35512059 PMCID: PMC9237668 DOI: 10.1093/plphys/kiac171] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
MicroRNA (miRNA)-mediated gene silencing is a master gene regulatory pathway in plant-pathogen interactions. The differential accumulation of miRNAs among plant varieties alters the expression of target genes, affecting plant defense responses and causing resistance differences among varieties. Botryosphaeria dothidea is an important phytopathogenic fungus of apple (Malus domestica). Malus hupehensis (Pamp.) Rehder, a wild apple species, is highly resistant, whereas the apple cultivar "Fuji" is highly susceptible. Here, we identified a 22-nt miRNA candidate named miRcand137 that compromises host resistance to B. dothidea infection and whose processing was affected by precursor sequence variation between M. hupehensis and "Fuji." miRcand137 guides the direct cleavage of and produced target-derived secondary siRNA against Ethylene response factor 14 (ERF14), a transcriptional activator of pathogenesis-related homologs that confers disease resistance to apple. We showed that miRcand137 acts as an inhibitor of apple immunity by compromising ERF14-mediated anti-fungal defense and revealed a negative association between miRcand137 expression and B. dothidea sensitivity in both resistant and susceptible apples. Furthermore, MIRCAND137 was transcriptionally activated by the invading fungi but not by the fungal elicitor, implying B. dothidea induced host miRcand137 as an infection strategy. We propose that the inefficient miRcand137 processing in M. hupehensis decreased pathogen-initiated miRcand137 accumulation, leading to higher resistance against B. dothidea.
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Affiliation(s)
- Xinyi Yu
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yingjun Hou
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Lifang Cao
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Tingting Zhou
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Sanhong Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Kaixu Hu
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Jingrui Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
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7
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Identification and Comparative Analysis of Conserved and Species-Specific microRNAs in Four Populus Sections. FORESTS 2022. [DOI: 10.3390/f13060873] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The conservation and diversity of microRNA (miRNA) families provide insights into the evolution of miRNA genes. However, there are few studies to explore the miRNA genes at the genus level in plants. Here, we identified 1194 miRNA loci in four Populus species P. deltoides, P. euphratica, P. tremula, and P. trichocarpa from Aigeiros, Turanga, Populus, and Tacamahaca sections, respectively, by combining de novo and homolog-based approaches. Our results indicated that a similar number of miRNA loci exist in each species (296–301 miRNA loci). Among the identified 143 miRNA families, 68 families are shared by the studied four species, and 31 families are species-specific, which might be related to local adaptation. Additionally, multiple miRNA-related single nucleotide polymorphisms (SNPs) were found, indicating that polymorphisms in pre-miRNA hairpins were likely to affect miRNA biogenesis. This study expanded the breadth and depth of miRNA annotations and provided valuable resources for further exploring the diversity and function of poplar miRNAs.
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8
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Zhang T, Zhai J, Zhang X, Ling L, Li M, Xie S, Song M, Ma C. Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:557-567. [PMID: 34332120 PMCID: PMC9801042 DOI: 10.1016/j.gpb.2021.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 12/15/2020] [Accepted: 03/06/2021] [Indexed: 01/26/2023]
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression. The large-scale detection and profiling of miRNAs have been accelerated with the development of high-throughput small RNA sequencing (sRNA-Seq) techniques and bioinformatics tools. However, generating high-quality comprehensive miRNA annotations remains challenging due to the intrinsic complexity of sRNA-Seq data and inherent limitations of existing miRNA prediction tools. Here, we present iwa-miRNA, a Galaxy-based framework that can facilitate miRNA annotation in plant species by combining computational analysis and manual curation. iwa-miRNA is specifically designed to generate a comprehensive list of miRNA candidates, bridging the gap between already annotated miRNAs provided by public miRNA databases and new predictions from sRNA-Seq datasets. It can also assist users in selecting promising miRNA candidates in an interactive mode, contributing to the accessibility and reproducibility of genome-wide miRNA annotation. iwa-miRNA is user-friendly and can be easily deployed as a web application for researchers without programming experience. With flexible, interactive, and easy-to-use features, iwa-miRNA is a valuable tool for the annotation of miRNAs in plant species with reference genomes. We also illustrate the application of iwa-miRNA for miRNA annotation using data from plant species with varying genomic complexity. The source codes and web server of iwa-miRNA are freely accessible at http://iwa-miRNA.omicstudio.cloud/.
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Affiliation(s)
- Ting Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling 712100, China,Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, China
| | - Jingjing Zhai
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling 712100, China,Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, China
| | - Xiaorong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling 712100, China,Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, China
| | - Lei Ling
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling 712100, China,Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, China
| | - Menghan Li
- College of Plant Science, Tibet Agricultural and Animal Husbandry University, Linzhi 860006, China
| | - Shang Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling 712100, China,Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, China
| | - Minggui Song
- College of Information Engineering, Northwest A&F University, Yangling 712100, China
| | - Chuang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling 712100, China,Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, China,Corresponding author.
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9
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Wong GY, Millar AA. TRUEE; a bioinformatic pipeline to define the functional microRNA targetome of Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1476-1492. [PMID: 35352405 PMCID: PMC9324967 DOI: 10.1111/tpj.15751] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Central to plant microRNA (miRNA) biology is the identification of functional miRNA-target interactions (MTIs). However, the complementarity basis of bioinformatic target prediction results in mostly false positives, and the degree of complementarity does not equate with regulation. Here, we develop a bioinformatic workflow named TRUEE (Targets Ranked Using Experimental Evidence) that ranks MTIs on the extent to which they are subjected to miRNA-mediated cleavage. It sorts predicted targets into high (HE) and low evidence (LE) groupings based on the frequency and strength of miRNA-guided cleavage degradome signals across multiple degradome experiments. From this, each target is assigned a numerical value, termed a Category Score, ranking the extent to which it is subjected to miRNA-mediated cleavage. As a proof-of-concept, the 428 Arabidopsis miRNAs annotated in miRBase were processed through the TRUEE pipeline to determine the miRNA 'targetome'. The majority of high-ranking Category Score targets corresponded to highly conserved MTIs, validating the workflow. Very few Arabidopsis-specific, Brassicaceae-specific, or Conserved-passenger miRNAs had HE targets with high Category Scores. In total, only several hundred MTIs were found to have Category Scores characteristic of currently known physiologically significance MTIs. Although non-exhaustive, clearly the number of functional MTIs is much narrower than many studies claim. Therefore, using TRUEE to numerically rank targets directly on experimental evidence has given insights into the scope of the functional miRNA targetome of Arabidopsis.
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Affiliation(s)
- Gigi Y. Wong
- Division of Plant Science, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - Anthony A. Millar
- Division of Plant Science, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
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10
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Fromm B, Høye E, Domanska D, Zhong X, Aparicio-Puerta E, Ovchinnikov V, Umu SU, Chabot PJ, Kang W, Aslanzadeh M, Tarbier M, Mármol-Sánchez E, Urgese G, Johansen M, Hovig E, Hackenberg M, Friedländer MR, Peterson KJ. MirGeneDB 2.1: toward a complete sampling of all major animal phyla. Nucleic Acids Res 2021; 50:D204-D210. [PMID: 34850127 PMCID: PMC8728216 DOI: 10.1093/nar/gkab1101] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/20/2021] [Accepted: 11/23/2021] [Indexed: 12/03/2022] Open
Abstract
We describe an update of MirGeneDB, the manually curated microRNA gene database. Adhering to uniform and consistent criteria for microRNA annotation and nomenclature, we substantially expanded MirGeneDB with 30 additional species representing previously missing metazoan phyla such as sponges, jellyfish, rotifers and flatworms. MirGeneDB 2.1 now consists of 75 species spanning over ∼800 million years of animal evolution, and contains a total number of 16 670 microRNAs from 1549 families. Over 6000 microRNAs were added in this update using ∼550 datasets with ∼7.5 billion sequencing reads. By adding new phylogenetically important species, especially those relevant for the study of whole genome duplication events, and through updating evolutionary nodes of origin for many families and genes, we were able to substantially refine our nomenclature system. All changes are traceable in the specifically developed MirGeneDB version tracker. The performance of read-pages is improved and microRNA expression matrices for all tissues and species are now also downloadable. Altogether, this update represents a significant step toward a complete sampling of all major metazoan phyla, and a widely needed foundation for comparative microRNA genomics and transcriptomics studies. MirGeneDB 2.1 is part of RNAcentral and Elixir Norway, publicly and freely available at http://www.mirgenedb.org/.
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Affiliation(s)
- Bastian Fromm
- The Arctic University Museum of Norway, UiT- The Arctic University of Norway, Tromsø, Norway.,Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Eirik Høye
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Diana Domanska
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway.,Department of Pathology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Xiangfu Zhong
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Ernesto Aparicio-Puerta
- Department of Genetics, Faculty of Sciences, MNAT Excellence Unit, University of Granada, Granada, Spain.,Biotechnology Institute, CIBM, Granada, Spain.,Biohealth Research Institute (ibs.GRANADA), University Hospitals of Granada, University of Granada, Granada, Spain
| | - Vladimir Ovchinnikov
- Computational and Molecular Evolutionary Biology Research Group, School of life sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK
| | - Sinan U Umu
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Peter J Chabot
- Department of Biological Sciences, Dartmouth College, Hanover, USA
| | - Wenjing Kang
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Morteza Aslanzadeh
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Marcel Tarbier
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, Sweden
| | - Emilio Mármol-Sánchez
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | | | - Morten Johansen
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Michael Hackenberg
- Department of Genetics, Faculty of Sciences, MNAT Excellence Unit, University of Granada, Granada, Spain.,Biotechnology Institute, CIBM, Granada, Spain.,Biohealth Research Institute (ibs.GRANADA), University Hospitals of Granada, University of Granada, Granada, Spain
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, USA
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11
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Fang L, Wang Y. MicroRNAs in Woody Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:686831. [PMID: 34531880 PMCID: PMC8438446 DOI: 10.3389/fpls.2021.686831] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 08/03/2021] [Indexed: 05/05/2023]
Abstract
MicroRNAs (miRNAs) are small (∼21-nucleotides) non-coding RNAs found in plant and animals. MiRNAs function as critical post-transcriptional regulators of gene expression by binding to complementary sequences in their target mRNAs, leading to mRNA destabilization and translational inhibition. Plant miRNAs have some distinct characteristics compared to their animal counterparts, including greater evolutionary conservation and unique miRNA processing methods. The lifecycle of a plant begins with embryogenesis and progresses through seed germination, vegetative growth, reproductive growth, flowering and fruiting, and finally senescence and death. MiRNAs participate in the transformation of plant growth and development and directly monitor progression of these processes and the expression of certain morphological characteristics by regulating transcription factor genes involved in cell growth and differentiation. In woody plants, a large and rapidly increasing number of miRNAs have been identified, but their biological functions are largely unknown. In this review, we summarize the progress of miRNA research in woody plants to date. In particular, we discuss the potential roles of these miRNAs in growth, development, and biotic and abiotic stresses responses in woody plants.
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Affiliation(s)
- Lisha Fang
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Yanmei Wang
- College of Forestry, Henan Agricultural University, Zhengzhou, China
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
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12
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Vivek AT, Kumar S. Computational methods for annotation of plant regulatory non-coding RNAs using RNA-seq. Brief Bioinform 2020; 22:6041165. [PMID: 33333550 DOI: 10.1093/bib/bbaa322] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 12/19/2022] Open
Abstract
Plant transcriptome encompasses numerous endogenous, regulatory non-coding RNAs (ncRNAs) that play a major biological role in regulating key physiological mechanisms. While studies have shown that ncRNAs are extremely diverse and ubiquitous, the functions of the vast majority of ncRNAs are still unknown. With ever-increasing ncRNAs under study, it is essential to identify, categorize and annotate these ncRNAs on a genome-wide scale. The use of high-throughput RNA sequencing (RNA-seq) technologies provides a broader picture of the non-coding component of transcriptome, enabling the comprehensive identification and annotation of all major ncRNAs across samples. However, the detection of known and emerging class of ncRNAs from RNA-seq data demands complex computational methods owing to their unique as well as similar characteristics. Here, we discuss major plant endogenous, regulatory ncRNAs in an RNA sample followed by computational strategies applied to discover each class of ncRNAs using RNA-seq. We also provide a collection of relevant software packages and databases to present a comprehensive bioinformatics toolbox for plant ncRNA researchers. We assume that the discussions in this review will provide a rationale for the discovery of all major categories of plant ncRNAs.
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Affiliation(s)
- A T Vivek
- National Institute of Plant Genome Research in New Delhi, India
| | - Shailesh Kumar
- National Institute of Plant Genome Research in New Delhi
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13
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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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14
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Gramzow L, Lobbes D, Innard N, Theißen G. Independent origin of MIRNA genes controlling homologous target genes by partial inverted duplication of antisense-transcribed sequences. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:401-419. [PMID: 31571291 DOI: 10.1111/tpj.14550] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/21/2019] [Accepted: 09/18/2019] [Indexed: 06/10/2023]
Abstract
Some microRNAs (miRNAs) are key regulators of developmental processes, mainly by controlling the accumulation of transcripts encoding transcription factors that are important for morphogenesis. MADS-box genes encode a family of transcription factors which control diverse developmental processes in flowering plants. Here we study the convergent evolution of two MIRNA (MIR) gene families, named MIR444 and MIR824, targeting members of the same clade of MIKCC -group MADS-box genes. We show that these two MIR genes most likely originated independently in monocots (MIR444) and in Brassicales (eudicots, MIR824). We provide evidence that, in both cases, the future target gene was transcribed in antisense prior to the evolution of the MIR genes. Both MIR genes then likely originated by a partial inverted duplication of their target genes, resulting in natural antisense organization of the newly evolved MIR gene and its target gene at birth. We thus propose a model for the origin of MIR genes, MEPIDAS (MicroRNA Evolution by Partial Inverted Duplication of Antisense-transcribed Sequences). MEPIDAS is a refinement of the inverted duplication hypothesis. According to MEPIDAS, a MIR gene evolves at a genomic locus at which the future target gene is also transcribed in the antisense direction. A partial inverted duplication at this locus causes the antisense transcript to fold into a stem-loop structure that is recognized by the miRNA biogenesis machinery to produce a miRNA that regulates the gene at this locus. Our analyses exemplify how to elucidate the origin of conserved miRNAs by comparative genomics and will guide future studies. OPEN RESEARCH BADGE: 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 https://www.ncbi.nlm.nih.gov/genbank/.
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Affiliation(s)
- Lydia Gramzow
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Dajana Lobbes
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Nathan Innard
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Günter Theißen
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743, Jena, Germany
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15
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Cavé-Radet A, Giraud D, Lima O, El Amrani A, Aïnouche M, Salmon A. Evolution of small RNA expression following hybridization and allopolyploidization: insights from Spartina species (Poaceae, Chloridoideae). PLANT MOLECULAR BIOLOGY 2020; 102:55-72. [PMID: 31748889 DOI: 10.1007/s11103-019-00931-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/09/2019] [Indexed: 06/10/2023]
Abstract
Differential expression of mi-RNAs targeting developmental processes and progressive downregulation of repeat-associated siRNAs following genome merger and genome duplication in the context of allopolyploid speciation in Spartina. The role of small RNAs on gene expression regulation and genome stability is arousing increased interest and is being explored in various plant systems. In spite of prominence of reticulate evolution and polyploidy that affects the evolutionary history of all plant lineages, very few studies analysed RNAi mechanisms with this respect. Here, we explored small RNAs diversity and expression in the context of recent allopolyploid speciation, using the Spartina system, which offers a unique opportunity to explore the immediate changes following hybridization and genome duplication. Small RNA-Seq analyses were conducted on hexaploid parental species (S. alterniflora and S. maritima), their F1 hybrid S. x townsendii, and the neoallododecaploid S. anglica. We identified 594 miRNAs, 2197 miRNA-target genes, and 3730 repeat-associated siRNAs (mostly targeting Class I/Copia-Ivana- Copia-SIRE and LINEs elements). For both mi- and ra-siRNAs, we detected differential expression patterns following genome merger and genome duplication. These misregulations include non-additive expression of miRNAs in the F1 hybrid and additional changes in the allopolyploid targeting developmental processes. Expression of repeat-associated siRNAs indicates a strengthen of transposable element repression during the allopolyploidization process. Altogether, these results confirm the central role small RNAs play in shaping regulatory changes in naturally formed recent allopolyploids.
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Affiliation(s)
- Armand Cavé-Radet
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Delphine Giraud
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Oscar Lima
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Abdelhak El Amrani
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Malika Aïnouche
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Armel Salmon
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France.
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16
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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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17
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Fridrich A, Hazan Y, Moran Y. Too Many False Targets for MicroRNAs: Challenges and Pitfalls in Prediction of miRNA Targets and Their Gene Ontology in Model and Non-model Organisms. Bioessays 2019; 41:e1800169. [PMID: 30919506 PMCID: PMC6701991 DOI: 10.1002/bies.201800169] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 01/28/2019] [Indexed: 12/20/2022]
Abstract
Short ("seed") or extended base pairing between microRNAs (miRNAs) and their target RNAs enables post-transcriptional silencing in many organisms. These interactions allow the computational prediction of potential targets. In model organisms, predicted targets are frequently validated experimentally; hence meaningful miRNA-regulated processes are reported. However, in non-models, these reports mostly rely on computational prediction alone. Many times, further bioinformatic analyses such as Gene Ontology (GO) enrichment are based on these in silico projections. Here such approaches are reviewed, their caveats are highlighted and the ease of picking false targets from predicted lists is demonstrated. Discoveries that shed new light on how miRNAs evolved to regulate targets in various phyletic groups are discussed, in addition to the pitfalls of target identification in non-model organisms. The goal is to prevent the misuse of bioinformatic tools, as they cannot bypass the biological understanding of miRNA-target regulation.
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Affiliation(s)
- Arie Fridrich
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Yael Hazan
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
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18
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Yu L, Guo R, Jiang Y, Ye X, Yang Z, Meng Y, Shao C. Genome-wide identification and characterization of novel microRNAs in seed development of soybean. Biosci Biotechnol Biochem 2019; 83:233-242. [PMID: 30355067 DOI: 10.1080/09168451.2018.1536513] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/03/2018] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in eukaryotes. However, the information about miRNAs population and their regulatory functions involving in soybean seed development remains incomplete. Base on the Dicer-like1-mediated cleavage signals during miRNA processing could be employed for novel miRNA discovery, a genome-wide search for miRNA candidates involved in seed development was carried out. As a result, 17 novel miRNAs, 14 isoforms of miRNA (isomiRs) and 31 previously validated miRNAs were discovered. These novel miRNAs and isomiRs represented tissue-specific expression and the isomiRs showed significantly higher abundance than that of their miRNA counterparts in different tissues. After target prediction and degradome sequencing data-based validation, 13 novel miRNA-target pairs were further identified. Besides, five targets of 22-nt iso-gma-miR393h were found to be triggered to produce secondary trans-acting siRNA (ta-siRNAs). Summarily, our results could expand the repertoire of miRNAs with potentially important functions in soybean.
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Affiliation(s)
- Lan Yu
- a College of Life Sciences , Huzhou University , Huzhou P.R. China
| | - Rongkai Guo
- b Shanghai Institute of Plant Physiology and Ecology , Chinese Academy of Sciences , Shanghai China
| | - Yeqin Jiang
- a College of Life Sciences , Huzhou University , Huzhou P.R. China
| | - Xinghuo Ye
- a College of Life Sciences , Huzhou University , Huzhou P.R. China
| | - Zhihong Yang
- a College of Life Sciences , Huzhou University , Huzhou P.R. China
| | - Yijun Meng
- c College of Life and Environmental Sciences , Hangzhou Normal University , Hangzhou P.R. China
| | - Chaogang Shao
- a College of Life Sciences , Huzhou University , Huzhou P.R. China
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19
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Abstract
Bioinformatic analysis of small RNA sequencing libraries consists of transforming a series of small RNA sequencing experiment fastq files into a table containing small RNA sequences and their abundance. This is achieved by cleaning the reads, aligning the cleaned reads to a reference, and parsing the alignment results. In this protocol we present the most common option, and the rationale, for each of these steps.
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20
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Devi K, Dey KK, Singh S, Mishra SK, Modi MK, Sen P. Identification and validation of plant miRNA from NGS data—an experimental approach. Brief Funct Genomics 2018; 18:13-22. [DOI: 10.1093/bfgp/ely034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 09/17/2018] [Accepted: 10/02/2018] [Indexed: 12/18/2022] Open
Affiliation(s)
- Kamalakshi Devi
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | - Kuntal Kumar Dey
- Distributed Information Centre, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | - Sanjay Singh
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | | | - Mahendra Kumar Modi
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
- Distributed Information Centre, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | - Priyabrata Sen
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
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21
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Chitarra W, Pagliarani C, Abbà S, Boccacci P, Birello G, Rossi M, Palmano S, Marzachì C, Perrone I, Gambino G. miRVIT: A Novel miRNA Database and Its Application to Uncover Vitis Responses to Flavescence dorée Infection. FRONTIERS IN PLANT SCIENCE 2018; 9:1034. [PMID: 30065744 PMCID: PMC6057443 DOI: 10.3389/fpls.2018.01034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/26/2018] [Indexed: 05/08/2023]
Abstract
Micro(mi)RNAs play crucial roles in plant developmental processes and in defense responses to biotic and abiotic stresses. In the last years, many works on small RNAs in grapevine (Vitis spp.) were published, and several conserved and putative novel grapevine-specific miRNAs were identified. In order to reorganize the high quantity of available data, we produced "miRVIT," the first database of all novel grapevine miRNA candidates characterized so far, and still not deposited in miRBase. To this aim, each miRNA accession was renamed, repositioned in the last version of the grapevine genome, and compared with all the novel and conserved miRNAs detected in grapevine. Conserved and novel miRNAs cataloged in miRVIT were then used for analyzing Vitis vinifera plants infected by Flavescence dorée (FD), one of the most severe phytoplasma diseases affecting grapevine. The analysis of small RNAs from healthy, recovered (plants showing spontaneous and stable remission of symptoms), and FD-infected "Barbera" grapevines showed that FD altered the expression profiles of several miRNAs, including those involved in cell development and photosynthesis, jasmonate signaling, and disease resistance response. The application of miRVIT in a biological context confirmed the effectiveness of the followed approach, especially for the identification of novel miRNA candidates in grapevine. miRVIT database is available at http://mirvit.ipsp.cnr.it. Highlights: The application of the newly produced database of grapevine novel miRNAs to the analysis of plants infected by Flavescence dorée reveals key roles of miRNAs in photosynthesis and jasmonate signaling.
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Affiliation(s)
- Walter Chitarra
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
- Viticultural and Enology Research Centre, Council for Agricultural Research and Economics, Conegliano, Italy
| | - Chiara Pagliarani
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | - Simona Abbà
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | - Paolo Boccacci
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | - Giancarlo Birello
- Research Institute on Sustainable Economic Growth, National Research Council of Italy, Turin, Italy
| | - Marika Rossi
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | - Sabrina Palmano
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | - Cristina Marzachì
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | - Irene Perrone
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
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22
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Tarver JE, Taylor RS, Puttick MN, Lloyd GT, Pett W, Fromm B, Schirrmeister BE, Pisani D, Peterson KJ, Donoghue PCJ. Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss. Genome Biol Evol 2018; 10:1457-1470. [PMID: 29788279 PMCID: PMC6007596 DOI: 10.1093/gbe/evy096] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2018] [Indexed: 12/18/2022] Open
Abstract
microRNAs are conserved noncoding regulatory factors implicated in diverse physiological and developmental processes in multicellular organisms, as causal macroevolutionary agents and for phylogeny inference. However, the conservation and phylogenetic utility of microRNAs has been questioned on evidence of pervasive loss. Here, we show that apparent widespread losses are, largely, an artefact of poorly sampled and annotated microRNAomes. Using a curated data set of animal microRNAomes, we reject the view that miRNA families are never lost, but they are rarely lost (92% are never lost). A small number of families account for a majority of losses (1.7% of families account for >45% losses), and losses are associated with lineages exhibiting phenotypic simplification. Phylogenetic analyses based on the presence/absence of microRNA families among animal lineages, and based on microRNA sequences among Osteichthyes, demonstrate the power of these small data sets in phylogenetic inference. Perceptions of widespread evolutionary loss of microRNA families are due to the uncritical use of public archives corrupted by spurious microRNA annotations, and failure to discriminate false absences that occur because of incomplete microRNAome annotation.
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Affiliation(s)
- James E Tarver
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Richard S Taylor
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Mark N Puttick
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
- Department of Biology and Biochemistry, University of Bath, United Kingdom
| | - Graeme T Lloyd
- School of Earth and Environment, University of Leeds, United Kingdom
| | - Walker Pett
- Department of Ecology, Evolution and Organismal Biology, Iowa State University
| | - Bastian Fromm
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Norway
| | - Bettina E Schirrmeister
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Davide Pisani
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire
| | - Philip C J Donoghue
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
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23
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24
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Chaves I, Costa BV, Rodrigues AS, Bohn A, Miguel CM. miRPursuit-a pipeline for automated analyses of small RNAs in model and nonmodel plants. FEBS Lett 2017; 591:2261-2268. [PMID: 28686301 DOI: 10.1002/1873-3468.12746] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/30/2017] [Accepted: 07/03/2017] [Indexed: 11/07/2022]
Abstract
miRPursuit is a pipeline developed for running end-to-end analyses of high-throughput small RNA (sRNA) sequence data in model and nonmodel plants, from raw data to identified and annotated conserved and novel sequences. It consists of a series of UNIX shell scripts, which connect open-source sRNA analysis software. The involved parameters can be combined with convenient workflow management by users without advanced computational skills. miRPursuit presents several advantages when compared to other tools, including the possibility of processing several sRNA libraries in parallel, thus easily allowing a comparison of the differences in sRNA read accumulation among sRNA libraries. We validate miRPursuit by using datasets from a model plant and discuss its performance with the analysis of sRNAs from non-model species.
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Affiliation(s)
- Inês Chaves
- Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Bruno Vasques Costa
- Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Andreia S Rodrigues
- Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Andreas Bohn
- Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Célia M Miguel
- Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal.,Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa (FCUL), Lisboa, Portugal
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