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Tripathi AM, Singh R, Verma AK, Singh A, Mishra P, Dwivedi V, Narayan S, Gandhivel VHS, Shirke PA, Shivaprasad PV, Roy S. Indian Himalayan natural Arabidopsis thaliana accessions with abolished miR158 levels exhibit robust miR173-initiated trans-acting cascade silencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:855-874. [PMID: 36883862 DOI: 10.1111/tpj.16175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/13/2023] [Accepted: 03/03/2023] [Indexed: 05/27/2023]
Abstract
Small RNAs (sRNAs) such as microRNAs (miRNAs) and small interfering RNAs (siRNAs) are short 20-24-nucleotide non-coding RNAs. They are key regulators of gene expression in plants and other organisms. Several 22-nucleotide miRNAs trigger biogenesis cascades of trans-acting secondary siRNAs, which are involved in various developmental and stress responses. Here we show that Himalayan Arabidopsis thaliana accessions having natural mutations in the miR158 locus exhibit robust cascade silencing of the pentatricopeptide repeat (PPR)-like locus. Furthermore, we show that these cascade sRNAs trigger tertiary silencing of a gene involved in transpiration and stomatal opening. The natural deletions or insertions in MIR158 led to improper processing of miR158 precursors, thereby blocking synthesis of mature miR158. Reduced miR158 levels led to increased levels of its target, a pseudo-PPR gene that is targeted by tasiRNAs generated by the miR173 cascade in other accessions. Using sRNA datasets derived from Indian Himalayan accessions, as well as overexpression and knockout lines of miR158, we show that absence of miR158 led to buildup of pseudo-PPR-derived tertiary sRNAs. These tertiary sRNAs mediated robust silencing of a gene involved in stomatal closure in Himalayan accessions lacking miR158 expression. We functionally validated the tertiary phasiRNA that targets NHX2, which encodes a Na+ -K+ /H+ antiporter protein, thereby regulating transpiration and stomatal conductance. Overall, we report the role of the miRNA-TAS-siRNA-pseudogene-tertiary phasiRNA-NHX2 pathway in plant adaptation.
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Affiliation(s)
- Abhinandan Mani Tripathi
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rajneesh Singh
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ashwani Kumar Verma
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Akanksha Singh
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Parneeta Mishra
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Varun Dwivedi
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Shiv Narayan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Plant Physiology Laboratory, CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Vivek Hari Sundar Gandhivel
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Pramod Arvind Shirke
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Plant Physiology Laboratory, CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Padubidri V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Sribash Roy
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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Jiang L, Fu Y, Sun P, Tian X, Wang G. Identification of microRNA158 from Anthurium andraeanum and Its Function in Cold Stress Tolerance. PLANTS (BASEL, SWITZERLAND) 2022; 11:3371. [PMID: 36501408 PMCID: PMC9735552 DOI: 10.3390/plants11233371] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Anthurium andraeanum is a tropical flower with high ornamental and economic value. Cold stress is one of the major abiotic stresses affecting the quality and value of A. andraeanum; thus, improving the cold tolerance of this species is an important breeding objective. MicroRNAs (miRNAs) have a critical role in plant abiotic stress responses, but their specific molecular regulatory mechanisms are largely unknown, including those related to the cold stress response in A. andraeanum. Here, we identified and cloned the precursor of miR158 from A. andraeanum (Aa-miR158). Both Aa-miR158 and its target gene (c48247) had higher expression levels in strong leaves than in other tissues or organs. Further study revealed that the transcript level of Aa-miR158 was increased by cold stress. Heterologous overexpression of Aa-miR158 improved cold stress tolerance in Arabidopsis, which was associated with decreases in the malondialdehyde (MDA) concentration and relative electrical conductivity (REC) as well as increases in peroxidase (POD) and catalase (CAT) activity. Moreover, overexpressing Aa-miR158 significantly increased the expression of endogenous genes related to cold stress tolerance and reactive oxygen species (ROS) levels in transgenic Arabidopsis under cold stress. Overall, our results demonstrate that Aa-miR158 is significantly involved in the cold stress response and provide a new strategy for cold tolerance breeding of A. andraeanum.
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Chaudhary V, Jangra S, Yadav NR. In silico Identification of miRNAs and Their Targets in Cluster Bean for Their Role in Development and Physiological Responses. Front Genet 2022; 13:930113. [PMID: 35846150 PMCID: PMC9280363 DOI: 10.3389/fgene.2022.930113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/08/2022] [Indexed: 11/17/2022] Open
Abstract
Cluster bean popularly known as “guar” is a drought-tolerant, annual legume that has recently emerged as an economically important crop, owing to its high protein and gum content. The guar gum has wide range of applications in food, pharma, and mining industries. India is the leading exporter of various cluster bean-based products all across the globe. Non-coding RNAs (miRNAs) are involved in regulating the expression of the target genes leading to variations in the associated pathways or final protein concentrations. The understanding of miRNAs and their associated targets in cluster bean is yet to be used to its full potential. In the present study, cluster bean EST (Expressed Sequence Tags) database was exploited to identify the miRNA and their predicted targets associated with metabolic and biological processes especially response to diverse biotic and abiotic stimuli using in silico approach. Computational analysis based on cluster bean ESTs led to the identification of 57 miRNAs along with their targets. To the best of our knowledge, this is the first report on identification of miRNAs and their targets using ESTs in cluster bean. The miRNA related to gum metabolism was also identified. Most abundant miRNA families predicted in our study were miR156, miR172, and miR2606. The length of most of the mature miRNAs was found to be 21nt long and the range of minimal folding energy (MFE) was 5.8–177.3 (−kcal/mol) with an average value of 25.4 (−kcal/mol). The identification of cluster bean miRNAs and their targets is predicted to hasten the miRNA discovery, resulting in better knowledge of the role of miRNAs in cluster bean development, physiology, and stress responses.
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Chowdhury MR, Bahadur RP, Basak J. Genome-wide prediction of cauliflower miRNAs and lncRNAs and their roles in post-transcriptional gene regulation. PLANTA 2021; 254:72. [PMID: 34519918 DOI: 10.1007/s00425-021-03689-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
We have predicted miRNAs, their targets and lncRNAs from the genome of Brassica oleracea along with their functional annotation. Selected miRNAs and their targets are experimentally validated. Roles of these non-coding RNAs in post-transcriptional gene regulation are also deciphered. Cauliflower (Brassica oleracea var. Botrytis) is an important vegetable crop for its dietary and medicinal values with rich source of vitamins, dietary fibers, flavonoids and antioxidants. MicroRNAs (miRNAs) are small non-coding RNAs (ncRNAs), which regulate gene expression by inhibiting translation or by degrading messenger RNAs (mRNAs). On the other hand, long non-coding RNAs (lncRNAs) are responsible for the up regulation and the down regulation of transcription. Although the genome of cauliflower is reported, yet the roles of these ncRNAs in post-transcriptional gene regulation (PTGR) remain elusive. In this study, we have computationally predicted 355 miRNAs, of which 280 miRNAs are novel compared to miRBase 22.1. All the predicted miRNAs belong to 121 different families. We have also identified 934 targets of 125 miRNAs along with their functional annotation. These targets are further classified into biological processes, molecular functions and cellular components. Moreover, we have predicted 634 lncRNAs, of which 61 are targeted by 30 novel miRNAs. Randomly chosen 10 miRNAs and 10 lncRNAs are experimentally validated. Five miRNA targets including squamosa promoter-binding-like protein 9, homeobox-leucine zipper protein HDG12-like, NAC domain-containing protein 100, CUP-SHAPED COTYLEDON 1 and kinesin-like protein NACK2 of four miRNAs including bol-miR156a, bol-miR162a, bol-miR164d and bol-miR2673 are also experimentally validated. We have built network models of interactions between miRNAs and their target mRNAs, as well as between miRNAs and lncRNAs. Our findings enhance the knowledge of non-coding genome of cauliflower and their roles in PTGR, and might play important roles in improving agronomic traits of this economically important crop.
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Affiliation(s)
- Moumita Roy Chowdhury
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Jolly Basak
- Department of Biotechnology, Visva-Bharati University, Santiniketan, 731235, India.
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Chapado LA, Martín-Hernández R, Hernández de la Red S, Tomé-Carneiro J, Gil-Zamorano J, Ruiz-Roso MB, Del Saz A, Crespo MC, Del Pozo-Acebo L, Arantes Ferreira Peres W, de la Peña G, López de Las Hazas MC, Dávalos A. Connection between miRNA Mediation and the Bioactive Effects of Broccoli ( Brassica oleracea var. italica): Exogenous miRNA Resistance to Food Processing and GI Digestion. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:9326-9337. [PMID: 34358423 DOI: 10.1021/acs.jafc.1c04087] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Broccoli (Brassica oleracea var. italica) and its bioactive compounds are associated with beneficial health effects, which might be enabled, at least in part, through miRNA regulation, despite recent controversial studies suggesting that exogenous dietary miRNAs may reach host circulation and target cells to regulate gene expression. Here, a computational analysis was performed to explore the processes and pathways associated with genes targeted either by (1) host-expressed miRNAs (endogenous) modulated by the bioactive compounds in broccoli or (2) miRNAs derived from broccoli (exogenous). In addition, the stability of exogenous miRNAs from broccoli was assessed after broccoli was subjected to the usual processing methods and in vitro digestion-simulating gastrointestinal (GI) conditions. Overall, bioinformatic results show that the anticarcinogenic and cancer-preventive properties attributed to cruciferous vegetables might be mediated, at least in part, through miRNA-related mechanisms. Moreover, results show that broccoli-derived miRNAs can survive common food-processing conditions and GI digestion.
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Affiliation(s)
- Luis A Chapado
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Ctra. De Cantoblanco 8, 28049 Madrid, Spain
| | - Roberto Martín-Hernández
- Bioinformatics and Biostatistics Unit, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, 28049 Madrid, Spain
| | - Silvia Hernández de la Red
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Ctra. De Cantoblanco 8, 28049 Madrid, Spain
| | - João Tomé-Carneiro
- Laboratory of Functional Foods, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, 28049 Madrid, Spain
| | - Judit Gil-Zamorano
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Ctra. De Cantoblanco 8, 28049 Madrid, Spain
| | - María Belén Ruiz-Roso
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Ctra. De Cantoblanco 8, 28049 Madrid, Spain
| | - Andrea Del Saz
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Ctra. De Cantoblanco 8, 28049 Madrid, Spain
| | - M Carmen Crespo
- Laboratory of Functional Foods, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, 28049 Madrid, Spain
| | - Lorena Del Pozo-Acebo
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Ctra. De Cantoblanco 8, 28049 Madrid, Spain
| | - Wilza Arantes Ferreira Peres
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Ctra. De Cantoblanco 8, 28049 Madrid, Spain
- Institute of Nutrition Josué de Castro, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
| | - Gema de la Peña
- Department of Biochemistry-Research, Hospital Universitario Ramón y Cajal & Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - María-Carmen López de Las Hazas
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Ctra. De Cantoblanco 8, 28049 Madrid, Spain
| | - Alberto Dávalos
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Ctra. De Cantoblanco 8, 28049 Madrid, Spain
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Bhardwaj E, Lal M, Anand S, Das S. Independent recurrent evolution of MICRORNA genes converging onto similar non-canonical organisation across green plant lineages is driven by local and segmental duplication events in species, family and lineages. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110661. [PMID: 33218629 DOI: 10.1016/j.plantsci.2020.110661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/02/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
The relationship between evolutionary history, organisation and transcriptional regulation of genes are intrinsically linked. These have been well studied in canonically organised protein-coding genes but not of MIRNAs. In the present study, we investigated the non-canonical arrangement of MIRNAs across taxonomic boundaries from algae to angiosperms employing a combination of genome organization, phylogeny and synteny. We retrieved the complete dataset of MIRNA from twenty-five species to identify and classify based on organisational patterns. The median size of cluster was between 2-5 kb and between 1-20 % of all MIRNAs are organized in head-to-head (with bidirectional promoter), head-to-tail (tandem), and overlapping manner. Although majority of the clusters are composed of MIRNA homologs, 25% of all clusters comprises of non-homologous genes with a potential of generating functional and regulatory complexity. A comparison of phylogeny and organizational patterns revealed that multiple independent events, some of which are species-specific, and some ancient, in different lineages, are responsible for non-canonical organization. Detailed investigation of MIR395 family across the plants revealed a complex origin of non-canonical arrangement through ancient and recent, segmental and local duplications; analysis of MIR399 family revealed major expansion occurred prior to monocot-dicot split, with few lineage-specific events. Evolution of "convergent" organization pattern of non-canonical arrangement originating from independent loci through recurrent event highlights our poor understanding of evolutionary process of MIRNA genes. The present investigation thus paves way for comparative functional genomics to understand the role of non-canonical organization on transcriptional regulation and regulatory diversity in MIRNA gene families.
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Affiliation(s)
- Ekta Bhardwaj
- Department of Botany, University of Delhi, Delhi, 110 007, India
| | - Mukund Lal
- Department of Botany, University of Delhi, Delhi, 110 007, India
| | - S Anand
- Department of Botany, University of Delhi, Delhi, 110 007, India
| | - Sandip Das
- Department of Botany, University of Delhi, Delhi, 110 007, India.
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Patil PG, Singh NV, Parashuram S, Bohra A, Mundewadikar DM, Sangnure VR, Babu KD, Sharma J. Genome wide identification, characterization and validation of novel miRNA-based SSR markers in pomegranate ( Punica granatum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:683-696. [PMID: 32255932 PMCID: PMC7113349 DOI: 10.1007/s12298-020-00790-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 01/13/2020] [Accepted: 02/25/2020] [Indexed: 05/21/2023]
Abstract
A total of 17,439 mature miRNAs (~ 21 nt) earlier generated through RNA seq in the pomegranate were used for in silico analysis. After complexity reduction, a total of 1922 representative mature miRNAs were selected and used as query sequences against pomegranate genome to retrieve 2540 homologous contigs with flanking regions (~ 800). By using pre-miRNA prediction web server, a total of 1028 true contigs harbouring pri-miRNAs encoding 1162 pre-miRNAs were identified. Survey of these sequences for SSRs yielded a total of 1358 and 238 SSRs specific to pri-miRNA and pre-miRNAs, respectively. Of these, primer pairs were designed for 897 pri-miRNA and 168 pre-miRNA SSRs. In pri-miRNA sequences, hexa-nucleotides repeats were found to be most abundant (44.18%) followed by mono- (18.41%) and di-nucleotide (17.01%), which is also observed in pre-miRNA sequences. Further, a set of 51 randomly selected pre-miRNA-SSRs was examined for marker polymorphism. The experimental validation of these markers on eight pomegranate genotypes demonstrated 92.15% polymorphism. Utility of these functional markers was confirmed via examination of genetic diversity of 18 pomegranate genotypes using 15 miRNA-SSRs. Further, potential application of miRNA-SSRs for discovery of trait specific candidate genes was showed by validating 51 mature miRNA against publically available 2047 EST sequences of pomegranate by target and network analysis. In summary, the current study offers novel functional molecular markers for pomegranate genetic improvement.
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Affiliation(s)
- Prakash G. Patil
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 Maharashtra India
| | - N. V. Singh
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 Maharashtra India
| | - Shilpa Parashuram
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 Maharashtra India
| | - Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024 Uttar Pradesh India
| | | | - Vipul R. Sangnure
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 Maharashtra India
| | - K. Dhinesh Babu
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 Maharashtra India
| | - Jyotsana Sharma
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 Maharashtra India
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Ahmed W, Li R, Xia Y, Bai G, Siddique KHM, Zhang H, Zheng Y, Yang X, Guo P. Comparative Analysis of miRNA Expression Profiles Between Heat-Tolerant and Heat-Sensitive Genotypes of Flowering Chinese Cabbage Under Heat Stress Using High-Throughput Sequencing. Genes (Basel) 2020; 11:E264. [PMID: 32121287 PMCID: PMC7140848 DOI: 10.3390/genes11030264] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/19/2020] [Accepted: 02/19/2020] [Indexed: 12/19/2022] Open
Abstract
Heat stress disturbs cellular homeostasis, thus usually impairs yield of flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee). MicroRNAs (miRNAs) play a significant role in plant responses to different stresses by modulating gene expression at the post-transcriptional level. However, the roles that miRNAs and their target genes may play in heat tolerance of flowering Chinese cabbage remain poorly characterized. The current study sequenced six small RNA libraries generated from leaf tissues of flowering Chinese cabbage collected at 0, 6, and 12 h after 38 °C heat treatment, and identified 49 putative novel miRNAs and 43 known miRNAs that differentially expressed between heat-tolerant and heat-sensitive flowering Chinese cabbage. Among them, 14 novel and nine known miRNAs differentially expressed only in the heat-tolerant genotype under heat-stress, therefore, their target genes including disease resistance protein TAO1-like, RPS6, reticuline oxidase-like protein, etc. might play important roles in enhancing heat-tolerance. Gene Ontology (GO) analysis revealed that targets of these differentially expressed miRNAs may play key roles in responses to temperature stimulus, cell part, cellular process, cell, membrane, biological regulation, binding, and catalytic activities. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified their important functions in signal transduction, environmental adaptation, global and overview maps, as well as in stress adaptation and in MAPK signaling pathways such as cell death. These findings provide insight into the functions of the miRNAs in heat stress tolerance of flowering Chinese cabbage.
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Affiliation(s)
- Waqas Ahmed
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Ronghua Li
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Yanshi Xia
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Guihua Bai
- United States Department of Agriculture - Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas 66506, United States of America
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture & Environment, The University of Western Australia, LB 5005, Perth WA 6001, Australia
| | - Hua Zhang
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510308, China
| | - Yansong Zheng
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510308, China
| | - Xinquan Yang
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Peiguo Guo
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou 510006, China
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The green peach aphid gut contains host plant microRNAs identified by comprehensive annotation of Brassica oleracea small RNA data. Sci Rep 2019; 9:18904. [PMID: 31827121 PMCID: PMC6906386 DOI: 10.1038/s41598-019-54488-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/05/2019] [Indexed: 12/28/2022] Open
Abstract
Like all organisms, aphids, plant sap-sucking insects that house a bacterial endosymbiont called Buchnera, are members of a species interaction network. Ecological interactions across such networks can result in phenotypic change in network members mediated by molecular signals, like microRNAs. Here, we interrogated small RNA data from the aphid, Myzus persicae, to determine the source of reads that did not map to the aphid or Buchnera genomes. Our analysis revealed that the pattern was largely explained by reads that mapped to the host plant, Brassica oleracea, and a facultative symbiont, Regiella. To start elucidating the function of plant small RNA in aphid gut, we annotated 213 unique B. oleracea miRNAs; 32/213 were present in aphid gut as mature and star miRNAs. Next, we predicted targets in the B. oleracea and M. persicae genomes for these 32 plant miRNAs. We found that plant targets were enriched for genes associated with transcription, while the distribution of targets in the aphid genome was similar to the functional distribution of all genes in the aphid genome. We discuss the potential of plant miRNAs to regulate aphid gene expression and the mechanisms involved in processing, export and uptake of plant miRNAs by aphids.
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Li J, Lei L, Ye F, Zhou Y, Chang H, Zhao G. Nutritive implications of dietary microRNAs: facts, controversies, and perspectives. Food Funct 2019; 10:3044-3056. [PMID: 31066412 DOI: 10.1039/c9fo00216b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As a group of non-coding RNA molecules, microRNAs have recently become more well-known due to their pivotal role in gene regulation. A large number of endogenous microRNAs naturally occur in the human body, and some of them act as regulatory targets of diet and its components. The wide presence of microRNAs in various food materials has inspired food scientists and nutritionists to explore their nutritive and bioactive significance. This article comprehensively reports updated insights into the accessibility, stability, absorbability, and bioactivity of dietary microRNAs by combining the current knowledge into figures and tables for reader's convenience. As one frontier in food science and nutrition, the research platform on dietary microRNAs is imperfect and even defective as indicated by the inconsistent and even contradictory results concluded by different investigations. The pros and cons as well as the limitations of current investigations have been critically discussed with attention chiefly paid to experimental designs and protocols. Moreover, future research directions have been recommended. Thus, this paper may not only provide a quick glance at the state-of-the-art of dietary microRNAs but also guide further research to clarify the present controversies and make the results more credible and persuasive.
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Affiliation(s)
- Jianting Li
- College of Food Science, Southwest University, Chongqing 400715, People's Republic of China.
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11
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Ahmed W, Xia Y, Zhang H, Li R, Bai G, Siddique KHM, Guo P. Identification of conserved and novel miRNAs responsive to heat stress in flowering Chinese cabbage using high-throughput sequencing. Sci Rep 2019; 9:14922. [PMID: 31624298 PMCID: PMC6797766 DOI: 10.1038/s41598-019-51443-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 10/01/2019] [Indexed: 12/12/2022] Open
Abstract
Plant microRNAs (miRNAs) are noncoding and endogenous key regulators that play significant functions in regulating plant responses to stress, and plant growth and development. Heat stress is a critical abiotic stress that reduces the yield and quality of flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee). However, limited information is available on whether miRNAs are involved in the regulation of heat stress in B. campestris. A high-throughput sequencing approach was used to identify novel and conserved heat-responsive miRNAs in four small RNA libraries of flowering Chinese cabbage using leaves collected at 0 h, 1 h, 6 h and 12 h after a 38 °C heat-stress treatment. The analysis identified 41 conserved miRNAs (belonging to 19 MIR families), of which MIR156, MIR159, MIR168, MIR171 and MIR1885 had the most abundant molecules. Prediction and evaluation of novel miRNAs using the unannotated reads resulted in 18 candidate miRNAs. Differential expression analysis showed that most of the identified miRNAs were downregulated in heat-treated groups. To better understand functional importance, bioinformatic analysis predicted 432 unique putative target miRNAs involved in cells, cell parts, catalytic activity, cellular processes and abiotic stress responses. Furthermore, the Kyoto Encyclopedia of Genes and Genomes maps of flowering Chinese cabbage identified the significant role of miRNAs in stress adaptation and stress tolerance, and in several mitogen-activated protein kinases signaling pathways including cell death. This work presents a comprehensive study of the miRNAs for understanding the regulatory mechanisms and their participation in the heat stress of flowering Chinese cabbage.
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Affiliation(s)
- Waqas Ahmed
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Yanshi Xia
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Hua Zhang
- Guangzhou Academy of Agricultural Sciences, Guangzhou, 510308, China
| | - Ronghua Li
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Guihua Bai
- United States Department of Agriculture - Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas, 66506, United States of America
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture & Environment, The University of Western Australia, LB 5005, Perth, WA, 6001, Australia
| | - Peiguo Guo
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, 510006, China.
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12
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Ahmed W, Xia Y, Li R, Bai G, Siddique KHM, Guo P. Non-coding RNAs: Functional roles in the regulation of stress response in Brassica crops. Genomics 2019; 112:1419-1424. [PMID: 31430515 DOI: 10.1016/j.ygeno.2019.08.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 07/03/2019] [Accepted: 08/16/2019] [Indexed: 12/22/2022]
Abstract
Brassica crops face a combination of different abiotic and biotic stresses in the field that can reduce plant growth and development by affecting biochemical and morpho-physiological processes. Emerging evidence suggests that non-coding RNAs (ncRNAs), especially microRNAs (miRNAs) and long ncRNAs (lncRNAs), play a significant role in the modulation of gene expression in response to plant stresses. Recent advances in computational and experimental approaches are of great interest for identifying and functionally characterizing ncRNAs. While progress in this field is limited, numerous ncRNAs involved in the regulation of gene expression in response to stress have been reported in Brassica. In this review, we summarize the modes of action and functions of stress-related miRNAs and lncRNAs in Brassica as well as the approaches used to identify ncRNAs.
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Affiliation(s)
- Waqas Ahmed
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Yanshi Xia
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Ronghua Li
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Guihua Bai
- United States Department of Agriculture - Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas 66506, United States
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture & Environment, The University of Western Australia, LB 5005, Perth, WA 6001, Australia
| | - Peiguo Guo
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China.
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13
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Dudink E, Florijn B, Weijs B, Duijs J, Luermans J, Peeters F, Schurgers L, Wildberger J, Schotten U, Bijkerk R, Crijns HJ, van Zonneveld AJ. Vascular Calcification and not Arrhythmia in Idiopathic Atrial Fibrillation Associates with Sex Differences in Diabetic Microvascular Injury miRNA Profiles. Microrna 2019; 8:127-134. [PMID: 30465521 DOI: 10.2174/2211536608666181122125208] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/17/2018] [Accepted: 11/16/2018] [Indexed: 01/09/2023]
Abstract
BACKGROUND Atrial Fibrillation (AF) in patients without concomitant cardiovascular pathophysiological disease, is called idiopathic Atrial Fibrillation (iAF). Nonetheless, iAF patients have often times subclinical coronary (micro) vascular dysfunction and, particularly in women, a higher prevalence of subsequent cardiovascular comorbidities. Previously, we identified a plasma miRNA association with diabetes and microvascular injury in Diabetic Nephropathy (DN) patients. Therefore, in this study we assessed whether plasma levels of these diabetic, microvascular injury associated miRNAs reflect microvascular integrity in iAF patients, associated with the presence of paroxysmal arrhythmia or instead are determined by concealed coronary artery disease. METHODS Circulating levels of a pre-selected set of diabetic, (micro) vascular injury associated miRNAs, were measured in 59 iAF patients compared to 176 Sinus Rhythm (SR) controls. Furthermore, the presence of coronary artery and aortic calcification in each patient was assessed using Cardiac Computed Tomography Angiography (CCTA). RESULTS Paroxysmal arrhythmia in iAF patients did not result in significant miRNA expression profile differences in iAF patients compared to SR controls. Nonetheless, coronary artery calcification (CAC) was associated with higher levels of miRNAs-103, -125a-5p, -221 and -223 in men. In women, CAC was associated with higher plasma levels of miRNA-27a and miRNA-126 and correlated with Agatston scores. Within the total population, ascending Aortic Calcification (AsAC) patients displayed increased plasma levels of miRNA-221, while women, in particular, demonstrated a Descending Aorta Calcification (DAC) associated increase in miRNA-212 levels. CONCLUSIONS Diabetic microvascular injury associated miRNAs in iAF are associated with subclinical coronary artery disease in a sex-specific way and confirm the notion that biological sex identifies iAF subgroups that may require dedicated clinical care.
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Affiliation(s)
- Elton Dudink
- Department of Cardiology, Maastricht University Medical Center and Cardiovascular Research Institute Maastricht, P. Debyelaan 25, 6229 HX, Maastricht, Netherlands
| | - Barend Florijn
- Department of Internal Medicine (Nephrology), Leiden University Medical Center and Einthoven Laboratory for Vascular and Regenerative Medicine, Albinusdreef 2, 2333 ZA, Leiden, Netherlands
| | - Bob Weijs
- Department of Cardiology, Maastricht University Medical Center and Cardiovascular Research Institute Maastricht, P. Debyelaan 25, 6229 HX, Maastricht, Netherlands
| | - Jacques Duijs
- Department of Internal Medicine (Nephrology), Leiden University Medical Center and Einthoven Laboratory for Vascular and Regenerative Medicine, Albinusdreef 2, 2333 ZA, Leiden, Netherlands
| | - Justin Luermans
- Department of Cardiology, Maastricht University Medical Center and Cardiovascular Research Institute Maastricht, P. Debyelaan 25, 6229 HX, Maastricht, Netherlands
| | - Frederique Peeters
- Department of Cardiology, Maastricht University Medical Center and Cardiovascular Research Institute Maastricht, P. Debyelaan 25, 6229 HX, Maastricht, Netherlands
| | - Leon Schurgers
- Department of Biochemistry,Maastricht University and Cardiovascular Research Institute Maastricht, Universiteitssingel 50, 6229 ER, Maastricht, Netherlands
| | - Joachim Wildberger
- Department of Radiology and Nuclear Medicine, Maastricht University Medical Center and Cardiovascular Research Institute Maastricht, P. Debyelaan 25, 6229 HX, Maastricht, Netherlands
| | - Ulrich Schotten
- Department of Physiology, Maastricht University and Cardiovascular Research Institute Maastricht, Universiteitssingel 50, 6229 ER, Maastricht, Netherlands
| | - Roel Bijkerk
- Department of Internal Medicine (Nephrology), Leiden University Medical Center and Einthoven Laboratory for Vascular and Regenerative Medicine, Albinusdreef 2, 2333 ZA, Leiden, Netherlands
| | - Harry J Crijns
- Department of Cardiology, Maastricht University Medical Center and Cardiovascular Research Institute Maastricht, P. Debyelaan 25, 6229 HX, Maastricht, Netherlands
| | - Anton Jan van Zonneveld
- Department of Internal Medicine (Nephrology), Leiden University Medical Center and Einthoven Laboratory for Vascular and Regenerative Medicine, Albinusdreef 2, 2333 ZA, Leiden, Netherlands
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14
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Liu X, Chen M, Zhou X, Cao Z. Identification of novel miRNAs and their target genes from Populus szechuanica infected with Melampsora larici-populina. Mol Biol Rep 2019; 46:3083-3092. [PMID: 30859446 DOI: 10.1007/s11033-019-04746-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/05/2019] [Indexed: 01/21/2023]
Abstract
Two novel miRNAs were selected from a pre-constructed RNA library of Populus szechuanica infected with the foliar rust fungus Melampsora larici-populina in order to detect the genes regulated as targets of the miRNAs novel_mir_11 and novel_mir_357. The novel miRNAs were identified from P. szechuanica using stem-loop methods and their precursors were able to fold into a complete stem loop structure. The predicted target genes of the novel miRNAs were verified with RNA ligase-mediated 5' rapid amplification of cDNA ends (RLM-5'RACE). The full-length sequences of target genes, RPM1 and RPS2/5, in P. szechuanica were obtained through rapid amplification of cDNA ends (RACE) and officially named PsRPM1 and PsRPS2/5. These genes contain nucleotide binding site-leucine-rich repeats (NBS-LRR) domains typical of resistance genes. The expression levels of miRNAs and their target genes in different periods post infection were analysed with quantitative real-time PCR (qRT-PCR). After infection with the foliar rust fungus, the expression levels of the novel miRNAs and their target genes were dynamic. Both novel_mir_11 and novel_mir_357 negatively regulated the expression of their target genes. In this study, the regulatory effects of two novel miRNAs through their target genes were characterized to provide further mechanistic information regarding the interaction between Populus and a foliar rust fungus. Results of this study improve our understanding of the defence response mechanisms of Populus and will stimulate future work to characterize strategies to prevent and control Populus diseases.
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Affiliation(s)
- Xin Liu
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Min Chen
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xue Zhou
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhimin Cao
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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15
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Wu J, Liu C, Liu Z, Li S, Li D, Liu S, Huang X, Liu S, Yukawa Y. Pol III-Dependent Cabbage BoNR8 Long ncRNA Affects Seed Germination and Growth in Arabidopsis. PLANT & CELL PHYSIOLOGY 2019; 60:421-435. [PMID: 30462304 DOI: 10.1093/pcp/pcy220] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 11/02/2018] [Indexed: 05/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) are non-protein-coding transcripts longer than 200 nt that are distributed widely in organisms and play many physiological roles. The BoNR8 lncRNA is a 272 nt long transcript yielded by RNA polymerase III in cabbage that was identified as the closest homolog of the AtR8 lncRNA in Arabidopsis. The BoNR8 lncRNA was expressed extensively in the epidermal tissue in the root elongation zone of germinated seeds, and its accumulation was induced by abiotic stresses, auxins and ABA. To investigate the correlation between the BoNR8 lncRNA and germination, BoNR8-overexpressing Arabidopsis plants (BoNR8-AtOX) were prepared. Three independent BoNR8-AtOX lines showed less primary root elongation, incomplete silique development and decreased germination rates. The germination efficiencies were affected strongly by ABA and slightly by salt stress, and ABA-related gene expression was changed in the BoNR8-AtOX lines.
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Affiliation(s)
- Juan Wu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry of Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, PR, Harbin, China
| | - Chunxiao Liu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
| | - Ziguang Liu
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry of Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, PR, Harbin, China
| | - Shuang Li
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan
| | - Dandan Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
| | - Shengyi Liu
- Mudanjiang Medical University, Mudanjiang, Heilongjiang, China
| | - Xiaoqing Huang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
| | - ShenKui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A and F University, Lin'an, Hangzhou, China
| | - Yasushi Yukawa
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan
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16
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Leijten W, Koes R, Roobeek I, Frugis G. Translating Flowering Time From Arabidopsis thaliana to Brassicaceae and Asteraceae Crop Species. PLANTS 2018; 7:plants7040111. [PMID: 30558374 PMCID: PMC6313873 DOI: 10.3390/plants7040111] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/07/2018] [Accepted: 12/13/2018] [Indexed: 12/31/2022]
Abstract
Flowering and seed set are essential for plant species to survive, hence plants need to adapt to highly variable environments to flower in the most favorable conditions. Endogenous cues such as plant age and hormones coordinate with the environmental cues like temperature and day length to determine optimal time for the transition from vegetative to reproductive growth. In a breeding context, controlling flowering time would help to speed up the production of new hybrids and produce high yield throughout the year. The flowering time genetic network is extensively studied in the plant model species Arabidopsis thaliana, however this knowledge is still limited in most crops. This article reviews evidence of conservation and divergence of flowering time regulation in A. thaliana with its related crop species in the Brassicaceae and with more distant vegetable crops within the Asteraceae family. Despite the overall conservation of most flowering time pathways in these families, many genes controlling this trait remain elusive, and the function of most Arabidopsis homologs in these crops are yet to be determined. However, the knowledge gathered so far in both model and crop species can be already exploited in vegetable crop breeding for flowering time control.
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Affiliation(s)
- Willeke Leijten
- ENZA Zaden Research & Development B.V., Haling 1E, 1602 DB Enkhuizen, The Netherlands.
| | - Ronald Koes
- Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | - Ilja Roobeek
- ENZA Zaden Research & Development B.V., Haling 1E, 1602 DB Enkhuizen, The Netherlands.
| | - Giovanna Frugis
- Istituto di Biologia e Biotecnologia Agraria (IBBA), Operative Unit of Rome, Consiglio Nazionale delle Ricerche (CNR), Via Salaria Km. 29,300 ⁻ 00015, Monterotondo Scalo, Roma, Italy.
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17
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Megha S, Basu U, Joshi RK, Kav NNV. Physiological studies and genome-wide microRNA profiling of cold-stressed Brassica napus. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 132:1-17. [PMID: 30170322 DOI: 10.1016/j.plaphy.2018.08.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/26/2018] [Accepted: 08/21/2018] [Indexed: 05/27/2023]
Abstract
Temperature extremes, including cold, adversely impact plant growth and development. Plant responses to cold stress (CS) are regulated at both transcriptional and post-transcriptional levels. MicroRNAs (miRNAs), small non-coding RNAs, are known to be involved in post-transcriptional regulation of various developmental processes and metal stress in Brassica napus L. (canola), however, their role in response to CS is largely unknown. In this study, changes in various physiological parameters and endogenous abundance of miRNAs were characterized in spring canola seedlings (DH12075) exposed to 4 °C for 0-48 h. Cold stress induced electrolyte leakage, increased the levels of malondialdheyde and antioxidant enzymes and reduced photosynthetic efficiency. Using small RNA sequencing, 70 known and 126 novel miRNAs were identified in CS leaf tissues and among these, 25 known and 104 novel miRNAs were differentially expressed. Quantitative real-time (qRT) PCR analysis of eight selected miRNAs confirmed their CS responsiveness. Furthermore, the expression of six out of eight miRNAs exhibited an opposite trend in a winter variety of canola, 'Mendel', when compared to 'DH12075'. This first study on the B. napus miRNAome provides a framework for further functional analysis of these miRNAs and their targets in response to CS which may contribute towards the future development of cold resilient crops.
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Affiliation(s)
- Swati Megha
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Urmila Basu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Raj Kumar Joshi
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Nat N V Kav
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
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18
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Marakli S. Identification and functional analyses of new sesame miRNAs (Sesamum indicum L.) and their targets. Mol Biol Rep 2018; 45:2145-2155. [PMID: 30209739 DOI: 10.1007/s11033-018-4373-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/06/2018] [Indexed: 12/20/2022]
Abstract
Plant microRNAs (miRNAs) have been commonly investigated during many years. Hundreds of miRNAs have been identified in many different plant species but there is very little information about the function of sesame (Sesamum indicum L.) miRNAs. For this purpose, in silico prediction of novel sesame miRNAs based on BLAST searches of the expressed sequence tag database was performed, using stringent criterias for miRNA annotation. The secondary structures of their precursor sequences, potential target genes of conserved and novel miRNAs were predicted and subjected to Gene Ontology (GO) annotation. mir447 and mir8140 were reported for the first time in sesame. Enrichment analysis of the GO with biological processes, cellular component and molecular functions revealed that these target genes were potentially involved in different metabolic pathways such as transcription factors, metabolism, growth and development, stress-related and even plant hormones. Results are valuable for figure out the gene regulation mechanism in sesame, using in the medicinal aspect of this plant species. Furthermore, these miRNAs and their profiled targets could provide the improvement of regulation and management, and even development of desirable traits in this plant.
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Affiliation(s)
- Sevgi Marakli
- Faculty of Arts and Sciences, Department of Biology, Amasya University, Ipekkoy, 05100, Amasya, Turkey.
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19
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Han J, Chu Q, Huo R, Xu T. Inducible microRNA-122 modulates RIG-I signaling pathway via targeting DAK in miiuy croaker after poly(I:C) stimulation. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 78:52-60. [PMID: 28923593 DOI: 10.1016/j.dci.2017.09.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 06/07/2023]
Abstract
MicroRNA-122 (miR-122) was originally identified in mouse and then lots of researches on miR-122 had been performed in mammals. However, the functional study of miR-122 were restricted in fish. In miiuy croaker, miR-122 is sensitive to poly(I:C) stimulation. In this study, a combination of bioinformatics and experimental techniques were used to investigate the functions of miR-122. DAK is a putative target gene of miR-122 which was predicted by bioinformatics, and further the luciferase reporter assays were used to confirm the target sites in DAK 3'untranslated region. The inhibiting effect of miR-122 mimics or pre-miR-122 on DAK presented the dose and time dependent manners, and the pre-miR-122 showed stronger inhibiting effect on DAK than the miR-122 mimics. Therefore, the miR-122 participate in regulating RIG-I-like receptors signaling pathway via inhibiting DAK which is the inhibitors of MDA5. The expression of miR-122 and DAK showed negative relationship in both miiuy croaker spleen and macrophages, which imply that miR-122 may regulate DAK at the post-transcriptional level. These results will enhance our understanding about the regulation of miRNAs on immune response in fish.
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Affiliation(s)
- Jingjing Han
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Qing Chu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Ruixuan Huo
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Tianjun Xu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China.
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20
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Otsuka K, Yamamoto Y, Matsuoka R, Ochiya T. Maintaining good miRNAs in the body keeps the doctor away?: Perspectives on the relationship between food-derived natural products and microRNAs in relation to exosomes/extracellular vesicles. Mol Nutr Food Res 2017; 62. [PMID: 28594130 DOI: 10.1002/mnfr.201700080] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 05/24/2017] [Accepted: 05/26/2017] [Indexed: 12/21/2022]
Abstract
During the last decade, it has been uncovered that microRNAs (miRNAs), a class of small non-coding RNAs, are related to many diseases including cancers. With an increase in reports describing the dysregulation of miRNAs in various tumor types, it has become abundantly clear that miRNAs play significant roles in the formation and progression of cancers. Intriguingly, miRNAs are present in body fluids because they are packed in exosomes/extracellular vesicles and released from all types of cells. The miRNAs in the fluids are measured in a relatively simple way and the profile of miRNAs is likely to be an indicator of health condition. In recent years, various studies have demonstrated that some naturally occurring compounds can control tumor-suppressive and oncogenic miRNAs in a positive manner, suggesting that food-derived compounds could maintain the expression levels of miRNAs and help maintain good health. Therefore, our daily food and compounds in food are of great interest. In addition, exogenous diet-derived miRNAs have been indicated to function in the regulation of target mammalian transcripts in the body. These findings highlight the possibility of diet for good health through the regulation of miRNAs, and we also discuss the perspective of food application and health promotion.
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Affiliation(s)
- Kurataka Otsuka
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan.,R&D Division, Kewpie Corporation Sengawa Kewport, Tokyo, Japan
| | - Yusuke Yamamoto
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | | | - Takahiro Ochiya
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
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21
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Gul Z, Barozai MYK, Din M. In-silico based identification and functional analyses of miRNAs and their targets in Cowpea ( Vigna unguiculata L.). AIMS GENETICS 2017; 4:138-165. [PMID: 31435506 PMCID: PMC6690248 DOI: 10.3934/genet.2017.2.138] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 06/15/2017] [Indexed: 11/18/2022]
Abstract
Cowpea (Vigna unguiculata L.) is an important leguminous plant and a good diet due to presence of carbohydrate and high protein contents. Currently, only few cowpea microRNAs (miRNAs) are reported. This study is intended to identify and functionally analyze new miRNAs and their targets in cowpea. An in-silico based homology search approach was applied and a total of 46 new miRNAs belonging to 45 families were identified and functionally annotated from the cowpea expressed sequence tags (ESTs). All these potential miRNAs are reported here for the first time in cowpea. The 46 new miRNAs were also observed with stable hairpin structures with minimum free energy, ranging from -10 to -132 kcal mol-1 with an average of -40 kcal mol-1. The length of new cowpea miRNAs are ranged from 18 to 26 nt with an average of 21 nt. The cowpea miRNA-vun-mir4414, is found as pre-miRNA cluster for the first time in cowpea. Furthermore, a set of 138 protein targets were also identified for these newly identified 46 cowpea miRNAs. These targets have significant role in various biological processes, like metabolism, transcription regulation as transcription factor, cell transport, signal transduction, growth & development and structural proteins. These findings are the significant basis to utilize and manage this important leguminous plant-cowpea for better nutritional properties and tolerance for biotic and abiotic stresses.
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Affiliation(s)
- Zareen Gul
- Department of Botany, University of Balochistan, Sariab Road, Quetta, Pakistan
| | | | - Muhammad Din
- Department of Botany, University of Balochistan, Sariab Road, Quetta, Pakistan
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22
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Baghban Kohnehrouz B, Bastami M, Nayeri S. In Silico Identification of Novel microRNAs and Targets Using EST Analysis in Allium cepa L. Interdiscip Sci 2017; 10:771-780. [PMID: 28660536 DOI: 10.1007/s12539-017-0240-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 05/16/2017] [Accepted: 05/22/2017] [Indexed: 12/26/2022]
Abstract
microRNAs (miRNAs) are a newly discovered class of non-coding small RNAs roughly 22 nucleotides long. Increasing evidence has shown that miRNAs play multiple roles in biological processes, including development, cell proliferation, apoptosis and stress responses. The identification of miRNAs and their targets is an important need to understand their roles in the development and physiology of sweet onion (Allium cepa). In this research, several computational approaches were combined to make concise prediction of the potential miRNAs and their targets. We used previously known miRNAs from other plant species against Expressed Sequence Tags (EST) database to search for the potential miRNAs. As a result, nine potential miRNAs were identified in eight ESTs of A. cepa, belonging to eight families. We could further BLAST the mRNA database and found total 154 number of the potential targets in A. cepa based on these potential miRNAs. According to the mRNA target information provided by NCBI, most of the target mRNAs appeared to be involved in plant growth, signal transduction, development, and stress responses. Gene ontology (GO) analysis implicated these targets in 32 biological processes such as protein ubiquitination, plant hormone signalling pathways and heme biosynthesis.
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Affiliation(s)
| | - Meysam Bastami
- Department of Agricultural Biotechnology, Faculty of Engineering, Imam Khomeini International University, 34149, Qazvin, Iran
| | - Shahnoush Nayeri
- Department of Biotechnology, Faculty of New Technologies and Energy Engineering, Shahid Beheshti University, 19839, Tehran, Iran
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23
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Ma Z, Jiang J, Hu Z, Lyu T, Yang Y, Jiang J, Cao J. Over-expression of miR158 causes pollen abortion in Brassica campestris ssp. chinensis. PLANT MOLECULAR BIOLOGY 2017; 93:313-326. [PMID: 27909970 DOI: 10.1007/s11103-016-0563-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 11/12/2016] [Indexed: 06/06/2023]
Abstract
We identified and cloned the two precursors of miR158 and its target gene in Brassica campestris ssp. chinensis, which both had high relative expression in the inflorescences. Further study revealed that over-expression of miR158 caused reduced pollen varbility, which was caused by the degradation of pollen contents from the binucleate microspore stage. These results first suggest the role of miR158 in pollen development of Brassica campestris ssp. chinensis. MicroRNAs (miRNAs) play crucial roles in many important growth and development processes both in plants and animals by regulating the expression of their target genes via mRNA cleavage or translational repression. In this study, miR158, a Brassicaceae specific miRNA, was functionally characterized with regard to its role in pollen development of non-heading Chinese cabbage (Brassica campestris ssp. chinensis). Two family members of miR158 in B. campestris, namely bra-miR158a1 and bra-miR158a2, and their target gene bra027656, which encodes a pentatricopeptide repeat (PPR) containing protein, were identified. Then, qRT-PCR analysis and GUS-reporter system revealed that both bra-miR158 and its target gene had relatively high expression levels in the inflorescences. Further study revealed that over-expression of miR158 caused reduced pollen varbility and pollen germination ratio, and the degradation of pollen contents from the binucleate microspore stage was also found in those deformed pollen grains, which led to pollen shrinking and collapse in later pollen development stage. These results first shed light on the importance of miR158 in pollen development of Brassica campestris ssp. chinensis.
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Affiliation(s)
- Zhiming Ma
- Lab of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
| | - Jianxia Jiang
- Lab of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
| | - Ziwei Hu
- Lab of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
| | - Tianqi Lyu
- Lab of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
| | - Yang Yang
- Lab of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
| | - Jingjing Jiang
- State Key Lab of Agrobiotechnology, Shenzhen Base, Shenzhen Research Institute, Chinese University of Hong Kong, Shenzhen, 518057, China
| | - Jiashu Cao
- Lab of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China.
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Din M, Barozai MYK, Baloch IA. Profiling and annotation of microRNAs and their putative target genes in chilli ( Capsicum annuum L.) using ESTs. GENE REPORTS 2016. [DOI: 10.1016/j.genrep.2016.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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25
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Wang L, Du H, Wuyun TN. Genome-Wide Identification of MicroRNAs and Their Targets in the Leaves and Fruits of Eucommia ulmoides Using High-Throughput Sequencing. FRONTIERS IN PLANT SCIENCE 2016; 7:1632. [PMID: 27877179 PMCID: PMC5099690 DOI: 10.3389/fpls.2016.01632] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/17/2016] [Indexed: 05/03/2023]
Abstract
MicroRNAs (miRNAs), a group of endogenous small non-coding RNAs, play important roles in plant growth, development, and stress response processes. Eucommia ulmoides Oliver (hardy rubber tree) is one of the few woody plants capable of producing trans-1, 4-polyisoprene (TPI), also known as Eu-rubber, which has been utilized as an industrial raw material and is extensively cultivated in China. However, the mechanism of TPI biosynthesis has not been identified in E. ulmoides. To characterize small RNAs and their targets with potential biological roles involved in the TPI biosynthesis in E. ulmoides, in the present study, eight small RNA libraries were constructed and sequenced from young and mature leaves and fruits of E. ulmoides. Further analysis identified 34 conserved miRNAs belonging to 20 families (two unclassified families), and 115 novel miRNAs seemed to be specific to E. ulmoides. Among these miRNAs, fourteen conserved miRNAs and 49 novel miRNAs were significantly differentially expressed and identified as Eu-rubber accumulation related miRNAs. Based on the E. ulmoides genomic data, 202 and 306 potential target genes were predicted for 33 conserved and 92 novel miRNAs, respectively; the predicted targets are mostly transcription factors and functional genes, which were enriched in metabolic pathways and biosynthesis of secondary metabolites. Noticeably, based on the expression patterns of miRNAs and their target genes in combination with the Eu-rubber accumulation, the negative correlation of expression of six miRNAs (Eu-miR14, Eu-miR91, miR162a, miR166a, miR172c, and miR396a) and their predicted targets serving as potential regulators in Eu-rubber accumulation. This study is the first to detect conserved and novel miRNAs and their potential targets in E. ulmoides and identify several candidate genes potentially controlling rubber accumulation, and thus provide molecular evidence for understanding the roles of miRNAs in regulating the TPI biosynthesis in E. ulmoides.
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Affiliation(s)
- Lin Wang
- Non-timber Forest Research and Development Center, Chinese Academy of ForestryZhengzhou, China
- The Eucommia Engineering Research Center of State Forestry AdministrationZhengzhou, China
| | - Hongyan Du
- Non-timber Forest Research and Development Center, Chinese Academy of ForestryZhengzhou, China
- The Eucommia Engineering Research Center of State Forestry AdministrationZhengzhou, China
| | - Ta-na Wuyun
- Non-timber Forest Research and Development Center, Chinese Academy of ForestryZhengzhou, China
- The Eucommia Engineering Research Center of State Forestry AdministrationZhengzhou, China
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26
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Han J, Xu G, Xu T. The miiuy croaker microRNA transcriptome and microRNA regulation of RIG-I like receptor signaling pathway after poly(I:C) stimulation. FISH & SHELLFISH IMMUNOLOGY 2016; 54:419-426. [PMID: 27131903 DOI: 10.1016/j.fsi.2016.04.126] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/18/2016] [Accepted: 04/26/2016] [Indexed: 06/05/2023]
Abstract
MicroRNAs (miRNAs) as endogenous small non-coding RNAs play key regulatory roles in diverse biological processes via degrading the target mRNAs or inhibiting protein translation. Previously many researchers have reported the identification, characteristic of miRNAs and the interaction with its target gene. But, the study on the regulation of miRNAs to biological processes via regulatory the key signaling pathway was still limited. In order to comprehend the regulatory mechanism of miRNAs, two small RNA libraries from the spleen of miiuy croaker individuals with or without poly(I:C) infection were constructed. The 197 conserved miRNAs and 75 novel miRNAs were identified, and 14 conserved and 8 novel miRNAs appeared significant variations. Those differently expressed miRNAs relate to immune regulation of miiuy croaker. Furthermore, expressions of four differently expressed miRNAs were validated by qRT-PCR, and the result was consistent with sequencing data. The target genes of the differently expressed miRNAs in the two libraries were predicted, and some candidate target genes were involved in the RIG-I-like receptor (RLR) signaling pathway. The negative regulation of miRNAs to target genes were confirmed by comparing the expression pattern of miRNAs and their target genes. The results of regulating target genes were that firstly directly or indirectly activating the downstream signaling cascades and subsequent inducting the type I interferon, inflammatory cytokines and apoptosis. These studies could help us to deeper understand the roles of miRNAs played in the fish immune system, and provide a new way to investigate the defense mechanism of fish.
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Affiliation(s)
- Jingjing Han
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Guoliang Xu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Tianjun Xu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China.
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27
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Abstract
Foods provide fats, carbohydrates, and proteins as well as vitamins, minerals and trace elements. These dietary factors may influence cellular processes by regulating endogenous microRNA expression. MicroRNAs are non-coding regulatory molecules which affect gene expression at the post transcriptional level. It has been shown that plant and animal derived foods also contain microRNA. Yet, it is unclear if and to what extent plant and animal food derived microRNAs are absorbed by mammals. Thus, future studies need to better address absorption, tissue distribution and function of dietary plant and animal derived microRNAs in the context of human health and disease.
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Affiliation(s)
- Anika E Wagner
- Institute of Human Nutrition and Food Science, Christian-Albrechts-University, Hermann-Rodewald-Str. 6, 24118 Kiel, Germany.
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Rogans SJ, Rey C. Unveiling the Micronome of Cassava (Manihot esculenta Crantz). PLoS One 2016; 11:e0147251. [PMID: 26799216 PMCID: PMC4723133 DOI: 10.1371/journal.pone.0147251] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 01/03/2016] [Indexed: 12/03/2022] Open
Abstract
MicroRNAs (miRNAs) are an important class of endogenous non-coding single-stranded small RNAs (21-24 nt in length), which serve as post-transcriptional negative regulators of gene expression in plants. Despite the economic importance of Manihot esculenta Crantz (cassava) only 153 putative cassava miRNAs (from multiple germplasm) are available to date in miRBase (Version 21), and identification of a number of miRNAs from the cassava EST database have been limited to comparisons with Arabidopsis. In this study, mature sequences of all known plant miRNAs were used as a query for homologous searches against cassava EST and GSS databases, and additional identification of novel and conserved miRNAs were gleaned from next generation sequencing (NGS) of two cassava landraces (T200 from southern Africa and TME3 from West Africa) at three different stages post explant transplantation and acclimatization. EST and GSS derived data revealed 259 and 32 miRNAs in cassava, and one of the miRNA families (miR2118) from previous studies has not been reported in cassava. NGS data collectively displayed expression of 289 conserved miRNAs in leaf tissue, of which 230 had not been reported previously. Of the 289 conserved miRNAs identified in T200 and TME3, 208 were isomiRs. Thirty-nine novel cassava-specific miRNAs of low abundance, belonging to 29 families, were identified. Thirty-eight (98.6%) of the putative new miRNAs identified by NGS have not been previously reported in cassava. Several miRNA targets were identified in T200 and TME3, highlighting differential temporal miRNA expression between the two cassava landraces. This study contributes to the expanding knowledge base of the micronome of this important crop.
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Affiliation(s)
- Sarah Jane Rogans
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Chrissie Rey
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
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29
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Jian H, Wang J, Wang T, Wei L, Li J, Liu L. Identification of Rapeseed MicroRNAs Involved in Early Stage Seed Germination under Salt and Drought Stresses. FRONTIERS IN PLANT SCIENCE 2016; 7:658. [PMID: 27242859 PMCID: PMC4865509 DOI: 10.3389/fpls.2016.00658] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 04/29/2016] [Indexed: 05/18/2023]
Abstract
Drought and salinity are severe and wide-ranging abiotic stresses that substantially affect crop germination, development and productivity, and seed germination is the first critical step in plant growth and development. To comprehensively investigate small-RNA targets and improve our understanding of miRNA-mediated post-transcriptional regulation networks during Brassica napus seed imbibition under drought and salt stresses, we constructed three small-RNA libraries from B. napus variety ZS11 embryos exposed to salt (200 mM NaCl, denoted "S"), drought (200 g L(-1) PEG-6000, denoted "D"), and distilled water (denoted "CK") during imbibition and sequenced them using an Illumina Genome Analyzer. A total of 11,528,557, 12,080,081, and 12,315,608 raw reads were obtained from the CK, D, and S libraries, respectively. Further analysis identified 85 known miRNAs belonging to 31 miRNA families and 882 novel miRNAs among the three libraries. Comparison of the D and CK libraries revealed significant down-regulation of six miRNA families, miR156, miR169, miR860, miR399, miR171, and miR395, whereas only miR172 was significantly up-regulated. In contrast, comparison of the S library with the CK library showed significant down-regulation of only two miRNA families: miRNA393 and miRNA399. Putative targets for 336, 376, and 340 novel miRNAs were successfully predicted in the CK, D, and S libraries, respectively, and 271 miRNA families and 20 target gene families [including disease resistance protein (DIRP), drought-responsive family protein (DRRP), early responsive to dehydration stress protein (ERD), stress-responsive alpha-beta barrel domain protein (SRAP), and salt tolerance homolog2 (STH2)] were confirmed as being core miRNAs and genes involved in the seed imbibition response to salt and drought stresses. The sequencing results were partially validated by quantitative RT-PCR for both conserved and novel miRNAs as well as the predicted target genes. Our data suggest that diverse and complex miRNAs are involved in seed imbibition, indicating that miRNAs are involved in plant hormone regulation, and may play important roles during seed germination under salt- or drought-stress conditions.
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Wei R, Qiu D, Wilson IW, Zhao H, Lu S, Miao J, Feng S, Bai L, Wu Q, Tu D, Ma X, Tang Q. Identification of novel and conserved microRNAs in Panax notoginseng roots by high-throughput sequencing. BMC Genomics 2015; 16:835. [PMID: 26490136 PMCID: PMC4618736 DOI: 10.1186/s12864-015-2010-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 10/03/2015] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are small, non-coding RNAs that are important regulators of gene expression, and play major roles in plant development and their response to the environment. Root extracts from Panax notoginseng contain triterpene saponins as their principal bioactive constituent, and demonstrate medicinal properties. To investigate the novel and conserved miRNAs in P. notoginseng, three small RNA libraries constructed from 1-, 2-, and 3-year-old roots in which root saponin levels vary underwent high-throughput sequencing. METHODS P. notoginseng roots, purified from 1-, 2-, and 3-year-old roots, were extracted for RNA, respectively. Three small libraries were constructed and subjected to next generation sequencing. RESULTS Sequencing of the three libraries generated 67,217,124 clean reads from P. notoginseng roots. A total of 316 conserved miRNAs (belonging to 67 miRNA families and one unclassified family) and 52 novel miRNAs were identified. MIR156 and MIR166 were the largest miRNA families, while miR156i and miR156g showed the highest abundance of miRNA species. Potential miRNA target genes were predicted and annotated using Cluster of Orthologous Groups, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes. Comparing these miRNAs between root samples revealed 33 that were differentially expressed between 2- and 1-year-old roots (8 increased, 25 decreased), 27 differentially expressed between 3- and 1-year-old roots (7 increased, 20 decreased), and 29 differentially expressed between 3- and 2-year-old roots (8 increased, 21 decreased). Two significantly differentially expressed miRNAs and four miRNAs predicted to target genes involved in the terpenoid backbone biosynthesis pathway were selected and validated by quantitative reverse transcription PCR. Furthermore, the expression patterns of these six miRNAs were analyzed in P. notoginseng roots, stems, and leaves at different developmental stages. CONCLUSIONS This study identified a large number of P. notoginseng miRNAs and their target genes, functional annotations, and gene expression patterns. It provides the first known miRNA profiles of the P. notoginseng root development cycle.
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Affiliation(s)
- Rongchang Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China. .,Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China.
| | - Deyou Qiu
- Department of Molecular Biology, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Iain W Wilson
- CSIRO Agriculture, PO Box 1600, Canberra, ACT 2001, Australia.
| | - Huan Zhao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
| | - Jianhua Miao
- Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China.
| | - Shixin Feng
- Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China.
| | - Longhua Bai
- Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China.
| | - Qinghua Wu
- Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China.
| | - Dongping Tu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
| | - Xiaojun Ma
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
| | - Qi Tang
- Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China. .,Hunan Provincial Key Laboratory of Crop Germplasm innovation and Utilization and National Chinese Medicinal Herbs (Hunan) Technology Center, Hunan Agricultural University, Changsha, 410128, China.
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31
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Li J, Gao Y, Xu T. Comparative genomic and evolution of vertebrate NOD1 and NOD2 genes and their immune response in miiuy croaker. FISH & SHELLFISH IMMUNOLOGY 2015; 46:387-397. [PMID: 26108036 DOI: 10.1016/j.fsi.2015.06.026] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 06/16/2015] [Accepted: 06/19/2015] [Indexed: 06/04/2023]
Abstract
The nucleotide-binding oligomerization domain proteins NOD1 and NOD2 are important cytoplasmic pathogen recognition receptors which sense microbial infections molecules to induce innate immune response. In this study, the sequence analysis showed that NOD1 and NOD2 genes in miiuy croaker (miichthys miiuy, mmiNOD1 and mmiNOD2) share some highly conserved motifs that crucial for recognizing the bacterial and viral components. Quantitative expression analysis revealed mmiNOD1 and mmiNOD2 had the highest level of expression in liver. Induction experiments with Vibrio anguillarum indicated the different expression levels of mmiNOD1 and mmiNOD2 in liver, spleen and kidney. The expressions of mmiNOD1 and mmiNOD2 increased more significantly after Poly(I:C) stimulation, meanwhile, we carried out the expression analysis at the transcriptome level and the regulation of microRNAs. In addition, the evolutionary analysis showed that the ancestral lineages of NOD1 in bony fish detected one positively selected site, however, both the current lineages of NOD1 and NOD2 genes in bony fish underwent purifying selection indicating that NOD1 gene in the ancestor of bony fish experienced positive selection. To further understand the evolutionary pattern of NOD1 and NOD2 in vertebrates, we were the first to conduct comparative genomic analysis by comparing the number and synteny of NOD1 and NOD2. Combining the duplication of NOD1, the lost of NOD2 and the more conserved synteny of NOD2 than NOD1, we proposed that the hypothetical evolutionary pattern is different between NOD1 and NOD2.
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Affiliation(s)
- Jinrui Li
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan 316022, China
| | - Yunhang Gao
- College of Animal Science and Veterinary Medicine, Jilin Agriculture University, Changchun 130118, China
| | - Tianjun Xu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan 316022, China.
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32
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Pan L, Wang X, Jin J, Yu X, Hu J. Bioinformatic identification and expression analysis of Nelumbo nucifera microRNA and their targets. APPLICATIONS IN PLANT SCIENCES 2015; 3:apps.1500046. [PMID: 26421251 PMCID: PMC4578376 DOI: 10.3732/apps.1500046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 08/12/2015] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY Sacred lotus (Nelumbo nucifera) is a perennial aquatic herbaceous plant of ecological, ornamental, and economic importance. MicroRNAs (miRNAs) play an important role in plant development. However, reports of miRNAs and their role in sacred lotus have been limited. METHODS Using the homology search of known miRNAs with genome and transcriptome contig sequences, we employed a pipeline to identify miRNAs in N. nucifera. We also predicted the targets of these miRNAs. RESULTS We found 106 conserved miRNAs in N. nucifera, and 456 of their miRNA targets were annotated. Quantitative real-time PCR (qRT-PCR) analysis revealed the different expression levels of the 10 selected conserved miRNAs in tissues of young leaves, stems, and flowers of N. nucifera. Negative correlation of expression level between five miRNAs and their target genes was also revealed. DISCUSSION Combining bioinformatics and experiment analysis, we identified the miRNAs in N. nucifera. The results can be used as a workbench for further investigation of the roles of miRNAs in N. nucifera.
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Affiliation(s)
- Lei Pan
- Hubei Province Engineering Research Center of Legume Plants, School of Life Sciences, Jianghan University, Wuhan 430056, People’s Republic of China
| | - Xiaolei Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Jing Jin
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Xiaolu Yu
- Hubei Province Engineering Research Center of Legume Plants, School of Life Sciences, Jianghan University, Wuhan 430056, People’s Republic of China
| | - Jihong Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
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Nithin C, Patwa N, Thomas A, Bahadur RP, Basak J. Computational prediction of miRNAs and their targets in Phaseolus vulgaris using simple sequence repeat signatures. BMC PLANT BIOLOGY 2015; 15:140. [PMID: 26067253 PMCID: PMC4464996 DOI: 10.1186/s12870-015-0516-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/29/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are endogenous, noncoding, short RNAs directly involved in regulating gene expression at the post-transcriptional level. In spite of immense importance, limited information of P. vulgaris miRNAs and their expression patterns prompted us to identify new miRNAs in P. vulgaris by computational methods. Besides conventional approaches, we have used the simple sequence repeat (SSR) signatures as one of the prediction parameter. Moreover, for all other parameters including normalized Shannon entropy, normalized base pairing index and normalized base-pair distance, instead of taking a fixed cut-off value, we have used 99% probability range derived from the available data. RESULTS We have identified 208 mature miRNAs in P. vulgaris belonging to 118 families, of which 201 are novel. 97 of the predicted miRNAs in P. vulgaris were validated with the sequencing data obtained from the small RNA sequencing of P. vulgaris. Randomly selected predicted miRNAs were also validated using qRT-PCR. A total of 1305 target sequences were identified for 130 predicted miRNAs. Using 80% sequence identity cut-off, proteins coded by 563 targets were identified. The computational method developed in this study was also validated by predicting 229 miRNAs of A. thaliana and 462 miRNAs of G. max, of which 213 for A. thaliana and 397 for G. max are existing in miRBase 20. CONCLUSIONS There is no universal SSR that is conserved among all precursors of Viridiplantae, but conserved SSR exists within a miRNA family and is used as a signature in our prediction method. Prediction of known miRNAs of A. thaliana and G. max validates the accuracy of our method. Our findings will contribute to the present knowledge of miRNAs and their targets in P. vulgaris. This computational method can be applied to any species of Viridiplantae for the successful prediction of miRNAs and their targets.
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Affiliation(s)
- Chandran Nithin
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.
| | - Nisha Patwa
- Department of Biotechnology, Visva-Bharati, Santiniketan, 731235, India.
| | - Amal Thomas
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.
| | - Jolly Basak
- Department of Biotechnology, Visva-Bharati, Santiniketan, 731235, India.
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High-throughput sequence analysis of small RNAs in skotomorphogenic seedlings of Brassica rapa ssp. rapa. Gene 2014; 548:68-74. [PMID: 25016069 DOI: 10.1016/j.gene.2014.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 06/26/2014] [Accepted: 07/07/2014] [Indexed: 01/08/2023]
Abstract
Skotomorphogenic development is the process by which seedlings adapt to a stressful dark environment. Such metabolic responses to abiotic stresses in plants are known to be regulated in part by microRNAs (miRNAs); however, little is known about the involvement of miRNAs in the regulation of skotomorphogenesis. To identify miRNAs at the genome-wide level in skotomorphogenic seedlings of turnip (Brassica rapa subsp. rapa), an important worldwide root vegetable, we used Solexa sequencing to sequence a small RNA library from seedlings grown in the dark for 4 days. Deep sequencing showed that the small RNAs (sRNAs) were predominantly 21 to 24 nucleotides long. Specifically, 13,319,035 reads produced 359,531 unique sRNAs including rRNA, tRNA, miRNA, small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), and unannotated sRNAs. Sequence analysis identified 96 conserved miRNAs belonging to 36 miRNA families and 576 novel miRNAs. qRT-PCR confirmed that the miRNAs were expressed during skotomorphogenesis similar to the trends shown by the Solexa sequencing results. A total of 2013 potential targets were predicted, and the targets of BrmiR157, BrmiR159 and BrmiR160 were proved to be regulated by miRNA-guided cleavage. These results show that specific regulatory miRNAs are present in skotomorphogenic seedlings of turnip and may play important roles in growth, development, and response to dark environment.
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Han J, Xie H, Sun Q, Wang J, Lu M, Wang W, Guo E, Pan J. Bioinformatic identification and experimental validation of miRNAs from foxtail millet (Setaria italica). Gene 2014; 546:367-77. [PMID: 24862217 DOI: 10.1016/j.gene.2014.05.050] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 05/20/2014] [Accepted: 05/22/2014] [Indexed: 02/06/2023]
Abstract
MiRNAs are a novel group of non-coding small RNAs that negatively regulate gene expression. Many miRNAs have been identified and investigated extensively in plant species with sequenced genomes. However, few miRNAs have been identified in foxtail millet (Setaria italica), which is an ancient cereal crop of great importance for dry land agriculture. In this study, 271 foxtail millet miRNAs belonging to 44 families were identified using a bioinformatics approach. Twenty-three pairs of sense/antisense miRNAs belonging to 13 families, and 18 miRNA clusters containing members of 8 families were discovered in foxtail millet. We identified 432 potential targets for 38 miRNA families, most of which were predicted to be involved in plant development, signal transduction, metabolic pathways, disease resistance, and environmental stress responses. Gene ontology (GO) analysis revealed that 101, 56, and 23 target genes were involved in molecular functions, biological processes, and cellular components, respectively. We investigated the expression patterns of 43 selected miRNAs using qRT-PCR analysis. All of the miRNAs were expressed ubiquitously with many exhibiting different expression levels in different tissues. We validated five predicted targets of four miRNAs using the RNA ligase mediated rapid amplification of cDNA end (5'-RLM-RACE) method.
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Affiliation(s)
- Jun Han
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
| | - Hao Xie
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Qingpeng Sun
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Jun Wang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi 046011, China
| | - Min Lu
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Weixiang Wang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Erhu Guo
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi 046011, China
| | - Jinbao Pan
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
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A genome-wide perspective of miRNAome in response to high temperature, salinity and drought stresses in Brassica juncea (Czern) L. PLoS One 2014; 9:e92456. [PMID: 24671003 PMCID: PMC3966790 DOI: 10.1371/journal.pone.0092456] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 02/21/2014] [Indexed: 11/23/2022] Open
Abstract
Micro RNAs (miRNAs) are involved in diverse biological processes including adaptive response towards abiotic stresses. To unravel small RNAs and more specifically miRNAs that can potentially regulate determinants of abiotic stress tolerance, next generation sequencing of B. juncea seedlings subjected to high temperature, high salt and drought conditions was carried out. With the help of UEA sRNA workbench software package, 51 conserved miRNAs belonging to 30 miRNA families were identified. As there was limited genomic information available for B. juncea, we generated and assembled its genome sequence at a low coverage. Using the generated sequence and other publically available Brassica genomic/transcriptomic resources as mapping reference, 126 novel (not reported in any plant species) were discovered for the first time in B. juncea. Further analysis also revealed existence of 32 and 37 star sequences for conserved and novel miRNAs, respectively. The expression of selected conserved and novel miRNAs under conditions of different abiotic stresses was revalidated through universal TaqMan based real time PCR. Putative targets of identified conserved and novel miRNAs were predicted in B. rapa to gain insights into functional roles manifested by B. juncea miRNAs. Furthermore, SPL2-like, ARF17-like and a NAC domain containing protein were experimentally validated as targets of miR156, miR160 and miR164 respectively. Investigation of gene ontologies linked with targets of known and novel miRNAs forecasted their involvement in various biological functions.
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Characterization of conserved microRNAs from five different cucurbit species using computational and experimental analysis. Biochimie 2014; 102:137-44. [PMID: 24657600 DOI: 10.1016/j.biochi.2014.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 03/04/2014] [Indexed: 10/25/2022]
Abstract
MicroRNAs (miRNAs) are ∼21 nt non-coding small RNAs which regulate gene expression at the post-transcriptional level in plants and animals. Until recently, only limited numbers of miRNAs were identified in Cucurbitaceae, a large flowering plant family. In this study, 220 potential miRNA candidates were identified from five species of Cucurbitaceae family using a comparative genome-based computational analysis. A comprehensive bioinformatic analysis of EST (expressed sequence tag) and GSS (genomic survey sequence) data of five cucurbit species showed that at least 41, 108, 21, 17 and 33 miRNAs existed in Cucumis sativus, Cucumis melo, Citrullus lanatus, Siraitia grosvenorii and Cucurbita pepo, respectively. Quantitative real-time PCR (qRT-PCR) analysis revealed the differentially expression levels of miRNAs in the four tissues of cucumber and melon. These identified miRNAs in the five species potentially targeted 578 protein-coding genes and one target of the C. melo miRNA cme-miR160a-5p was verified by 5' RLM-RACE. GO and KEGG analysis suggested that many melon miRNAs might involve in nucleotide metabolism, oxidative phosphorylation, cell redox homeostasis and signal transduction.
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38
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Geng M, Li H, Jin C, Liu Q, Chen C, Song W, Wang C. Genome-wide identification and characterization of miRNAs in the hypocotyl and cotyledon of cauliflower (Brassica oleracea L. var. botrytis) seedlings. PLANTA 2014; 239:341-356. [PMID: 24170336 DOI: 10.1007/s00425-013-1986-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Accepted: 10/15/2013] [Indexed: 06/02/2023]
Abstract
MicroRNAs (miRNAs) are a class of small endogenous, non-coding RNAs that have key regulatory functions in plant growth, development, and other biological processes. Hypocotyl and cotyledon are the two major tissues of cauliflower (Brassica oleracea L. var. botrytis) seedlings. Tissue culture experiments have indicated that the regenerative abilities of these two tissues are significantly different. However, the characterization of miRNAs and their roles in regulating organ development in cauliflower remain unexplored. In the present study, two small RNA libraries were sequenced by Solexa sequencing technology. 99 known miRNAs belonging to 28 miRNA families were identified, in which 6 miRNA families were detected only in Brassicaceae. A total of 162 new miRNA sequences with single nucleotide substitutions corresponding to the known miRNAs, and 32 potentially novel miRNAs were also first discovered. Comparative analysis indicated that 42 of 99 known miRNAs and 17 of 32 novel miRNAs exhibited significantly differential expression between hypocotyl and cotyledon, and the differential expression of several miRNAs was further validated by stem-loop RT-PCR. In addition, 235 targets for 89 known miRNAs and 198 targets for 24 novel miRNAs were predicted, and their functions were further discussed. The expression patterns of several representative targets were also confirmed by qRT-PCR analysis. The results identified that the transcriptional expression patterns of miRNAs were negatively correlated with their targets. These findings gave new insights into the characteristics of miRNAs in cauliflower, and provided important clues to elucidate the roles of miRNAs in the tissue differentiation and development of cauliflower.
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Affiliation(s)
- Meijuan Geng
- College of Life Sciences, Nankai University, Tianjin, 300071, China
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39
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Panda D, Dehury B, Sahu J, Barooah M, Sen P, Modi MK. Computational identification and characterization of conserved miRNAs and their target genes in garlic (Allium sativum L.) expressed sequence tags. Gene 2014; 537:333-42. [PMID: 24434367 DOI: 10.1016/j.gene.2014.01.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 12/03/2013] [Accepted: 01/04/2014] [Indexed: 01/22/2023]
Abstract
The endogenous small non-coding functional microRNAs (miRNAs) are short in size, range from ~21 to 24 nucleotides in length, play a pivotal role in gene expression in plants and animals by silencing genes either by destructing or blocking of translation of homologous mRNA. Although various high-throughput, time consuming and expensive techniques like forward genetics and direct cloning are employed to detect miRNAs in plants but comparative genomics complemented with novel bioinformatic tools pave the way for efficient and cost-effective identification of miRNAs through homologous sequence search with previously known miRNAs. In this study, an attempt was made to identify and characterize conserved miRNAs in garlic expressed sequence tags (ESTs) through computational means. For identification of novel miRNAs in garlic, a total 3227 known mature miRNAs of plant kingdom Viridiplantae were searched for homology against 21,637 EST sequences resulting in identification of 6 potential miRNA candidates belonging to 6 different miRNA families. The psRNATarget server predicted 33 potential target genes and their probable functions for the six identified miRNA families in garlic. Most of the garlic miRNA target genes seem to encode transcription factors as well as genes involved in stress response, metabolism, plant growth and development. The results from the present study will shed more light on the understanding of molecular mechanisms of miRNA in garlic which may aid in the development of novel and precise techniques to understand some post-transcriptional gene silencing mechanism in response to stress tolerance.
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Affiliation(s)
- Debashis Panda
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India
| | - Budheswar Dehury
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India
| | - Jagajjit Sahu
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India
| | - Madhumita Barooah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India
| | - Priyabrata Sen
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India
| | - Mahendra K Modi
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India.
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Din M, Barozai MYK. Profiling and characterization of eggplant (Solanum melongena L.) microRNAs and their targets. Mol Biol Rep 2014; 41:889-94. [PMID: 24390233 DOI: 10.1007/s11033-013-2932-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 12/20/2013] [Indexed: 11/26/2022]
Abstract
MicroRNAs (miRNAs) are small, non-protein coding and functional RNAs. They play negative regulatory role in gene regulation. They are endogenous in nature and are ~21 nucleotides in length. They are reported in many plant species, but still missing and need to be identified in other important plants like; eggplant. The comparative genomic methodology due to their conserved nature is a reasonable approach for the novel miRNAs discovery. In this research, total 76 novel miRNAs from 67 families were identified in the important vegetable eggplant (Solanum melongena L.). All precursor miRNAs form stable minimum free energy secondary structures and the mature miRNAs reside in the stem regions. Furthermore, eight miRNAs were randomly selected and experimentally validated through RT-PCR. A total of 345 putative targets were also identified for the novel 76 eggplant miRNAs. Their targets are involved in regulation, metabolism, transcription factors, growth and development and other physiological processes. These findings provide a baseline to unravel the miRNAs role in eggplant and utilize them for the improvement of the plant biology.
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Affiliation(s)
- Muhammad Din
- Department of Botany, University of Balochistan, Sariab Road, Quetta, Pakistan
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41
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Li X, Hou Y, Zhang L, Zhang W, Quan C, Cui Y, Bian S. Computational identification of conserved microRNAs and their targets from expression sequence tags of blueberry (Vaccinium corybosum). PLANT SIGNALING & BEHAVIOR 2014; 9:e29462. [PMID: 25763692 PMCID: PMC4203583 DOI: 10.4161/psb.29462] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/03/2014] [Accepted: 06/04/2014] [Indexed: 05/21/2023]
Abstract
MicroRNAs (miRNAs) are a class of endogenous, approximately 21nt in length, non-coding RNA, which mediate the expression of target genes primarily at post-transcriptional levels. miRNAs play critical roles in almost all plant cellular and metabolic processes. Although numerous miRNAs have been identified in the plant kingdom, the miRNAs in blueberry, which is an economically important small fruit crop, still remain totally unknown. In this study, we reported a computational identification of miRNAs and their targets in blueberry. By conducting an EST-based comparative genomics approach, 9 potential vco-miRNAs were discovered from 22,402 blueberry ESTs according to a series of filtering criteria, designated as vco-miR156-5p, vco-miR156-3p, vco-miR1436, vco-miR1522, vco-miR4495, vco-miR5120, vco-miR5658, vco-miR5783, and vco-miR5986. Based on sequence complementarity between miRNA and its target transcript, 34 target ESTs from blueberry and 70 targets from other species were identified for the vco-miRNAs. The targets were found to be involved in transcription, RNA splicing and binding, DNA duplication, signal transduction, transport and trafficking, stress response, as well as synthesis and metabolic process. These findings will greatly contribute to future research in regard to functions and regulatory mechanisms of blueberry miRNAs.
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Affiliation(s)
- Xuyan Li
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
| | - Yanming Hou
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
| | - Li Zhang
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
| | - Wenhao Zhang
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
| | - Chen Quan
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
| | - Yuhai Cui
- Agriculture and Agri-Food Canada; Southern Crop Protection and Food Research Centre; London, ON Canada
- Department of Biology; Western University; London, ON Canada
| | - Shaomin Bian
- College of Plant Science; Jilin University; Changchun, Jilin, PR China
- Correspondence to: Shaomin Bian,
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Din M, Barozai MYK. Profiling microRNAs and their targets in an important fleshy fruit: tomato (Solanum lycopersicum). Gene 2013; 535:198-203. [PMID: 24315821 DOI: 10.1016/j.gene.2013.11.034] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 11/11/2013] [Accepted: 11/14/2013] [Indexed: 12/11/2022]
Abstract
Tomato (Solanum lycopersicum) is an important and the most useful plant based diet. It is widely used for its antioxidant property. Presently, only two digits, tomato microRNAs (miRNAs) are reported in miRBase: a miRNA database. This study is aimed to profile and characterize more miRNAs and their targets in tomato. A comprehensive comparative genomic approach is applied and a total of 109 new miRNAs belonging to 106 families are identified and characterized from the tomato expressed sequence tags (ESTs). All these potential miRNAs are profiled for the first time in tomato. The profiled miRNAs are also observed with stable stem-loop structures (Precursor-miRNAs), whose length ranges from 45 to 329 nucleotides (nt) with an average of 125 nt. The mature miRNAs are found in the stem of pre-miRNAs and their length ranges from 19 to 24 nt with an average of 21 nt. Furthermore, twelve miRNAs are randomly selected and experimentally validated through RT-PCR. A total of 406 putative targets are also predicted for the newly 109 tomato miRNAs. These targets are involved in structural protein, metabolism, transcription factor, growth & development, stress related, signaling pathways, storage proteins and other vital processes. Some important proteins like; 9-cisepoxycarotenoid dioxygenase (NCED), transcription factor MYB, ATP-binding cassette transporters, terpen synthase, 14-3-3 and TIR-NBS proteins are also predicted as putative targets for tomato miRNAs. These findings improve a baseline data of miRNAs and their targets in tomato. This baseline data can be utilized to fine tune this important fleshy fruit for nutritional & antioxidant properties and also under biotic & abiotic stresses.
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Affiliation(s)
- Muhammad Din
- Department of Botany, University of Balochistan, Sariab Road Quetta, Pakistan
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Lukasik A, Pietrykowska H, Paczek L, Szweykowska-Kulinska Z, Zielenkiewicz P. High-throughput sequencing identification of novel and conserved miRNAs in the Brassica oleracea leaves. BMC Genomics 2013; 14:801. [PMID: 24245539 PMCID: PMC3840582 DOI: 10.1186/1471-2164-14-801] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 11/14/2013] [Indexed: 11/20/2022] Open
Abstract
Background Plant microRNAs are short (~21 nt) non-coding molecules that regulate gene expression by targeting the mRNA cleavage or protein translation inhibition. In this manner, they play many important roles in the cells of living organisms. One of the plant species in which the entire set of miRNAs has not been yet completely identified is Brassica oleracea var. capitata (cabbage). For this reason and for the economic and nutritional importance of this food crop, high-throughput small RNAs sequencing has been performed to discover the novel and conserved miRNAs in mature cabbage leaves. Results In this study, raw reads generated from three small RNA libraries were bioinformatically processed and further analyzed to select sequences homologous to known B. oleracea and other plant miRNAs. As a result of this analysis, 261 conserved miRNAs (belonging to 62 families) have been discovered. MIR169, MIR167 and MIR166 were the largest miRNA families, while the highest abundance molecules were miR167, miR166, miR168c and miR157a. Among the generated sequencing reads, miRNAs* were also found, such as the miR162c*, miR160a* and miR157a*. The unannotated tags were used in the prediction and evaluation of novel miRNAs, which resulted in the 26 potential miRNAs proposal. The expressions of 13 selected miRNAs were analyzed by northern blot hybridization. The target prediction and annotation for identified miRNAs were performed, according to which discovered molecules may target mRNAs encoding several potential proteins – e.g., transcription factors, polypeptides that regulate hormone stimuli and abiotic stress response, and molecules participating in transport and cell communication. Additionally, KEGG maps analysis suggested that the miRNAs in cabbage are involved in important processing pathways, including glycolysis, glycerolipid metabolism, flavonoid biosynthesis and oxidative phosphorylation. Conclusions Conclusively, for the first time, the large set of miRNAs was identified in mature cabbage leaves. Potential targets designation for these miRNAs may suggest their essential role in many plants primary biological processes. Presented study not only supplements the knowledge about B. oleracea miRNAs, but additionally it may be used in other research concerning the improvement of the cabbage cultivation.
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Affiliation(s)
| | | | | | | | - Piotr Zielenkiewicz
- Institute of Biophysics and Biochemistry, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
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Barozai MYK, Din M, Baloch IA. Structural and functional based identification of the bean (Phaseolus) microRNAs and their targets from expressed sequence tags. ACTA ACUST UNITED AC 2013; 14:11-8. [PMID: 23605779 DOI: 10.1007/s10969-013-9152-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 04/01/2013] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) are small, 18-26 nucleotides long, non-coding RNAs that play role in post-transcriptional gene regulation. Many of these are evolutionarily conserved. This suggests a powerful approach to predict new miRNAs in other species. In this research, structural and functional approaches were combined to make computational prediction of potential miRNAs and their targets in Bean (Phaseolus). Total 55 novel miRNAs were detected from 38 miRNAs families in Bean (Phaseolus). These families are; miR156, 160, 164, 168, 170, 171, 172, 319, 393, 396, 397, 398, 408, 414, 438, 444, 535, 1310, 1424, 1426, 1848, 1860, 1863, 2055, 2091, 2093, 2094, 2102, 2103, 2105, 2864, 2866, 2925, 2926, 4221, 4245, 4246 and 4250. In the 55 putative miRNAs; 28 miRNAs belong to Phaseolus acutifolius, 23 to Phaseolus vulgaris, 4 to Phaseolus coccineus. All the mature miRNAs reside in the stem portion of the hairpin structures. Total 146 potential protein targets were predicted for these miRNAs.
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Li C, Zhu Y, Guo X, Sun C, Luo H, Song J, Li Y, Wang L, Qian J, Chen S. Transcriptome analysis reveals ginsenosides biosynthetic genes, microRNAs and simple sequence repeats in Panax ginseng C. A. Meyer. BMC Genomics 2013; 14:245. [PMID: 23577925 PMCID: PMC3637502 DOI: 10.1186/1471-2164-14-245] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Accepted: 04/02/2013] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Panax ginseng C. A. Meyer is one of the most widely used medicinal plants. Complete genome information for this species remains unavailable due to its large genome size. At present, analysis of expressed sequence tags is still the most powerful tool for large-scale gene discovery. The global expressed sequence tags from P. ginseng tissues, especially those isolated from stems, leaves and flowers, are still limited, hindering in-depth study of P. ginseng. RESULTS Two 454 pyrosequencing runs generated a total of 2,423,076 reads from P. ginseng roots, stems, leaves and flowers. The high-quality reads from each of the tissues were independently assembled into separate and shared contigs. In the separately assembled database, 45,849, 6,172, 4,041 and 3,273 unigenes were only found in the roots, stems, leaves and flowers database, respectively. In the jointly assembled database, 178,145 unigenes were observed, including 86,609 contigs and 91,536 singletons. Among the 178,145 unigenes, 105,522 were identified for the first time, of which 65.6% were identified in the stem, leaf or flower cDNA libraries of P. ginseng. After annotation, we discovered 223 unigenes involved in ginsenoside backbone biosynthesis. Additionally, a total of 326 potential cytochrome P450 and 129 potential UDP-glycosyltransferase sequences were predicted based on the annotation results, some of which may encode enzymes responsible for ginsenoside backbone modification. A BLAST search of the obtained high-quality reads identified 14 potential microRNAs in P. ginseng, which were estimated to target 100 protein-coding genes, including transcription factors, transporters and DNA binding proteins, among others. In addition, a total of 13,044 simple sequence repeats were identified from the 178,145 unigenes. CONCLUSIONS This study provides global expressed sequence tags for P. ginseng, which will contribute significantly to further genome-wide research and analyses in this species. The novel unigenes identified here enlarge the available P. ginseng gene pool and will facilitate gene discovery. In addition, the identification of microRNAs and the prediction of targets from this study will provide information on gene transcriptional regulation in P. ginseng. Finally, the analysis of simple sequence repeats will provide genetic makers for molecular breeding and genetic applications in this species.
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Affiliation(s)
- Chunfang Li
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Yingjie Zhu
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Xu Guo
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Chao Sun
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Hongmei Luo
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Jingyuan Song
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Ying Li
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Lizhi Wang
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Jun Qian
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Shilin Chen
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
- China Academy of Chinese Medical Sciences, Institute of Chinese Materia Medica, Beijing, 100700, China
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Hu J, Sun L, Ding Y. Identification of conserved microRNAs and their targets in chickpea (Cicer arietinum L.). PLANT SIGNALING & BEHAVIOR 2013; 8:e23604. [PMID: 23333975 PMCID: PMC7030309 DOI: 10.4161/psb.23604] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The microRNAs (miRNAs) are a new class of non-protein coding small RNAs that regulate gene expression at the post-transcriptional level in plants. Although thousands of miRNAs have been identified in many plant species, little studies have been reported about chickpea microRNAs. In this study, 28 potential miRNA candidates belonging to 20 families were identified from 16 ESTs and 12 GSSs in chickpea using a comparative genome-based computational analysis. A total of 664 miRNA targets were predicted and some of them encoded transcription factors as well as genes that function in stress response, signal transduction, methylation and a variety of other metabolic processes. These findings lay the foundation for further understanding of miRNA function in the development of chickpea.
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Affiliation(s)
- Jihong Hu
- State Key Laboratory of Hybrid Rice; College of Life Sciences; Wuhan University; Wuhan, P.R. China
- Correspondence to: Jihong Hu,
| | - Lulu Sun
- State Key Laboratory of Hybrid Rice; College of Life Sciences; Wuhan University; Wuhan, P.R. China
| | - Yi Ding
- State Key Laboratory of Hybrid Rice; College of Life Sciences; Wuhan University; Wuhan, P.R. China
- Correspondence to: Yi Ding,
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Identification of conserved microRNAs and their targets in the model legume Lotus japonicus. J Biotechnol 2013; 164:520-4. [DOI: 10.1016/j.jbiotec.2013.01.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 01/30/2013] [Accepted: 01/30/2013] [Indexed: 11/19/2022]
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Dehury B, Panda D, Sahu J, Sahu M, Sarma K, Barooah M, Sen P, Modi MK. In silico identification and characterization of conserved miRNAs and their target genes in sweet potato (Ipomoea batatas L.) expressed sequence tags (ESTs). PLANT SIGNALING & BEHAVIOR 2013; 8:e26543. [PMID: 24067297 PMCID: PMC4091516 DOI: 10.4161/psb.26543] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The endogenous small non-coding micro RNAs (miRNAs), which are typically ~21-24 nt nucleotides, play a crucial role in regulating the intrinsic normal growth of cells and development of the plants as well as in maintaining the integrity of genomes. These small non-coding RNAs function as the universal specificity factors in post-transcriptional gene silencing. Discovering miRNAs, identifying their targets, and further inferring miRNA functions is a routine process to understand normal biological processes of miRNAs and their roles in the development of plants. Comparative genomics based approach using expressed sequence tags (EST) and genome survey sequences (GSS) offer a cost-effective platform for identification and characterization of miRNAs and their target genes in plants. Despite the fact that sweet potato (Ipomoea batatas L.) is an important staple food source for poor small farmers throughout the world, the role of miRNA in various developmental processes remains largely unknown. In this paper, we report the computational identification of miRNAs and their target genes in sweet potato from their ESTs. Using comparative genomics-based approach, 8 potential miRNA candidates belonging to miR168, miR2911, and miR156 families were identified from 23 406 ESTs in sweet potato. A total of 42 target genes were predicted and their probable functions were illustrated. Most of the newly identified miRNAs target transcription factors as well as genes involved in plant growth and development, signal transduction, metabolism, defense, and stress response. The identification of miRNAs and their targets is expected to accelerate the pace of miRNA discovery, leading to an improved understanding of the role of miRNA in development and physiology of sweet potato, as well as stress response.
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