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Mehtab-Singh, Tripathi RK, Bekele WA, Tinker NA, Singh J. Differential expression and global analysis of miR156/SQUAMOSA promoter binding-like proteins (SPL) module in oat. Sci Rep 2024; 14:9928. [PMID: 38688976 PMCID: PMC11061197 DOI: 10.1038/s41598-024-60739-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/26/2024] [Indexed: 05/02/2024] Open
Abstract
SQUAMOSA promoter binding-like proteins (SPLs) are important transcription factors that influence growth phase transition and reproduction in plants. SPLs are targeted by miR156 but the SPL/miR156 module is completely unknown in oat. We identified 28 oat SPL genes (AsSPLs) distributed across all 21 oat chromosomes except for 4C and 6D. The oat- SPL gene family represented six of eight SPL phylogenetic groups, with no AsSPLs in groups 3 and 7. A novel oat miR156 (AsmiR156) family with 21 precursors divided into 7 groups was characterized. A total of 16 AsSPLs were found to be targeted by AsmiR156. Intriguingly, AsSPL3s showed high transcript abundance during early inflorescence (GS-54), as compared to the lower abundance of AsmiR156, indicating their role in reproductive development. Unravelling the SPL/miR156 regulatory hub and alterations in expression patterns of AsSPLs could provide an essential toolbox for genetic improvement in the cultivated oat.
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Affiliation(s)
- Mehtab-Singh
- Plant Science Department, McGill University, 21111 Rue Lakeshore, Montreal, QC, H9X 3V9, Canada
| | - Rajiv K Tripathi
- Plant Science Department, McGill University, 21111 Rue Lakeshore, Montreal, QC, H9X 3V9, Canada
| | - Wubishet A Bekele
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
| | - Nicholas A Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
| | - Jaswinder Singh
- Plant Science Department, McGill University, 21111 Rue Lakeshore, Montreal, QC, H9X 3V9, Canada.
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2
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Rao S, Balyan S, Bansal C, Mathur S. An Integrated Bioinformatics and Functional Approach for miRNA Validation. Methods Mol Biol 2022; 2408:253-281. [PMID: 35325428 DOI: 10.1007/978-1-0716-1875-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
MicroRNAs (miRNAs) are small (20-24 nucleotides) non-coding ribo-regulatory molecules with significant roles in regulating target mRNA and long non-coding RNAs at transcriptional and post-transcriptional levels. Rapid advancement in the small RNA sequencing methods with integration of degradome sequencing has accelerated the understanding of miRNA-mediated regulatory hubs in plants and yielded extensive annotation of miRNAs and corresponding targets. However, it is becoming clear that large numbers of such annotations are questionable. Therefore, it is imperative to adopt reliable and strict bioinformatics pipelines for miRNA identification. Furthermore, sensitive methods are needed for validation and functional characterization of miRNA and its target(s). In this chapter, we have provided a comprehensive and streamlined methodology for miRNA identification and its functional validation in plants. This includes a combination of various in silico and experimental methodologies. To identify miRNA compendium from large-scale Next-Generation Sequencing (NGS) small RNA datasets, the miR-PREFeR (miRNA PREdiction From small RNA-Seq data) bioinformatics tool has been described. Also, a homology-based search protocol for finding members of a specific miRNA family has been discussed. The chapter also includes techniques to ascertain miRNA:target pair specificity using in silico target prediction from degradome NGS libraries using CleaveLand pipeline, miRNA:target validation by in planta transient assays, 5' RLM-RACE and expression analysis as well as functional techniques like miRNA overexpression, short tandem target mimic and resistant target approaches. The proposed strategy offers a reliable and sensitive way for miRNA:target identification and validation. Additionally, we strongly promulgate the use of multiple methodologies to validate a miRNA as well as its target.
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Affiliation(s)
- Sombir Rao
- National Institute of Plant Genome Research, New Delhi, India
| | - Sonia Balyan
- National Institute of Plant Genome Research, New Delhi, India
| | - Chandni Bansal
- National Institute of Plant Genome Research, New Delhi, India
| | - Saloni Mathur
- National Institute of Plant Genome Research, New Delhi, India.
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3
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Buch DU, Sharma OA, Pable AA, Barvkar VT. Characterization of microRNA genes from Pigeonpea (Cajanus cajan L.) and understanding their involvement in drought stress. J Biotechnol 2020; 321:23-34. [PMID: 32610182 DOI: 10.1016/j.jbiotec.2020.06.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNA) are non-coding 20-24 nucleotide long RNAs regulating gene expression. In this study, we have characterized and analysed expression of miRNAs in Pigeonpea by using bioinformatics and experimental tools. We identified 116 miRNAs belonging to 32 phylogenetic families. Further, transcription start sites of miRNA genes revealed abundance and unique arrangement of adenine at +1 and thymine at -1 position. Promoter analysis exhibited presence of 19 most prevalent motifs which comprises majorly of TATA box and MYC domains. In total, 252 miRNA-targets were identified and found to be involved in various developmental processes and stress responses. Moreover, genome-wide localization studies demonstrated clustering of cca-miRNA 395 and 169 genes. The tandem and segmental duplication events were observed suggesting miRNA genes have been originated parallelly with protein coding genes. The expression analysis revealed induction of cca-miR169a, 398a and 408 miRNAs under drought stress highlighting their involvement. Conversely, down-regulation of their putative targets (NFYA, SOD, and UCLA, respectively) confirmed regulatory role of miRNAs in their expression emphasising the negative relationship between these miRNAs and targets in Pigeonpea. This study reports vast repertoire of miRNA genes which further can be experimentally characterized to elucidate their functions in various biological processes and can be recommended for Pigeonpea improvement programs.
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Affiliation(s)
- Drushtant U Buch
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India.
| | - Oshin A Sharma
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India.
| | - Anupama A Pable
- Department of Microbiology, Savitribai Phule Pune University, Pune, 411007, India.
| | - Vitthal T Barvkar
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India.
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4
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Martins TF, Souza PFN, Alves MS, Silva FDA, Arantes MR, Vasconcelos IM, Oliveira JTA. Identification, characterization, and expression analysis of cowpea (Vigna unguiculata [L.] Walp.) miRNAs in response to cowpea severe mosaic virus (CPSMV) challenge. PLANT CELL REPORTS 2020; 39:1061-1078. [PMID: 32388590 DOI: 10.1007/s00299-020-02548-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/04/2020] [Accepted: 04/25/2020] [Indexed: 06/11/2023]
Abstract
Cowpea miRNAs and Argonaute genes showed differential expression patterns in response to CPSMV challenge Several biotic stresses affect cowpea production and yield. CPSMV stands out for causing severe negative impacts on cowpea. Plants have two main induced immune systems. In the basal system (PTI, PAMP-triggered immunity), plants recognize and respond to conserved molecular patterns associated with pathogens (PAMPs). The second type (ETI, Effector-triggered immunity) is induced after plant recognition of specific factors from pathogens. RNA silencing is another important defense mechanism in plants. Our research group has been using biochemical and proteomic approaches to learn which proteins and pathways are involved and could explain why some cowpea genotypes are resistant whereas others are susceptible to CPSMV. This current study was conducted to determine the role of cowpea miRNA in the interaction between a resistant cowpea genotype (BRS-Marataoã) and CPSMV. Previously identified and deposited plant microRNA sequences were used to find out all possible microRNAs in the cowpea genome. This search detected 617 mature microRNAs, which were distributed in 89 microRNA families. Next, 4 out of these 617 miRNAs and their possible target genes that encode the proteins Kat-p80, DEAD-Box, GST, and SPB9, all involved in the defense response of cowpea to CPSMV, had their expression compared between cowpea leaves uninoculated and inoculated with CPSMV. Additionally, the differential expression of genes that encode the Argonaute (AGO) proteins 1, 2, 4, 6, and 10 is reported. In summary, the studied miRNAs and AGO 2 and AGO4 associated genes showed differential expression patterns in response to CPSMV challenge, which indicate their role in cowpea defense.
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Affiliation(s)
- Thiago F Martins
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE, Brazil
| | - Pedro F N Souza
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE, Brazil
| | - Murilo S Alves
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE, Brazil
| | - Fredy Davi A Silva
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE, Brazil
| | - Mariana R Arantes
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE, Brazil
| | - Ilka M Vasconcelos
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE, Brazil
| | - Jose T A Oliveira
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE, Brazil.
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5
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Rao S, Balyan S, Jha S, Mathur S. Novel insights into expansion and functional diversification of MIR169 family in tomato. PLANTA 2020; 251:55. [PMID: 31974682 DOI: 10.1007/s00425-020-03346-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/13/2020] [Indexed: 05/23/2023]
Abstract
MAIN CONCLUSION Expansion of MIR169 members by duplication and new mature forms, acquisition of new promoters, differential precursor-miRNA processivity and engaging novel targets increase the functional diversification of MIR169 in tomato. MIR169 family is an evolutionarily conserved miRNA family in plants. A systematic in-depth analysis of MIR169 family in tomato is lacking. We report 18 miR169 precursors, annotating new loci for MIR169a, b and d, as well as 3 novel mature isoforms (MIR169f/g/h). The family has expanded by both tandem- and segmental-duplication events during evolution. A tandem-pair MIR169b/b-1 and MIR169b-2/h is polycistronic in nature coding for three MIR169b isoforms and a new variant miR169h, that is evidently absent in the wild relatives S. pennellii and S. pimpinellifolium. Seven novel miR169 targets including RNA-binding protein, protein-phosphatase, aminotransferase, chaperone, tetratricopeptide-repeat-protein, and transcription factors ARF-9B and SEPELLATA-3 were established by efficient target cleavage in the presence of specific precursors as well as increased target abundance upon miR169 chelation by short-tandem-target-mimic construct in transient assays. Comparative antagonistic expression profiles of MIR169:target pairs suggest MIR169 family as ubiquitous regulator of various abiotic stresses (heat, cold, dehydration and salt) and developmental pathways. This regulation is partly brought about by acquisition of new promoters as demonstrated by promoter MIR169:GUS reporter assays as well as differential processivity of different precursors and miRNA cleavage efficiencies. Thus, the current study augments the functional horizon of MIR169 family with applications for stress tolerance in crops.
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Affiliation(s)
- Sombir Rao
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110 067, India
| | - Sonia Balyan
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110 067, India
| | - Sarita Jha
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110 067, India
| | - Saloni Mathur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110 067, India.
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6
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Marakli S. In silico determination of transposon-derived miRNAs and targets in Aegilops species. J Biomol Struct Dyn 2019; 38:3098-3109. [PMID: 31402758 DOI: 10.1080/07391102.2019.1654409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Transposable elements (TEs) are found almost in all living organism, shaping organisms' genomes. miRNAs are noncoding RNA types which are especially important in gene expression regulations. Many previously determined plant miRNAs are identical/homologous to transposons (TE-MIR). The aim of this study was computational characterization of novel TE-related miRNAs and their targets in Aegilops genome by using stringent criteria. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed by BLAST2GO. Seventeen novel TE-related miRNAs in Aegilops genome were identified for the first time. GO analyses indicated that 40 targets played different roles in biological processes, cellular components and molecular functions. Moreover, these genes were involved in 10 metabolic pathways such as purine metabolism, nitrogen metabolism, oxidative phosphorylation, etc. as a result of KEGG analyses. Identification of miRNAs and their targets are significant to understand miRNA-TEs relationships and even how TEs affect plant growth and development. Obtaining results of this study are expected to provide possible new insight into Aegilops and its related species, wheat, with respect to miRNAs evolution and domestication.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sevgi Marakli
- Department of Medical Services and Techniques, Amasya University, Sabuncuoglu Serefeddin Health Services Vocational School, Amasya, Turkey.,Amasya University, Central Research Laboratory, Amasya, Turkey
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7
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Sharma C, Saripalli G, Kumar S, Gautam T, Kumar A, Rani S, Jain N, Prasad P, Raghuvanshi S, Jain M, Sharma JB, Prabhu KV, Sharma PK, Balyan HS, Gupta PK. A study of transcriptome in leaf rust infected bread wheat involving seedling resistance gene Lr28. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:1046-1064. [PMID: 32291004 DOI: 10.1071/fp17326] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 04/09/2018] [Indexed: 05/02/2023]
Abstract
Leaf rust disease causes severe yield losses in wheat throughout the world. During the present study, high-throughput RNA-Seq analysis was used to gain insights into the role of Lr28 gene in imparting seedling leaf rust resistance in wheat. Differential expression analysis was conducted using a pair of near-isogenic lines (NILs) (HD 2329 and HD 2329+Lr28) at early (0h before inoculation (hbi), 24 and 48h after inoculation (hai)) and late stages (72, 96 and 168 hai) after inoculation with a virulent pathotype of pathogen Puccinia triticina. Expression of a large number of genes was found to be affected due to the presence/absence of Lr28. Gene ontology analysis of the differentially expressed transcripts suggested enrichment of transcripts involved in carbohydrate and amino acid metabolism, oxidative stress and hormone metabolism, in resistant and/or susceptible NILs. Genes encoding receptor like kinases (RLKs) (including ATP binding; serine threonine kinases) and other kinases were the most abundant class of genes, whose expression was affected. Genes involved in reactive oxygen species (ROS) homeostasis and several genes encoding transcription factors (TFs) (most abundant being WRKY TFs) were also identified along with some ncRNAs and histone variants. Quantitative real-time PCR was also used for validation of 39 representative selected genes. In the long term, the present study should prove useful in developing leaf rust resistant wheat cultivars through molecular breeding.
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Affiliation(s)
- Chanchal Sharma
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
| | - Santosh Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Tinku Gautam
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
| | - Avneesh Kumar
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
| | - Sushma Rani
- Division of Genetics, Indian Agricultural Research Institute (IARI), Pusa, New Delhi, 110022, India
| | - Neelu Jain
- Division of Genetics, Indian Agricultural Research Institute (IARI), Pusa, New Delhi, 110022, India
| | - Pramod Prasad
- Regional Station, Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, 171002, India
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - J B Sharma
- Division of Genetics, Indian Agricultural Research Institute (IARI), Pusa, New Delhi, 110022, India
| | - K V Prabhu
- Division of Genetics, Indian Agricultural Research Institute (IARI), Pusa, New Delhi, 110022, India
| | - P K Sharma
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
| | - H S Balyan
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
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8
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Zuo J, Wang Y, Zhu B, Luo Y, Wang Q, Gao L. sRNAome and transcriptome analysis provide insight into chilling response of cowpea pods. Gene 2018; 671:142-151. [PMID: 29792949 DOI: 10.1016/j.gene.2018.05.064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/04/2018] [Accepted: 05/16/2018] [Indexed: 12/11/2022]
Abstract
Cowpea is an important horticultural crop in tropical and subtropical areas of Asia, Africa, and Latin America, as well as parts of southern Europe and Central and South America. Chilling injury is a common physiological hazard of cowpea in cold chain logistics which reduce the cowpea pods nutritional quality and product value. However, the molecular mechanism involved in chilling injury remains unclear in cowpea pods. RNA-Seq and sRNA-Seq technologies were employed to decipher the miRNAs and mRNAs expression profiles and their regulatory networks in cowpea pods involved in chilling stress. Differentially expressed miRNAs and mRNA profiles were obtained based on cluster analysis, miRNAs and target genes were found to show coherent relationships in the regulatory networks of chilling injury. Furthermore, we found that numerous miRNAs and nat-siRNAs' targets were predicted to be key enzymes involved in the redox reactions such as POD, CAT, AO and LOX, energy metabolism such as ATPase, FAD and NAD related enzymes and different transcription factors such as WRKY, bHLH, MYB, ERF and NAC which play important roles in chilling injury.
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Affiliation(s)
- Jinhua Zuo
- Key laboratory of the vegetable postharvest treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; Boyce Thompson Institute for Plant Research, Cornell University Campus, Ithaca, NY 14853, USA.
| | - Yunxiang Wang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China
| | - Benzhong Zhu
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yunbo Luo
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Qing Wang
- Key laboratory of the vegetable postharvest treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Lipu Gao
- Key laboratory of the vegetable postharvest treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
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9
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Vivek A. In silico identification and characterization of microRNAs based on EST and GSS in orphan legume crop, Lens culinaris medik. (Lentil). ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.aggene.2018.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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10
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Gupta OP, Nigam D, Dahuja A, Kumar S, Vinutha T, Sachdev A, Praveen S. Regulation of Isoflavone Biosynthesis by miRNAs in Two Contrasting Soybean Genotypes at Different Seed Developmental Stages. FRONTIERS IN PLANT SCIENCE 2017; 8:567. [PMID: 28450878 PMCID: PMC5390031 DOI: 10.3389/fpls.2017.00567] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 03/29/2017] [Indexed: 05/20/2023]
Abstract
Owing to the presence of nutritionally important, health-promoting bioactive compounds, especially isoflavones, soybean has acquired the status of a functional food. miRNAs are tiny riboregulator of gene expression by either decreasing and/or increasing the expression of their corresponding target genes. Despite several works on identification and functional characterization of plant miRNAs, the role of miRNAs in the regulation of isoflavones metabolism is still a virgin field. In the present study, we identified a total of 31 new miRNAs along with their 245 putative target genes from soybean seed-specific ESTs using computational approach. The Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that miRNA putatively regulates metabolism and genetic information processing. Out of that, a total of 5 miRNAs (Gma-miRNA12, Gma-miRNA24, Gma-miRNA26, Gma-miRNA28, and Gma-miRNA29) were predicted and validated for their probable role during isoflavone biosynthesis. We also validated their five target genes using RA-PCR, which is as good as 5'RLM-RACE. Temporal regulation [35 days after flowering, 45, 55, and 65 DAF] of miRNAs and their targets showed differential expression schema. Differential expression of Gma-miR26 and Gma-miRNA28 along with their corresponding target genes (Glyma.10G197900 and Glyma.09G127200) showed a direct relationship with the total isoflavone content. Therefore, understanding the miRNA-based genetic regulation of isoflavone pathway would assist in selection and manipulation to get high-performing soybean genotypes with better isoflavone yield.
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Affiliation(s)
- Om P. Gupta
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, Pusa CampusNew Delhi, India
| | - Deepti Nigam
- Centre for Agricultural Bio-Informatics, ICAR-Indian Agricultural Statistics Research Institute, Pusa CampusNew Delhi, India
| | - Anil Dahuja
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, Pusa CampusNew Delhi, India
| | - Sanjeev Kumar
- Centre for Agricultural Bio-Informatics, ICAR-Indian Agricultural Statistics Research Institute, Pusa CampusNew Delhi, India
| | - T. Vinutha
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, Pusa CampusNew Delhi, India
| | - Archana Sachdev
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, Pusa CampusNew Delhi, India
| | - Shelly Praveen
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, Pusa CampusNew Delhi, India
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11
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Djami-Tchatchou AT, Sanan-Mishra N, Ntushelo K, Dubery IA. Functional Roles of microRNAs in Agronomically Important Plants-Potential as Targets for Crop Improvement and Protection. FRONTIERS IN PLANT SCIENCE 2017; 8:378. [PMID: 28382044 PMCID: PMC5360763 DOI: 10.3389/fpls.2017.00378] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/06/2017] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs that have recently emerged as important regulators of gene expression, mainly through cleavage and/or translation inhibition of the target mRNAs during or after transcription. miRNAs play important roles by regulating a multitude of biological processes in plants which include maintenance of genome integrity, development, metabolism, and adaptive responses toward environmental stresses. The increasing population of the world and their food demands requires focused efforts for the improvement of crop plants to ensure sustainable food production. Manipulation of mRNA transcript abundance via miRNA control provides a unique strategy for modulating differential plant gene expression and miRNAs are thus emerging as the next generation targets for genetic engineering for improvement of the agronomic properties of crops. However, a deeper understanding of its potential and the mechanisms involved will facilitate the design of suitable strategies to obtain the desirable traits with minimum trade-offs in the modified crops. In this regard, this review highlights the diverse roles of conserved and newly identified miRNAs in various food and industrial crops and recent advances made in the uses of miRNAs to improve plants of agronomically importance so as to significantly enhance crop yields and increase tolerance to various environmental stress agents of biotic-or abiotic origin.
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Affiliation(s)
- Arnaud T. Djami-Tchatchou
- Department of Agriculture and Animal Health, University of South Africa (Florida Campus)Pretoria, South Africa
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and BiotechnologyNew Delhi, India
| | - Khayalethu Ntushelo
- Department of Agriculture and Animal Health, University of South Africa (Florida Campus)Pretoria, South Africa
| | - Ian A. Dubery
- Department of Biochemistry, University of Johannesburg (Auckland Park Kingsway Campus)Johannesburg, South Africa
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12
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Barraza A, Contreras-Cubas C, Estrada-Navarrete G, Reyes JL, Juárez-Verdayes MA, Avonce N, Quinto C, Díaz-Camino C, Sanchez F. The Class II Trehalose 6-phosphate Synthase Gene PvTPS9 Modulates Trehalose Metabolism in Phaseolus vulgaris Nodules. FRONTIERS IN PLANT SCIENCE 2016; 7:1589. [PMID: 27847509 PMCID: PMC5088437 DOI: 10.3389/fpls.2016.01589] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 10/07/2016] [Indexed: 05/21/2023]
Abstract
Legumes form symbioses with rhizobia, producing nitrogen-fixing nodules on the roots of the plant host. The network of plant signaling pathways affecting carbon metabolism may determine the final number of nodules. The trehalose biosynthetic pathway regulates carbon metabolism and plays a fundamental role in plant growth and development, as well as in plant-microbe interactions. The expression of genes for trehalose synthesis during nodule development suggests that this metabolite may play a role in legume-rhizobia symbiosis. In this work, PvTPS9, which encodes a Class II trehalose-6-phosphate synthase (TPS) of common bean (Phaseolus vulgaris), was silenced by RNA interference in transgenic nodules. The silencing of PvTPS9 in root nodules resulted in a reduction of 85% (± 1%) of its transcript, which correlated with a 30% decrease in trehalose contents of transgenic nodules and in untransformed leaves. Composite transgenic plants with PvTPS9 silenced in the roots showed no changes in nodule number and nitrogen fixation, but a severe reduction in plant biomass and altered transcript profiles of all Class II TPS genes. Our data suggest that PvTPS9 plays a key role in modulating trehalose metabolism in the symbiotic nodule and, therefore, in the whole plant.
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Affiliation(s)
- Aarón Barraza
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología/Universidad Nacional Autónoma de MéxicoCuernavaca, Mexico
| | - Cecilia Contreras-Cubas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología/Universidad Nacional Autónoma de MéxicoCuernavaca, Mexico
| | - Georgina Estrada-Navarrete
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología/Universidad Nacional Autónoma de MéxicoCuernavaca, Mexico
| | - José L. Reyes
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología/Universidad Nacional Autónoma de MéxicoCuernavaca, Mexico
| | - Marco A. Juárez-Verdayes
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología/Universidad Nacional Autónoma de MéxicoCuernavaca, Mexico
| | - Nelson Avonce
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de MorelosCuernavaca, Mexico
| | - Carmen Quinto
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología/Universidad Nacional Autónoma de MéxicoCuernavaca, Mexico
| | - Claudia Díaz-Camino
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología/Universidad Nacional Autónoma de MéxicoCuernavaca, Mexico
| | - Federico Sanchez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología/Universidad Nacional Autónoma de MéxicoCuernavaca, Mexico
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13
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Computational Identification, Target Prediction, and Validation of Conserved miRNAs in Insulin Plant (Costus pictus D. Don). Appl Biochem Biotechnol 2015; 178:513-26. [PMID: 26490377 DOI: 10.1007/s12010-015-1891-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 10/08/2015] [Indexed: 10/22/2022]
Abstract
Insulin plant (Costus pictus D. Don) is an economically important medicinal plant for the content of its high value secondary metabolites, bioactive compounds, and remarkable flowering features. MicroRNAs are a class of short (∼21 nucleotides), endogenous, noncoding RNA molecules that play a vital role in regulating gene expression. Here, we used a computer-based homology approach to identify conserved miRNAs in Transcribed Sequence Assemblies (TSA) of C. pictus. It led us to identify 42 miRNAs of 13 different families in C. pictus for the first time. Using quantitative polymerase chain reaction (qPCR) assays, we further confirmed the expression of 8 miRNAs (miR394, miR159b, miR166k, miR172, miR159f, miR166, miR144, and miR858) in young and mature leaf tissues. A total of 109 potential target genes of the identified miRNAs were subsequently predicted in rice (Oryza sativa L.) genome. The target genes encode transcription factors, enzymes, and various functional proteins involved in the regulation of several metabolic pathways. The findings in the present study lay the foundation for further research on miRNAs and miRNA-mediated gene regulation in this important medicinal plant.
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14
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An approach to identify the novel miRNA encoded from H. Annuus EST sequences. GENOMICS DATA 2015; 6:139-44. [PMID: 26697356 PMCID: PMC4664742 DOI: 10.1016/j.gdata.2015.09.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/06/2015] [Indexed: 01/15/2023]
Abstract
MicroRNAs are a newly discovered class of non-protein small RNAs with 22-24 nucleotides. They play multiple roles in biological processes including development, cell proliferation, apoptosis, stress responses and many other cell functions. In this research, several approaches were combined to make a computational prediction of potential miRNAs and their targets in Helianthus annuus (H. annuus). The already available information of the plant miRNAs present in miRBase v21 was used against expressed sequence tags (ESTs). A total of three miRNAs were detected from which one potential novel miRNA was identified following a range of strict filtering criteria. The target prediction was carried out for these three miRNAs having various targets. These targets were functionally annotated and GO terms were assigned. To study the conserved nature of the miRNAs, predicted phylogenetic analysis was carried out. These findings will significantly provide the broader picture for understanding the functions in H. annuus.
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15
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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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Das A, Chaudhury S, Kalita MC, Mondal TK. In silico identification, characterization and expression analysis of miRNAs in Cannabis sativa L. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.plgene.2015.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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Abreu PMV, Gaspar CG, Buss DS, Ventura JA, Ferreira PCG, Fernandes PMB. Carica papaya microRNAs are responsive to Papaya meleira virus infection. PLoS One 2014; 9:e103401. [PMID: 25072834 PMCID: PMC4114745 DOI: 10.1371/journal.pone.0103401] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 06/30/2014] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs are implicated in the response to biotic stresses. Papaya meleira virus (PMeV) is the causal agent of sticky disease, a commercially important pathology in papaya for which there are currently no resistant varieties. PMeV has a number of unusual features, such as residence in the laticifers of infected plants, and the response of the papaya to PMeV infection is not well understood. The protein levels of 20S proteasome subunits increase during PMeV infection, suggesting that proteolysis could be an important aspect of the plant defense response mechanism. To date, 10,598 plant microRNAs have been identified in the Plant miRNAs Database, but only two, miR162 and miR403, are from papaya. In this study, known plant microRNA sequences were used to search for potential microRNAs in the papaya genome. A total of 462 microRNAs, representing 72 microRNA families, were identified. The expression of 11 microRNAs, whose targets are involved in 20S and 26S proteasomal degradation and in other stress response pathways, was compared by real-time PCR in healthy and infected papaya leaf tissue. We found that the expression of miRNAs involved in proteasomal degradation increased in response to very low levels of PMeV titre and decreased as the viral titre increased. In contrast, miRNAs implicated in the plant response to biotic stress decreased their expression at very low level of PMeV and increased at high PMeV levels. Corroborating with this results, analysed target genes for this miRNAs had their expression modulated in a dependent manner. This study represents a comprehensive identification of conserved miRNAs inpapaya. The data presented here might help to complement the available molecular and genomic tools for the study of papaya. The differential expression of some miRNAs and identifying their target genes will be helpful for understanding the regulation and interaction of PMeV and papaya.
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Affiliation(s)
- Paolla M. V. Abreu
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Clicia G. Gaspar
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - David S. Buss
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - José A. Ventura
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
- Instituto Capixaba de Pesquisa, Assistência Técnica e Extensão Rural, Vitória, Espírito Santo, Brazil
| | - Paulo C. G. Ferreira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Patricia M. B. Fernandes
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
- * E-mail:
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18
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Yang H, Zhang R, Jing Y, Zhu L, Zhang W, Liu C, Wang J, Yang J, Zhang J, Zen K, Zhang C, Li D. Identification and characterization of microRNAs in the crab-eating macaque (Macaca fascicularis) using transcriptome analysis. Gene 2013; 536:308-15. [PMID: 24355555 DOI: 10.1016/j.gene.2013.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 11/26/2013] [Accepted: 12/06/2013] [Indexed: 01/15/2023]
Abstract
MicroRNAs (miRNAs), with an average length between 16 nt and 26 nt, are small non-coding RNAs that can repress gene expression on the post-transcriptional level. Macaca fascicularis (M. fascicularis), one of the most important nonhuman primate animal models, is widely used in basic and applied preclinical research, especially in studies that involve neuroscience and disease. However, due to the lack of a complete genome sequence, the miRNAs in M. fascicularis have not been completely characterized. In this study, 86 putative M. fascicularis miRNAs were identified using a strategy of our design. The expression of some of these miRNAs in the tissue was confirmed by qRT-PCR. The function and pathway of their targeted genes were analyzed to reveal the potential relevance of miRNA regulation on diseases and physiological processes. The current study provides insight into potential miRNAs and forms a useful knowledge base for the future understanding of the function of miRNAs in M. fascicularis.
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Affiliation(s)
- Hao Yang
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing 210093, China
| | - Rui Zhang
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing 210093, China
| | - Ying Jing
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing 210093, China
| | - Lin Zhu
- Institute of Discovery Biology, Jiangsu Simcere Pharmaceutical R&D Co., Ltd, 699-18 Xuan Wu Avenue, Nanjing 210042, China
| | - Wen Zhang
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing 210093, China
| | - Chang Liu
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing 210093, China
| | - Jin Wang
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing 210093, China
| | - Jie Yang
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing 210093, China
| | - Junfeng Zhang
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing 210093, China
| | - Ke Zen
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing 210093, China.
| | - Chenyu Zhang
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing 210093, China.
| | - Donghai Li
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing 210093, China.
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19
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Gao D, Qiu L, Hou Z, Zhang Q, Wu J, Gao Q, Song L. Computational Identification of MicroRNAs from the Expressed Sequence Tags of Toxic Dinoflagellate Alexandrium Tamarense. Evol Bioinform Online 2013; 9:479-85. [PMID: 24324323 PMCID: PMC3855098 DOI: 10.4137/ebo.s12899] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Micro ribonucleic acids (miRNAs) represent a class of small noncoding RNAs that play important roles in multiple biological processes by degrading targeted mRNAs or by repressing mRNA translation. In the case of algal lineages, especially dinoflagellates, knowledge regarding the miRNA system is still limited and its regulatory role remains unclear. In the present study, a computational approach was employed to screen miRNAs from the expressed sequence tags (ESTs) of Alexandrium tamarense. A total of 18 potential miRNAs were identified according to a range of filtering criteria. In addition, unique evolutionary features, such as miRNA gene duplication and sequence similarity to metazoan miRNAs, implied that the miRNA system in dinoflagellates is complex. Moreover, based on these 18 miRNA sequences, 42 potential target genes showing diverse functions in regulating growth and development were predicted in Thalassiosira pseudonana and Phaeodactylum tricornutum. Taken together, our data suggest the existence of miRNAs in dinoflagellates and provide clues for further functional studies on these predicted miRNAs.
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Affiliation(s)
- Dahai Gao
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences (IOCAS), Qingdao, People's Republic of China
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20
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Patanun O, Lertpanyasampatha M, Sojikul P, Viboonjun U, Narangajavana J. Computational identification of microRNAs and their targets in cassava (Manihot esculenta Crantz.). Mol Biotechnol 2013; 53:257-69. [PMID: 22388699 DOI: 10.1007/s12033-012-9521-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
MicroRNAs (miRNAs) are a newly discovered class of noncoding endogenous small RNAs involved in plant growth and development as well as response to environmental stresses. miRNAs have been extensively studied in various plant species, however, only few information are available in cassava, which serves as one of the staple food crops, a biofuel crop, animal feed and industrial raw materials. In this study, the 169 potential cassava miRNAs belonging to 34 miRNA families were identified by computational approach. Interestingly, mes-miR319b was represented as the first putative mirtron demonstrated in cassava. A total of 15 miRNA clusters involving 7 miRNA families, and 12 pairs of sense and antisense strand cassava miRNAs belonging to six different miRNA families were discovered. Prediction of potential miRNA target genes revealed their functions involved in various important plant biological processes. The cis-regulatory elements relevant to drought stress and plant hormone response were identified in the promoter regions of those miRNA genes. The results provided a foundation for further investigation of the functional role of known transcription factors in the regulation of cassava miRNAs. The better understandings of the complexity of miRNA-mediated genes network in cassava would unravel cassava complex biology in storage root development and in coping with environmental stresses, thus providing more insights for future exploitation in cassava improvement.
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Affiliation(s)
- Onsaya Patanun
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
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21
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Shui XR, Chen ZW, Li JX. MicroRNA prediction and its function in regulating drought-related genes in cowpea. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 210:25-35. [PMID: 23849110 DOI: 10.1016/j.plantsci.2013.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 05/02/2013] [Accepted: 05/04/2013] [Indexed: 05/26/2023]
Abstract
Cowpea has indigenous drought-tolerant characteristics, but the molecular mechanisms underlying the drought-tolerance are largely unknown. Drought sensitive and resistant cowpea have different responses regarding to drought stress. We applied homology search to predict miRNAs and their corresponding targets. The newly identified cowpea miRNAs were validated by real-time quantitative PCR in the leaves and roots of cowpea plants under drought treatment. Target gene prediction shows that a set of miRNA target genes are involved in the metabolic pathways regarding the physiological changes that are highly related to drought stress. We analyzed the expression levels of some important genes that participate in the physiological responses to drought stress and found that variations in their expression levels correspond well to the different responses of drought sensitive and resistant cowpea to drought stress. The expression levels of the target genes were negatively correlated to those of miRNAs. The same miRNA in different tissues responds differently to drought stress. Our results indicate that miRNAs play important roles in response to drought stress by regulating the expression levels of drought-related genes in cowpea.
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Affiliation(s)
- Xiao-Rong Shui
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
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22
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Kurtoglu KY, Kantar M, Lucas SJ, Budak H. Unique and conserved microRNAs in wheat chromosome 5D revealed by next-generation sequencing. PLoS One 2013; 8:e69801. [PMID: 23936103 PMCID: PMC3720673 DOI: 10.1371/journal.pone.0069801] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 06/12/2013] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs are a class of short, non-coding, single-stranded RNAs that act as post-transcriptional regulators in gene expression. miRNA analysis of Triticum aestivum chromosome 5D was performed on 454 GS FLX Titanium sequences of flow-sorted chromosome 5D with a total of 3,208,630 good quality reads representing 1.34x and 1.61x coverage of the short (5DS) and long (5DL) arms of the chromosome respectively. In silico and structural analyses revealed a total of 55 miRNAs; 48 and 42 miRNAs were found to be present on 5DL and 5DS respectively, of which 35 were common to both chromosome arms, while 13 miRNAs were specific to 5DL and 7 miRNAs were specific to 5DS. In total, 14 of the predicted miRNAs were identified in wheat for the first time. Representation (the copy number of each miRNA) was also found to be higher in 5DL (1,949) compared to 5DS (1,191). Targets were predicted for each miRNA, while expression analysis gave evidence of expression for 6 out of 55 miRNAs. Occurrences of the same miRNAs were also found in Brachypodium distachyon and Oryza sativa genome sequences to identify syntenic miRNA coding sequences. Based on this analysis, two other miRNAs: miR1133 and miR167 were detected in B. distachyon syntenic region of wheat 5DS. Five of the predicted miRNA coding regions (miR6220, miR5070, miR169, miR5085, miR2118) were experimentally verified to be located to the 5D chromosome and three of them : miR2118, miR169 and miR5085, were shown to be 5D specific. Furthermore miR2118 was shown to be expressed in Chinese Spring adult leaves. miRNA genes identified in this study will expand our understanding of gene regulation in bread wheat.
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Affiliation(s)
| | - Melda Kantar
- Faculty of Engineering and Natural Sciences, Sabanci University, Orhanlı, Tuzla, Istanbul, Turkey
| | - Stuart J. Lucas
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Sabanci University, Tuzla, Istanbul, Turkey
| | - Hikmet Budak
- Faculty of Engineering and Natural Sciences, Sabanci University, Orhanlı, Tuzla, Istanbul, Turkey
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Sabanci University, Tuzla, Istanbul, Turkey
- * E-mail:
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23
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Mathiyalagan R, Subramaniyam S, Natarajan S, Kim YJ, Sun MS, Kim SY, Kim YJ, Yang DC. Insilico profiling of microRNAs in Korean ginseng (Panax ginseng Meyer). J Ginseng Res 2013; 37:227-47. [PMID: 23717176 PMCID: PMC3659641 DOI: 10.5142/jgr.2013.37.227] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 11/20/2012] [Accepted: 12/10/2012] [Indexed: 01/07/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of recently discovered non-coding small RNA molecules, on average approximately 21 nucleotides in length, which underlie numerous important biological roles in gene regulation in various organisms. The miRNA database (release 18) has 18,226 miRNAs, which have been deposited from different species. Although miRNAs have been identified and validated in many plant species, no studies have been reported on discovering miRNAs in Panax ginseng Meyer, which is a traditionally known medicinal plant in oriental medicine, also known as Korean ginseng. It has triterpene ginseng saponins called ginsenosides, which are responsible for its various pharmacological activities. Predicting conserved miRNAs by homology-based analysis with available expressed sequence tag (EST) sequences can be powerful, if the species lacks whole genome sequence information. In this study by using the EST based computational approach, 69 conserved miRNAs belonging to 44 miRNA families were identified in Korean ginseng. The digital gene expression patterns of predicted conserved miRNAs were analyzed by deep sequencing using small RNA sequences of flower buds, leaves, and lateral roots. We have found that many of the identified miRNAs showed tissue specific expressions. Using the insilico method, 346 potential targets were identified for the predicted 69 conserved miRNAs by searching the ginseng EST database, and the predicted targets were mainly involved in secondary metabolic processes, responses to biotic and abiotic stress, and transcription regulator activities, as well as a variety of other metabolic processes.
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Affiliation(s)
- Ramya Mathiyalagan
- Korean Ginseng Center and Ginseng Resource Bank, Kyung Hee University, Yongin 449-701, Korea
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24
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Vishwakarma NP, Jadeja VJ. Identification of miRNA encoded by Jatropha curcas from EST and GSS. PLANT SIGNALING & BEHAVIOR 2013; 8:e23152. [PMID: 23299511 PMCID: PMC3657014 DOI: 10.4161/psb.23152] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 12/06/2012] [Indexed: 05/30/2023]
Abstract
miRNAs are endogenous approx 22 nucleotide RNA which mediates transcriptional or Post-transcriptional gene regulation and play a critical role in diverse aspects of plant development. miRNA identification in wet lab have various constraints, it is time consuming and expensive. It also faces the limitation of identifying miRNAs expressed at specific time and/or at special conditions. Due to the nature of strong conservation of miRNA in plant species, the use of comparative genomics approach for expressed sequence tags (ESTs), Genome Survey Sequence (GSS) and structural feature criteria filter has paved the way toward the identification of conserved miRNAs from the plant species whose genomes are not yet available in public domain. To identify the novel miRNA from Jatropha curcas, a total of 46862 EST sequences and 1569 GSS were searched for homology to previously known viridiplantae 2502 mature miRNA. After predicting the RNA secondary structure, 24 new potential miRNA were identified in J. curcas. Using the newly identified miRNA sequences, a total of 78 potential target genes were identified for 3 miRNA families. Most of the miRNA targeted genes were predicted to encode transcription factors that regulate cell growth and development, signaling, and metabolism. These findings considerably broaden the scope of understanding the functions of miRNA in J. curcas.
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Affiliation(s)
| | - Vasant J. Jadeja
- Department of Microbiology; Shree M. & N. Virani Science College; Rajkot, Gujarat, India
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25
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Identification and Characterization of MicroRNAs in Macaca fascicularis by EST Analysis. Comp Funct Genomics 2012; 2012:957607. [PMID: 22829752 PMCID: PMC3398586 DOI: 10.1155/2012/957607] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 04/16/2012] [Accepted: 04/30/2012] [Indexed: 01/18/2023] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs which repress gene expression at the posttranscriptional level. In this study, an expressed sequence tag (EST)-based combined method was applied for the detection of miRNAs in Macaca fascicularis which is used as a model animal extensively in medical experiments, particularly those involved with neuroscience and disease. Initially, previously known miRNA sequences from metazoans were used to blast with the EST databases of Macaca fascicularis, and then a range of filtering criteria was conducted to remove some pseudo ones. At last a total of 8 novel conserved miRNAs were identified; their functions were further predicted and analyzed. Together, our study provides insight into miRNAs and their functions in Macaca fascicularis, indicating that the EST analysis is an efficient and affordable alternative approach for identifying novel miRNA candidates.
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26
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Sahu S, Khushwaha A, Dixit R. Computational identification of miRNAs in medicinal plant Senecio vulgaris (Groundsel). Bioinformation 2011; 7:375-8. [PMID: 22347777 PMCID: PMC3280435 DOI: 10.6026/97320630007375] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 12/05/2011] [Indexed: 11/23/2022] Open
Abstract
RNAs Interference plays a very important role in gene silencing. In vitro identification of miRNAs is a slow process as it is difficult to isolate them. Nucleotide sequences of miRNAs are highly conserved among the plants and, this form the key feature behind the identification of miRNAs in plant species by homology alignment. In silico identification of miRNAs from EST database is emerging as a novel, faster and reliable approach. Here EST sequences of Senecio vulgaris (Groundsel) were searched against known miRNA sequences by using BLASTN tool. A total of 10 miRNAs were identified from 1956 EST sequences and 115 GSS sequences. The most stable miRNA identified is svu-mir-1. This approach will accelerate advance research in regulation of gene expression in Groundsel by interfering RNAs.
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Affiliation(s)
- Sarika Sahu
- Centre for Bioinformatics, Faculty of Biological Engineering, Shobhit University, Meerut
| | - Anjana Khushwaha
- Centre for Bioinformatics, Faculty of Biological Engineering, Shobhit University, Meerut
| | - Rekha Dixit
- School of Biotechnology, Faculty of Biological Engineering, Shobhit University, Meerut
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27
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Barrera-Figueroa BE, Gao L, Diop NN, Wu Z, Ehlers JD, Roberts PA, Close TJ, Zhu JK, Liu R. Identification and comparative analysis of drought-associated microRNAs in two cowpea genotypes. BMC PLANT BIOLOGY 2011; 11:127. [PMID: 21923928 PMCID: PMC3182138 DOI: 10.1186/1471-2229-11-127] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 09/17/2011] [Indexed: 05/18/2023]
Abstract
BACKGROUND Cowpea (Vigna unguiculata) is an important crop in arid and semi-arid regions and is a good model for studying drought tolerance. MicroRNAs (miRNAs) are known to play critical roles in plant stress responses, but drought-associated miRNAs have not been identified in cowpea. In addition, it is not understood how miRNAs might contribute to different capacities of drought tolerance in different cowpea genotypes. RESULTS We generated deep sequencing small RNA reads from two cowpea genotypes (CB46, drought-sensitive, and IT93K503-1, drought-tolerant) that grew under well-watered and drought stress conditions. We mapped small RNA reads to cowpea genomic sequences and identified 157 miRNA genes that belong to 89 families. Among 44 drought-associated miRNAs, 30 were upregulated in drought condition and 14 were downregulated. Although miRNA expression was in general consistent in two genotypes, we found that nine miRNAs were predominantly or exclusively expressed in one of the two genotypes and that 11 miRNAs were drought-regulated in only one genotype, but not the other. CONCLUSIONS These results suggest that miRNAs may play important roles in drought tolerance in cowpea and may be a key factor in determining the level of drought tolerance in different cowpea genotypes.
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Affiliation(s)
- Blanca E Barrera-Figueroa
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
- Departamento de Biotecnologia, Universidad del Papaloapan, Tuxtepec Oaxaca 68301, Mexico
| | - Lei Gao
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Ndeye N Diop
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Zhigang Wu
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Jeffrey D Ehlers
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Philip A Roberts
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Timothy J Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Jian-Kang Zhu
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Renyi Liu
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
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Kulcheski FR, de Oliveira LFV, Molina LG, Almerão MP, Rodrigues FA, Marcolino J, Barbosa JF, Stolf-Moreira R, Nepomuceno AL, Marcelino-Guimarães FC, Abdelnoor RV, Nascimento LC, Carazzolle MF, Pereira GAG, Margis R. Identification of novel soybean microRNAs involved in abiotic and biotic stresses. BMC Genomics 2011; 12:307. [PMID: 21663675 PMCID: PMC3141666 DOI: 10.1186/1471-2164-12-307] [Citation(s) in RCA: 201] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 06/10/2011] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Small RNAs (19-24 nt) are key regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in eukaryotes. Current studies have demonstrated that microRNAs (miRNAs) act in several plant pathways associated with tissue proliferation, differentiation, and development and in response to abiotic and biotic stresses. In order to identify new miRNAs in soybean and to verify those that are possibly water deficit and rust-stress regulated, eight libraries of small RNAs were constructed and submitted to Solexa sequencing. RESULTS The libraries were developed from drought-sensitive and tolerant seedlings and rust-susceptible and resistant soybeans with or without stressors. Sequencing the library and subsequent analyses detected 256 miRNAs. From this total, we identified 24 families of novel miRNAs that had not been reported before, six families of conserved miRNAs that exist in other plants species, and 22 families previously reported in soybean. We also observed the presence of several isomiRNAs during our analyses. To validate novel miRNAs, we performed RT-qPCR across the eight different libraries. Among the 11 miRNAs analyzed, all showed different expression profiles during biotic and abiotic stresses to soybean. The majority of miRNAs were up-regulated during water deficit stress in the sensitive plants. However, for the tolerant genotype, most of the miRNAs were down regulated. The pattern of miRNAs expression was also different for the distinct genotypes submitted to the pathogen stress. Most miRNAs were down regulated during the fungus infection in the susceptible genotype; however, in the resistant genotype, most miRNAs did not vary during rust attack. A prediction of the putative targets was carried out for conserved and novel miRNAs families. CONCLUSIONS Validation of our results with quantitative RT-qPCR revealed that Solexa sequencing is a powerful tool for miRNA discovery. The identification of differentially expressed plant miRNAs provides molecular evidence for the possible involvement of miRNAs in the process of water deficit- and rust-stress responses.
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Affiliation(s)
- Franceli R Kulcheski
- Centre of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Population, building 43431, Federal University of Rio Grande do Sul - UFRGS, P.O. Box 15005, CEP 91501-970, Porto Alegre, RS, Brazil
| | - Luiz FV de Oliveira
- Centre of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Population, building 43431, Federal University of Rio Grande do Sul - UFRGS, P.O. Box 15005, CEP 91501-970, Porto Alegre, RS, Brazil
- PPGGBM at Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Lorrayne G Molina
- Centre of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Population, building 43431, Federal University of Rio Grande do Sul - UFRGS, P.O. Box 15005, CEP 91501-970, Porto Alegre, RS, Brazil
- PPGGBM at Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Maurício P Almerão
- Centre of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Population, building 43431, Federal University of Rio Grande do Sul - UFRGS, P.O. Box 15005, CEP 91501-970, Porto Alegre, RS, Brazil
| | - Fabiana A Rodrigues
- EMBRAPA Soja, Rodovia Carlos João Strass, Distrito de Warta, CEP 86001-970, Londrina, PR, Brazil
| | - Juliana Marcolino
- EMBRAPA Soja, Rodovia Carlos João Strass, Distrito de Warta, CEP 86001-970, Londrina, PR, Brazil
| | - Joice F Barbosa
- EMBRAPA Soja, Rodovia Carlos João Strass, Distrito de Warta, CEP 86001-970, Londrina, PR, Brazil
| | - Renata Stolf-Moreira
- EMBRAPA Soja, Rodovia Carlos João Strass, Distrito de Warta, CEP 86001-970, Londrina, PR, Brazil
| | - Alexandre L Nepomuceno
- EMBRAPA Soja, Rodovia Carlos João Strass, Distrito de Warta, CEP 86001-970, Londrina, PR, Brazil
| | | | - Ricardo V Abdelnoor
- EMBRAPA Soja, Rodovia Carlos João Strass, Distrito de Warta, CEP 86001-970, Londrina, PR, Brazil
| | - Leandro C Nascimento
- Institute of Biology, Laboratory of Genomic and Expression, State University of Campinas, CEP 13083-970, Campinas, SP, Brazil
| | - Marcelo F Carazzolle
- Institute of Biology, Laboratory of Genomic and Expression, State University of Campinas, CEP 13083-970, Campinas, SP, Brazil
- National Center for High Performance Processing (CENAPAD-SP), State University of Campinas, CEP 13083-970, Campinas, SP, Brazil
| | - Gonçalo AG Pereira
- Institute of Biology, Laboratory of Genomic and Expression, State University of Campinas, CEP 13083-970, Campinas, SP, Brazil
| | - Rogério Margis
- Centre of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Population, building 43431, Federal University of Rio Grande do Sul - UFRGS, P.O. Box 15005, CEP 91501-970, Porto Alegre, RS, Brazil
- PPGGBM at Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
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Sahu S, Khushwaha A, Dixit R. Computational identification of miRNAs in medicinal plant Senecio vulgaris (Groundsel). Bioinformation 2011. [PMID: 22347777 DOI: 10.6026/bioinformation] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
RNAs Interference plays a very important role in gene silencing. In vitro identification of miRNAs is a slow process as it is difficult to isolate them. Nucleotide sequences of miRNAs are highly conserved among the plants and, this form the key feature behind the identification of miRNAs in plant species by homology alignment. In silico identification of miRNAs from EST database is emerging as a novel, faster and reliable approach. Here EST sequences of Senecio vulgaris (Groundsel) were searched against known miRNA sequences by using BLASTN tool. A total of 10 miRNAs were identified from 1956 EST sequences and 115 GSS sequences. The most stable miRNA identified is svu-mir-1. This approach will accelerate advance research in regulation of gene expression in Groundsel by interfering RNAs.
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