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Zhang X, Zhu X, Chen L, Fan H, Liu X, Yang N, Wang Y, Duan Y. Functional Identification of miR2119 Targeting ADHs in Modulating Soybean Resistance to Heterodera glycines. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:21461-21474. [PMID: 39311099 PMCID: PMC11450968 DOI: 10.1021/acs.jafc.4c05000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 09/07/2024] [Accepted: 09/17/2024] [Indexed: 10/03/2024]
Abstract
Soybean cyst nematode (SCN, Heterodera glycines) is a sedentary endoparasite nematode that results in severe economic losses in soybean crops. miRNAs play crucial roles in plant responses to nematode. However, the role of miR2119 responding to SCN stress in soybean. Here, we demonstrated that the transcript levels of polycistronic precursors containing miR2119 and miR398a were significantly reduced in soybean upon nematode infection. Promoter of the miR2119-398a precursor analysis was conducted containing a GUS reporter gene. GUS activity assays demonstrated a decrease in miR2119-398a promoter during SCN infection. Overexpression of polycistronic precursor miR2119-398a (OE-premiR2119-398a) and miR2119 precursor (OE-premiR2119) rendered soybean more susceptible to SCN. Conversely, silencing miR2119 (STTM2119) increased soybean resistance against SCN. Furthermore, RNA-seq analysis revealed that miR2119 is involved in many defense signaling pathways. GUS reporter gene assays demonstrated that miR2119 targets GmADH1.1a and GmADH1.1b. Functional analysis indicated that ADHs act as a major role in responding to H. glycines by modulating reactive oxygen species (ROS) levels. Together, the findings reveal a novel mechanism by which the polycistronic precursor miR2119-398a coordinately regulates in response to H. glycines. Additionally, miR2119 becomes an essential element contributing to H. glycines by modulating ADH activity and ROS homeostasis in soybean.
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Affiliation(s)
- Xiaoyu Zhang
- Nematology
Institute of Northern China, Shenyang Agricultural
University, Shenyang 110866, China
- College
of Plant Protection, Shenyang Agricultural
University, Shenyang 110866, China
| | - Xiaofeng Zhu
- Nematology
Institute of Northern China, Shenyang Agricultural
University, Shenyang 110866, China
- College
of Plant Protection, Shenyang Agricultural
University, Shenyang 110866, China
| | - Lijie Chen
- Nematology
Institute of Northern China, Shenyang Agricultural
University, Shenyang 110866, China
- College
of Plant Protection, Shenyang Agricultural
University, Shenyang 110866, China
| | - Haiyan Fan
- Nematology
Institute of Northern China, Shenyang Agricultural
University, Shenyang 110866, China
- College
of Plant Protection, Shenyang Agricultural
University, Shenyang 110866, China
| | - Xiaoyu Liu
- Nematology
Institute of Northern China, Shenyang Agricultural
University, Shenyang 110866, China
- College
of Sciences, Shenyang Agricultural University, Shenyang 110866, China
| | - Ning Yang
- Nematology
Institute of Northern China, Shenyang Agricultural
University, Shenyang 110866, China
- College
of Plant Protection, Shenyang Agricultural
University, Shenyang 110866, China
| | - Yuanyuan Wang
- Nematology
Institute of Northern China, Shenyang Agricultural
University, Shenyang 110866, China
- College
of Biological Science and Technology, Shenyang
Agricultural University, Shenyang 110866, China
| | - Yuxi Duan
- Nematology
Institute of Northern China, Shenyang Agricultural
University, Shenyang 110866, China
- College
of Plant Protection, Shenyang Agricultural
University, Shenyang 110866, China
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Unnikrishnan DK, Sreeharsha RV, Mudalkar S, Reddy AR. Flowering onset time is regulated by microRNA-mediated trehalose-6-phosphate signaling in Cajanus cajan L . under elevated CO 2. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:483-496. [PMID: 38633268 PMCID: PMC11018574 DOI: 10.1007/s12298-024-01434-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 02/24/2024] [Accepted: 03/05/2024] [Indexed: 04/19/2024]
Abstract
CO2 levels are known to have an impact on plant development and physiology. In the current study, we have investigated the effect of elevated CO2 on flowering and its regulation through miRNA mediated sugar signaling. We also unraveled small RNA transcriptome of pigeonpea under ambient and elevated CO2 conditions and predicted the targets for crucial miRNAs through computational methods. The results have shown that the delayed flowering in pigeonpea under elevated CO2 was due to an imbalance in C:N stoichiometry and differential expression pattern of aging pathway genes, including SQUAMOSA PROMOTER BINDING PROTEIN-LIKE. Furthermore, qRT PCR analysis has revealed the role of miR156 and miR172 in mediating trehalose-6-phosphate dependent flowering regulation. The current study is crucial in understanding the responses of flowering patterns in a legume crop to elevated CO2 which showed a significant impact on its final yields. Also, these findings are crucial in devising effective crop improvement strategies for developing climate resilient crops, including pigeonpea. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01434-9.
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Affiliation(s)
| | | | - Shalini Mudalkar
- Forest College and Research Institute, Hyderabad, Mulugu, Telangana 502279 India
| | - Attipalli R. Reddy
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 500049 India
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3
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Gutiérrez-García C, Ahmed SSSJ, Ramalingam S, Selvaraj D, Srivastava A, Paul S, Sharma A. Identification of microRNAs from Medicinal Plant Murraya koenigii by High-Throughput Sequencing and Their Functional Implications in Secondary Metabolite Biosynthesis. PLANTS (BASEL, SWITZERLAND) 2021; 11:plants11010046. [PMID: 35009050 PMCID: PMC8747174 DOI: 10.3390/plants11010046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/14/2021] [Accepted: 12/18/2021] [Indexed: 05/05/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNA molecules that play crucial post-transcriptional regulatory roles in plants, including development and stress-response signaling. However, information about their involvement in secondary metabolism is still limited. Murraya koenigii is a popular medicinal plant, better known as curry leaves, that possesses pharmaceutically active secondary metabolites. The present study utilized high-throughput sequencing technology to investigate the miRNA profile of M. koenigii and their association with secondary metabolite biosynthesis. A total of 343,505 unique reads with lengths ranging from 16 to 40 nt were obtained from the sequencing data, among which 142 miRNAs were identified as conserved and 7 as novel miRNAs. Moreover, 6078 corresponding potential target genes of M. koenigii miRNAs were recognized in this study. Interestingly, several conserved and novel miRNAs of M. koenigii were found to target key enzymes of the terpenoid backbone and the flavonoid biosynthesis pathways. Furthermore, to validate the sequencing results, the relative expression of eight randomly selected miRNAs was determined by qPCR. To the best of our knowledge, this is the first report of the M. koenigii miRNA profile that may provide useful information for further elucidation of the involvement of miRNAs in secondary metabolism. These findings might be crucial in the future to generate artificial-miRNA-based, genetically engineered M. koenigii plants for the overproduction of medicinally highly valuable secondary metabolites.
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Affiliation(s)
- Claudia Gutiérrez-García
- Tecnologico de Monterrey, Centre of Bioengineering, School of Engineering and Sciences, Queretaro CP 76130, Mexico;
| | - Shiek S. S. J. Ahmed
- Omics and Drug Discovery Lab, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam 603103, India;
| | - Sathishkumar Ramalingam
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore 641046, India; (S.R.); (D.S.)
| | - Dhivya Selvaraj
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore 641046, India; (S.R.); (D.S.)
| | - Aashish Srivastava
- Section of Bioinformatics, Clinical Laboratory, Haukeland University Hospital, 5021 Bergen, Norway;
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Sujay Paul
- Tecnologico de Monterrey, Centre of Bioengineering, School of Engineering and Sciences, Queretaro CP 76130, Mexico;
- Correspondence: (S.P.); (A.S.)
| | - Ashutosh Sharma
- Tecnologico de Monterrey, Centre of Bioengineering, School of Engineering and Sciences, Queretaro CP 76130, Mexico;
- Correspondence: (S.P.); (A.S.)
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4
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Rawal HC, Ali S, Mondal TK. miRPreM and tiRPreM: Improved methodologies for the prediction of miRNAs and tRNA-induced small non-coding RNAs for model and non-model organisms. Brief Bioinform 2021; 23:6420093. [PMID: 34734232 DOI: 10.1093/bib/bbab448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/15/2021] [Accepted: 09/28/2021] [Indexed: 11/12/2022] Open
Abstract
In recent years, microRNAs (miRNAs) and tRNA-derived RNA fragments (tRFs) have been reported extensively following different approaches of identification and analysis. Comprehensively analyzing the present approaches to overcome the existing variations, we developed a benchmarking methodology each for the identification of miRNAs and tRFs, termed as miRNA Prediction Methodology (miRPreM) and tRNA-induced small non-coding RNA Prediction Methodology (tiRPreM), respectively. We emphasized the use of respective genome of organism under study for mapping reads, sample data with at least two biological replicates, normalized read count support and novel miRNA prediction by two standard tools with multiple runs. The performance of these methodologies was evaluated by using Oryza coarctata, a wild rice species as a case study for model and non-model organisms. With organism-specific reference genome approach, 98 miRNAs and 60 tRFs were exclusively found. We observed high accuracy (13 out of 15) when tested these genome-specific miRNAs in support of analyzing the data with respective organism. Such a strong impact of miRPreM, we have predicted more than double number of miRNAs (186) as compared with the traditional approaches (79) and with tiRPreM, we have predicted all known classes of tRFs within the same small RNA data. Moreover, the methodologies presented here are in standard form in order to extend its applicability to different organisms rather than restricting to plants. Hence, miRPreM and tiRPreM can fulfill the need of a comprehensive methodology for miRNA prediction and tRF identification, respectively, for model and non-model organisms.
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Affiliation(s)
- Hukam Chand Rawal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India.,School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Shakir Ali
- School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India.,Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Tapan Kumar Mondal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India
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Chand Jha U, Nayyar H, Mantri N, Siddique KHM. Non-Coding RNAs in Legumes: Their Emerging Roles in Regulating Biotic/Abiotic Stress Responses and Plant Growth and Development. Cells 2021; 10:cells10071674. [PMID: 34359842 PMCID: PMC8306516 DOI: 10.3390/cells10071674] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 12/28/2022] Open
Abstract
Noncoding RNAs, including microRNAs (miRNAs), small interference RNAs (siRNAs), circular RNA (circRNA), and long noncoding RNAs (lncRNAs), control gene expression at the transcription, post-transcription, and translation levels. Apart from protein-coding genes, accumulating evidence supports ncRNAs playing a critical role in shaping plant growth and development and biotic and abiotic stress responses in various species, including legume crops. Noncoding RNAs (ncRNAs) interact with DNA, RNA, and proteins, modulating their target genes. However, the regulatory mechanisms controlling these cellular processes are not well understood. Here, we discuss the features of various ncRNAs, including their emerging role in contributing to biotic/abiotic stress response and plant growth and development, in addition to the molecular mechanisms involved, focusing on legume crops. Unravelling the underlying molecular mechanisms and functional implications of ncRNAs will enhance our understanding of the coordinated regulation of plant defences against various biotic and abiotic stresses and for key growth and development processes to better design various legume crops for global food security.
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MESH Headings
- Fabaceae/genetics
- Fabaceae/growth & development
- Fabaceae/metabolism
- Food Security
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Plant
- Humans
- MicroRNAs/classification
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Organ Specificity
- Protein Biosynthesis
- RNA, Circular/classification
- RNA, Circular/genetics
- RNA, Circular/metabolism
- RNA, Long Noncoding/classification
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Plant/classification
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Small Interfering/classification
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Species Specificity
- Stress, Physiological/genetics
- Transcription, Genetic
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Affiliation(s)
- Uday Chand Jha
- ICAR—Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
- Correspondence: (U.C.J.); (K.H.M.S.)
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh 160014, India;
| | - Nitin Mantri
- School of Science, RMIT University, Melbourne 3083, Australia;
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth 6001, Australia
- Correspondence: (U.C.J.); (K.H.M.S.)
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Paul S, Reyes-Pérez P, Angulo-Bejarano PI, Srivastava A, Ramalingam S, Sharma A. Characterization of microRNAs from neem ( Azadirachta indica) and their tissue-specific expression study in leaves and stem. 3 Biotech 2021; 11:277. [PMID: 34040926 DOI: 10.1007/s13205-021-02839-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/08/2021] [Indexed: 01/29/2023] Open
Abstract
Neem (Azadirachta indica) is a very popular traditional medicinal plant used since ancient times to treat numerous ailments. MicroRNAs (miRNAs) are highly conserved, non-coding, short RNA molecules that play important regulatory roles in plant development and metabolism. In this study, deploying a high stringent genome-wide computational-based approach and following a set of strict filtering norms a total of 44 potential conserved neem miRNAs belonging to 21 families and their corresponding 48 potential target transcripts were identified. Important targets include Squamosa promoter binding protein-like proteins, NAC, Scarecrow proteins, Auxin response factor, and F-box proteins. A biological network has also been developed to understand the miRNA-mediated gene regulation using the minimum free energy (MFE) values of the miRNA-target interaction. Moreover, six selected miRNAs were reported to be involved in secondary metabolism in other plant species (miR156a, miR156l, miR160, miR164, miR171, miR395) were validated by qPCR and their tissue-specific differential expression pattern was observed in leaves and stem. Except for ain-miR395, all the other miRNAs were found overexpressed in the stem as compared to leaves. To the best of our knowledge, this is the first report of neem miRNAs and we believe the finding of the present study will be useful for the functional genomic study of medicinal plants. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02839-z.
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Affiliation(s)
- Sujay Paul
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, 76130 Queretaro, CP Mexico
| | - Paula Reyes-Pérez
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, 76130 Queretaro, CP Mexico
| | - Paola Isabel Angulo-Bejarano
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, 76130 Queretaro, CP Mexico
| | - Aashish Srivastava
- Section of Bioinformatics, Clinical Laboratory, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Sathishkumar Ramalingam
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Ashutosh Sharma
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, 76130 Queretaro, CP Mexico
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7
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De la Rosa C, Lozano L, Castillo-Ramírez S, Covarrubias AA, Reyes JL. Origin and Evolutionary Dynamics of the miR2119 and ADH1 Regulatory Module in Legumes. Genome Biol Evol 2020; 12:2355-2369. [PMID: 33045056 PMCID: PMC7846098 DOI: 10.1093/gbe/evaa205] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2020] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs are important regulators of gene expression in eukaryotes. Previously, we reported that in Phaseolus vulgaris, the precursor for miR2119 is located in the same gene as miR398a, conceiving a dicistronic MIR gene. Both miRNA precursors are transcribed and processed from a single transcript resulting in two mature microRNAs that regulate the mRNAs encoding ALCOHOL DEHYDROGENASE 1 (ADH1) and COPPER-ZINC SUPEROXIDE DISMUTASE 1 (CSD1). Genes for miR398 are distributed throughout the spermatophytes; however, miR2119 is only found in Leguminosae species, indicating its recent emergence. Here, we used public databases to explore the presence of the miR2119 sequence in several plant species. We found that miR2119 is present only in specific clades within the Papilionoideae subfamily, including important crops used for human consumption and forage. Within this subfamily, MIR2119 and MIR398a are found together as a single gene in the genomes of the Millettioids and Hologalegina. In contrast, in the Dalbergioids MIR2119 is located in a different locus from MIR398a, suggesting this as the ancestral genomic organization. To our knowledge, this is a unique example where two separate MIRNA genes have merged to generate a single polycistronic gene. Phylogenetic analysis of ADH1 gene sequences in the Papilionoideae subfamily revealed duplication events resulting in up to four ADH1 genes in certain species. Notably, the presence of MIR2119 correlates with the conservation of target sites in particular ADH1 genes in each clade. Our results suggest that post-transcriptional regulation of ADH1 genes by miR2119 has contributed to shaping the expansion and divergence of this gene family in the Papilionoideae. Future experimental work on ADH1 regulation by miR2119 in more legume species will help to further understand the evolutionary history of the ADH1 gene family and the relevance of miRNA regulation in this process.
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Affiliation(s)
- Carlos De la Rosa
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis D. Colosio S/N entre Reforma y Sahuaripa, Col Centro, Hermosillo, Mexico
| | - Luis Lozano
- Luis Lozano Unidad de Análisis Bioinformáticos, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, México.,Santiago Castillo Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, Mexico
| | - Santiago Castillo-Ramírez
- Luis Lozano Unidad de Análisis Bioinformáticos, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, México.,Santiago Castillo Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, Mexico
| | - Alejandra A Covarrubias
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - José L Reyes
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Sangita Chowdhury Paul, Sharma A, Mehta R, Paul S. In silico Characterization of microRNAs and Their Target Transcripts from Cranberry (Vaccinium macrocarpon). CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720010120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Choudhary S, Thakur S, Majeed A, Bhardwaj P. Exploring microRNA profiles for circadian clock and flowering development regulation in Himalayan Rhododendron. Genomics 2019; 111:1456-1463. [DOI: 10.1016/j.ygeno.2018.09.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/23/2018] [Accepted: 09/25/2018] [Indexed: 12/19/2022]
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10
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DeBoer K, Melser S, Sperschneider J, Kamphuis LG, Garg G, Gao LL, Frick K, Singh KB. Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development. BMC Genomics 2019; 20:135. [PMID: 30764773 PMCID: PMC6376761 DOI: 10.1186/s12864-019-5521-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 02/07/2019] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Whilst information regarding small RNAs within agricultural crops is increasing, the miRNA composition of the nutritionally valuable pulse narrow-leafed lupin (Lupinus angustifolius) remains unknown. RESULTS By conducting a genome- and transcriptome-wide survey we identified 7 Dicer-like and 16 Argonaute narrow-leafed lupin genes, which were highly homologous to their legume counterparts. We identified 43 conserved miRNAs belonging to 16 families, and 13 novel narrow-leafed lupin-specific miRNAs using high-throughput sequencing of small RNAs from foliar and root and five seed development stages. We observed up-regulation of members of the miRNA families miR167, miR399, miR156, miR319 and miR164 in narrow-leafed lupin seeds, and confirmed expression of miR156, miR166, miR164, miR1507 and miR396 using quantitative RT-PCR during five narrow-leafed lupin seed development stages. We identified potential targets for the conserved and novel miRNAs and were able to validate targets of miR399 and miR159 using 5' RLM-RACE. The conserved miRNAs are predicted to predominately target transcription factors and 93% of the conserved miRNAs originate from intergenic regions. In contrast, only 43% of the novel miRNAs originate from intergenic regions and their predicted targets were more functionally diverse. CONCLUSION This study provides important insights into the miRNA gene regulatory networks during narrow-leafed lupin seed development.
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Affiliation(s)
- Kathleen DeBoer
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA 6009 Australia
| | - Su Melser
- CSIRO Agriculture and Food, Private Bag 5, Wembley, WA 6913 Australia
- Present address: INSERM U1215, Neurocentre Magendie, Bordeaux, France
| | - Jana Sperschneider
- Centre for Genomics, Metabolomics and Bioinformatics (CGMB), The Australian National University, Canberra, ACT 2601 Australia
| | - Lars G. Kamphuis
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA 6009 Australia
- CSIRO Agriculture and Food, Private Bag 5, Wembley, WA 6913 Australia
- Curtin University, Centre for Crop and Disease Management, Department of Environment and Agriculture, Bentley, WA 6102 Australia
| | - Gagan Garg
- CSIRO Agriculture and Food, Private Bag 5, Wembley, WA 6913 Australia
| | - Ling-Ling Gao
- CSIRO Agriculture and Food, Private Bag 5, Wembley, WA 6913 Australia
| | - Karen Frick
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA 6009 Australia
- CSIRO Agriculture and Food, Private Bag 5, Wembley, WA 6913 Australia
- The School of Plant Biology, University of Western Australia, Crawley, WA 6009 Australia
| | - Karam B. Singh
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA 6009 Australia
- CSIRO Agriculture and Food, Private Bag 5, Wembley, WA 6913 Australia
- Curtin University, Centre for Crop and Disease Management, Department of Environment and Agriculture, Bentley, WA 6102 Australia
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11
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Wei W, Li G, Jiang X, Wang Y, Ma Z, Niu Z, Wang Z, Geng X. Small RNA and degradome profiling involved in seed development and oil synthesis of Brassica napus. PLoS One 2018; 13:e0204998. [PMID: 30332454 PMCID: PMC6192625 DOI: 10.1371/journal.pone.0204998] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 09/18/2018] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNAs) play a prominent role in post-transcriptional gene expression regulation and have been involved in various biological and metabolic processes to regulate gene expression. For Brassica napus, improving seed-weight and oil-content is the main breeding goal. In order to better understand the regulation mechanism of miRNAs during seed-weight formation and oil-content accumulation in B. napus, in this study, a high-throughput sequencing technology was used to profile miRNAs expression of Brassica napus immature seeds from one to six weeks after flowering. A total of 1,276 miRNAs, including 1,248 novel and 28 known miRNAs, were obtained from both the high-seed-weight with low-oil-content RNA pool (S03) and the low-seed-weight with high-oil-content RNA pool (S04). Analysis of their expression profiles disclosed that 300 novel and two known miRNAs were differentially expressed between S03 and S04. For degradome analysis, 57 genes with 64 degradation sites were predicted to be targeted for degradation by these miRNAs. Further bioinformatics analysis indicated that these differentially expressed miRNAs might participate in regulation of myriad cellular and molecular processes, during seed development and oil synthesis. Finally, 6 target genes with potential roles in regulation of seed development and 9 other targets in seed oil synthesis, were further confirmed as candidate genes from small RNA and degradome sequencing.
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Affiliation(s)
- Wenhui Wei
- College of Life Science and Technology, Henan Institute of Science and Technology / Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Xinxiang, China
| | - Gan Li
- College of Life Science and Technology, Henan Institute of Science and Technology / Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Xinxiang, China
| | - Xiaoling Jiang
- College of Life Science and Technology, Henan Institute of Science and Technology / Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Xinxiang, China
| | - Yuquan Wang
- College of Life Science and Technology, Henan Institute of Science and Technology / Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Xinxiang, China
| | - Zhihui Ma
- College of Life Science and Technology, Henan Institute of Science and Technology / Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Xinxiang, China
| | - Zhipeng Niu
- College of Life Science and Technology, Henan Institute of Science and Technology / Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Xinxiang, China
| | - Zhiwei Wang
- College of Life Science and Technology, Henan Institute of Science and Technology / Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Xinxiang, China
| | - Xinxin Geng
- Applied Biotechnology Center, Wuhan Institute of Bioengineering, Wuhan, China
- * E-mail:
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Wu F, Luo K, Yan Z, Zhang D, Yan Q, Zhang Y, Yi X, Zhang J. Analysis of miRNAs and their target genes in five Melilotus albus NILs with different coumarin content. Sci Rep 2018; 8:14138. [PMID: 30237524 PMCID: PMC6147922 DOI: 10.1038/s41598-018-32153-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 09/03/2018] [Indexed: 11/14/2022] Open
Abstract
MicroRNAs (miRNAs) exhibit diverse and important roles in regulation of various biological processes at the post-transcriptional level in plants. In this study, Melilotus albus miRNA and their target genes were elucidated from five M. albus near-isogenic lines which differ in coumarin content to construct small RNA libraries through high-throughput sequencing. A total of 417 known miRNAs and 76 novel miRNAs were identified in M. albus. In addition, 4155 different target genes for 114 known miRNA families and 14 target genes for 2 novel miRNAs were identified in M. albus. Moreover, mtr-miR5248 and mtr-miR7701-5p target c35498_g3 and gma-miR396a-3p target c37211_g1 involved in coumarin biosynthesis were identified by using the differential expression of the miRNAs and their target genes correlation analysis. The abundance of miRNAs and potential target genes were validated by qRT-PCR analysis. We also found that there were both positive and negative expression changing patterns between miRNAs and their related target genes. Our first and preliminary study of miRNAs will contribute to our understanding of the functions and molecular regulatory mechanisms of miRNAs and their target genes, and provide information on regulating the complex coumarin pathway in M. albus for future research.
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Affiliation(s)
- Fan Wu
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Kai Luo
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Zhuanzhuan Yan
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Daiyu Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Qi Yan
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Yufei Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Xianfeng Yi
- Guangxi Institute of Animal Sciences, Nanning, 530001, P.R. China.
| | - Jiyu Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China.
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13
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Patwa N, Nithin C, Bahadur RP, Basak J. Identification and characterization of differentially expressed Phaseolus vulgaris miRNAs and their targets during mungbean yellow mosaic India virus infection reveals new insight into Phaseolus-MYMIV interaction. Genomics 2018; 111:1333-1342. [PMID: 30237075 DOI: 10.1016/j.ygeno.2018.09.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/17/2018] [Accepted: 09/09/2018] [Indexed: 02/06/2023]
Abstract
Phaseolus vulgaris is an economically important legume in tropical and subtropical regions of Asia, Africa, Latin-America and parts of USA and Europe. However, its production gets severely affected by mungbean yellow mosaic India virus (MYMIV). We aim to identify and characterize differentially expressed miRNAs during MYMIV-infection in P. vulgaris. A total of 422 miRNAs are identified of which 292 are expressed in both MYMIV-treated and mock-treated samples, 109 are expressed only in MYMIV-treated and 21 are expressed only in mock-treated samples. Selected up- and down-regulated miRNAs are validated by RT-qPCR. 3367 target ORFs are identified for 270 miRNAs. Selected targets are validated by 5' RLM-RACE. Differentially expressed miRNAs regulate transcription factors and are involved in improving stress tolerance to MYMIV. These findings will provide an insight into the role of miRNAs during MYMIV infection in P. vulgaris in particular and during any biotic stress conditions in Leguminosae family in general.
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Affiliation(s)
- Nisha Patwa
- Laboratory of Plant Stress Biology, Department of Biotechnology, Visva-Bharati, Santiniketan 731235, India
| | - Chandran Nithin
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, 721302, India
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, 721302, India
| | - Jolly Basak
- Laboratory of Plant Stress Biology, Department of Biotechnology, Visva-Bharati, Santiniketan 731235, India.
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14
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Ghorecha V, Zheng Y, Liu L, Sunkar R, Krishnayya NSR. MicroRNA dynamics in a wild and cultivated species of Convolvulaceae exposed to drought stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:291-300. [PMID: 28461718 PMCID: PMC5391358 DOI: 10.1007/s12298-017-0426-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 02/14/2017] [Accepted: 03/03/2017] [Indexed: 05/14/2023]
Abstract
Agricultural productivity is severely hampered by drought in many parts of the globe. It is well-known that wild plant species can tolerate drought better when compared with their closely related cultivated plant species. Better drought adaptation of wild species over cultivated ones is accounted for their ability to differentially regulate gene expression. miRNAs, known to regulate gene expression at the post-transcriptional level, are admitted to play an important role in plant adaptation to stresses. This study aims at evaluating miRNA dynamics in a drought-tolerant wild Ipomoea campanulata L. and drought-sensitive cultivated Jacquemontia pentantha (Jacq.) of the family Convolvulaceae under ex situ drought. Sequencing profiles revealed that 34 conserved miRNA families were analogous between the two species. Drought altered expression levels of several of these miRNAs in both the species. Drought-tolerant I. campanulata showed upregulation of miR398, miR168, miR858, miR162 and miR408, while miR394 and miR171 were downregulated. Drought-sensitive J. pentantha showed upregulation of miR394, miR156, miR160, miR164, miR167, miR172, miR319, miR395, miR396, miR403 and downregulation of miR157. Basal miRNA levels and their drought mediated regulation were very different between the two species. Differential drought sensitivities of these two plant species can be attributed to these innate variations in miRNA levels and their expression.
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Affiliation(s)
- Vallabhi Ghorecha
- Ecology Laboratory, Botany Department, Faculty of Science, M.S. University of Baroda, Baroda, 390002 India
| | - Yun Zheng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727, South Jingming Road, Kunming, 650500 Yunnan China
| | - Li Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727, South Jingming Road, Kunming, 650500 Yunnan China
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74074 USA
| | - N. S. R. Krishnayya
- Ecology Laboratory, Botany Department, Faculty of Science, M.S. University of Baroda, Baroda, 390002 India
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15
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Kundu A, Paul S, Dey A, Pal A. High throughput sequencing reveals modulation of microRNAs in Vigna mungo upon Mungbean Yellow Mosaic India Virus inoculation highlighting stress regulation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 257:96-105. [PMID: 28224923 DOI: 10.1016/j.plantsci.2017.01.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/23/2017] [Accepted: 01/28/2017] [Indexed: 05/21/2023]
Abstract
MicroRNAs (miRNAs) are 20-24 nucleotides long non-coding RNAs known to play important regulatory roles during biotic and abiotic stresses by controlling gene expression. Blackgram (Vigna mungo), an economically important grain legume is highly susceptible to pathogenic begomovirus Mungbean Yellow Mosaic India Virus (MYMIV) and resulting in high yield loss. In this study two different leaf-small-RNA libraries were prepared from the pooled RNA at three different time points of resistant V. mungo inbred line VM84 inoculated either with viruliferous or non-viruliferous whiteflies carrying MYMIV and performed high-throughput Illumina sequencing. Sequencing followed by bioinformatics analysis of the small RNA reads indicated that the expression patterns of most of the known and novel miRNAs were altered in resistant line over mock-inoculated sample during the plant virus incompatible interaction. Highly altered miRNAs belong to the families of miR156, miR159, miR160, miR166, miR398, miR1511, miR1514, miR2118 and novel vmu-miRn7, vmu-miRn8, vmu-miRn13 and vmu-miRn14. These results were validated using qPCR, and most of the miRNAs showed similar pattern of expression like that of Illumina reads. The expression patterns of some selected known and novel miRNAs were also compared between the infected MYMIV-resistant and -susceptible genotypes and most of these were modulated after MYMIV-inoculation. Target transcripts like NB-LRR, NAC, MYB, Zinc finger, CCAAT-box transcription factor, fructose 2-6 bisphosphate, HDZIP protein that confers immune response were predicted as targets amongst identified miRNAs using psRNATarget server. Some selected target transcripts including NB-LRR, ARF, SOD, SPB, Basic blue copper protein were validated and their differential expression were demonstrated between MYMIV-resistant and -susceptible V. mungo by qPCR data analyses. In the present study we have identified miRNAs that implicate in the regulation of MYMIV-induced stress response in V. mungo; and generated genomic resources for a non-model legume with the aid of bioinformatics tools supplemented by experimental validation.
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Affiliation(s)
- Anirban Kundu
- Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VII M, Kolkata, 700054, India; Ramakrishna Mission Vivekananda Centenary College, Rahara, Kolkata, 7000118, India
| | - Sujay Paul
- Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VII M, Kolkata, 700054, India; Laboratorio de Micología y Biotecnología, Universidad Nacional Agraria La Molina, Av. La Molina s/n, Lima, 12, Peru.
| | - Avishek Dey
- Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VII M, Kolkata, 700054, India
| | - Amita Pal
- Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VII M, Kolkata, 700054, India.
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16
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Wang W, Xia MX, Chen J, Yuan R, Deng FN, Shen FF. Gene Expression Characteristics and Regulation Mechanisms of Superoxide Dismutase and Its Physiological Roles in Plants under Stress. BIOCHEMISTRY (MOSCOW) 2017; 81:465-80. [PMID: 27297897 DOI: 10.1134/s0006297916050047] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Superoxide dismutases (SODs) are key enzymes functioning as the first line of antioxidant defense by virtue of the ability to convert highly reactive superoxide radicals to hydrogen peroxide and molecular oxygen. SOD plays a central role in protecting plants against the toxic effects of reactive oxygen species generated during normal cellular metabolic activity or as a result of various environmental stresses. Our review focuses on the characteristics of expression of SOD genes, the mechanisms regulating expression of SOD genes at transcriptional, posttranscriptional, and translation levels, and their functional role(s) during development and in response to biotic or abiotic stresses. We propose two important research directions: studying SOD at the genome-wide or proteome-wide level, and improving plant stress tolerances by selecting varieties using transgenic technology.
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Affiliation(s)
- W Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
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17
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Kundu A, Paul S, Pal A, Technology G. Mungbean Yellow Mosaic India Virus (MYMIV)-infection, Small RNA Library Construction and Deep Sequencing for MicroRNA Identification in Vigna mungo. Bio Protoc 2016. [DOI: 10.21769/bioprotoc.1961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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18
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Usha S, Jyothi MN, Sharadamma N, Dixit R, Devaraj VR, Nagesh Babu R. Identification of microRNAs and their targets in Finger millet by high throughput sequencing. Gene 2015; 574:210-6. [PMID: 26255946 DOI: 10.1016/j.gene.2015.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 08/03/2015] [Accepted: 08/05/2015] [Indexed: 12/27/2022]
Abstract
MicroRNAs are short non-coding RNAs which play an important role in regulating gene expression by mRNA cleavage or by translational repression. The majority of identified miRNAs were evolutionarily conserved; however, others expressed in a species-specific manner. Finger millet is an important cereal crop; nonetheless, no practical information is available on microRNAs to date. In this study, we have identified 95 conserved microRNAs belonging to 39 families and 3 novel microRNAs by high throughput sequencing. For the identified conserved and novel miRNAs a total of 507 targets were predicted. 11 miRNAs were validated and tissue specificity was determined by stem loop RT-qPCR, Northern blot. GO analyses revealed targets of miRNA were involved in wide range of regulatory functions. This study implies large number of known and novel miRNAs found in Finger millet which may play important role in growth and development.
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Affiliation(s)
- S Usha
- Post Graduate Department of Biochemistry, Maharani's Science College for Women, Bangalore 560001, India; Centre for Bioinformatics, Faculty of Biological Engineering, Shobhit University, Meerut, 250110 India
| | - M N Jyothi
- Post Graduate Department of Biochemistry, Maharani's Science College for Women, Bangalore 560001, India; Centre for Bioinformatics, Faculty of Biological Engineering, Shobhit University, Meerut, 250110 India
| | - N Sharadamma
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012 India
| | - Rekha Dixit
- Centre for Bioinformatics, Faculty of Biological Engineering, Shobhit University, Meerut, 250110 India
| | - V R Devaraj
- Department of Biochemistry, Central College Campus, Bangalore University, Bangalore 560001 India
| | - R Nagesh Babu
- Post Graduate Department of Biochemistry, Maharani's Science College for Women, Bangalore 560001, India.
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19
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Souframanien J, Reddy KS. De novo Assembly, Characterization of Immature Seed Transcriptome and Development of Genic-SSR Markers in Black Gram [Vigna mungo (L.) Hepper]. PLoS One 2015; 10:e0128748. [PMID: 26042595 PMCID: PMC4456365 DOI: 10.1371/journal.pone.0128748] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 05/01/2015] [Indexed: 12/02/2022] Open
Abstract
Black gram [V. mungo (L.) Hepper] is an important legume crop extensively grown in south and south-east Asia, where it is a major source of dietary protein for its predominantly vegetarian population. However, lack of genomic information and markers has become a limitation for genetic improvement of this crop. Here, we report the transcriptome sequencing of the immature seeds of black gram cv. TU94-2, by Illumina paired end sequencing technology to generate transcriptome sequences for gene discovery and genic-SSR marker development. A total of 17.2 million paired-end reads were generated and 48,291 transcript contigs (TCS) were assembled with an average length of 443 bp. Based on sequence similarity search, 33,766 TCS showed significant similarity to known proteins. Among these, only 29,564 TCS were annotated with gene ontology (GO) functional categories. A total number of 138 unique KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were identified, of which majority of TCS are grouped into purine metabolism (678) followed by pyrimidine metabolism (263). A total of 48,291 TCS were searched for SSRs and 1,840 SSRs were identified in 1,572 TCS with an average frequency of one SSR per 11.9 kb. The tri-nucleotide repeats were most abundant (35%) followed by di-nucleotide repeats (32%). PCR primer pairs were successfully designed for 933 SSR loci. Sequences analyses indicate that about 64.4% and 35.6% of the SSR motifs were present in the coding sequences (CDS) and untranslated regions (UTRs) respectively. Tri-nucleotide repeats (57.3%) were preferentially present in the CDS. The rate of successful amplification and polymorphism were investigated using selected primers among 18 black gram accessions. Genic-SSR markers developed from the Illumina paired end sequencing of black gram immature seed transcriptome will provide a valuable resource for genetic diversity, evolution, linkage mapping, comparative genomics and marker-assisted selection in black gram.
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Affiliation(s)
- J. Souframanien
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai-400085, India
- * E-mail:
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20
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High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute. Int J Genomics 2015; 2015:125048. [PMID: 25861616 PMCID: PMC4378336 DOI: 10.1155/2015/125048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 02/13/2015] [Accepted: 02/23/2015] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. A group of plant microRNAs are evolutionarily conserved; however, others are expressed in a species-specific manner. Jute is an agroeconomically important fibre crop; nonetheless, no practical information is available for microRNAs in jute to date. In this study, Illumina sequencing revealed a total of 227 known microRNAs and 17 potential novel microRNA candidates in jute, of which 164 belong to 23 conserved families and the remaining 63 belong to 58 nonconserved families. Among a total of 81 identified microRNA families, 116 potential target genes were predicted for 39 families and 11 targets were predicted for 4 among the 17 identified novel microRNAs. For understanding better the functions of microRNAs, target genes were analyzed by Gene Ontology and their pathways illustrated by KEGG pathway analyses. The presence of microRNAs identified in jute was validated by stem-loop RT-PCR followed by end point PCR and qPCR for randomly selected 20 known and novel microRNAs. This study exhaustively identifies microRNAs and their target genes in jute which will ultimately pave the way for understanding their role in this crop and other crops.
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21
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Identification of conserved and novel microRNAs in Catharanthus roseus by deep sequencing and computational prediction of their potential targets. Gene 2014; 554:181-95. [PMID: 25445288 DOI: 10.1016/j.gene.2014.10.046] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 10/08/2014] [Accepted: 10/25/2014] [Indexed: 12/14/2022]
Abstract
MicroRNAs are small endogenous non-coding RNAs of ~19-24 nucleotides and perform regulatory roles in many plant processes. To identify miRNAs involved in regulatory networks controlling diverse biological processes including secondary metabolism in Catharanthus roseus, an important medicinal plant, we employed deep sequencing of small RNA from leaf tissue. A total of 88 potential miRNAs comprising of 81 conserved miRNAs belonging to 35 families and seven novel miRNAs were identified. Precursors for 16 conserved and seven novel cro-miRNAs were identified, and their stem-loop hairpin structures were predicted. Selected cro-miRNAs were analyzed by stem-loop qRT-PCR and differential expression patterns were observed in different vegetative tissues of C. roseus. Targets were predicted for conserved and novel cro-miRNAs, which were found to be involved in diverse biological role(s) including secondary metabolism. Our study enriches available resources and information regarding miRNAs and their potential targets for better understanding of miRNA-mediated gene regulation in plants.
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22
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Bohra A, Jha UC, Kishor PBK, Pandey S, Singh NP. Genomics and molecular breeding in lesser explored pulse crops: current trends and future opportunities. Biotechnol Adv 2014; 32:1410-28. [PMID: 25196916 DOI: 10.1016/j.biotechadv.2014.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 08/29/2014] [Accepted: 09/01/2014] [Indexed: 12/17/2022]
Abstract
Pulses are multipurpose crops for providing income, employment and food security in the underprivileged regions, notably the FAO-defined low-income food-deficit countries. Owing to their intrinsic ability to endure environmental adversities and the least input/management requirements, these crops remain central to subsistence farming. Given their pivotal role in rain-fed agriculture, substantial research has been invested to boost the productivity of these pulse crops. To this end, genomic tools and technologies have appeared as the compelling supplement to the conventional breeding. However, the progress in minor pulse crops including dry beans (Vigna spp.), lupins, lablab, lathyrus and vetches has remained unsatisfactory, hence these crops are often labeled as low profile or lesser researched. Nevertheless, recent scientific and technological breakthroughs particularly the next generation sequencing (NGS) are radically transforming the scenario of genomics and molecular breeding in these minor crops. NGS techniques have allowed de novo assembly of whole genomes in these orphan crops. Moreover, the availability of a reference genome sequence would promote re-sequencing of diverse genotypes to unlock allelic diversity at a genome-wide scale. In parallel, NGS has offered high-resolution genetic maps or more precisely, a robust genetic framework to implement whole-genome strategies for crop improvement. As has already been demonstrated in lupin, sequencing-based genotyping of the representative sample provided access to a number of functionally-relevant markers that could be deployed straight away in crop breeding programs. This article attempts to outline the recent progress made in genomics of these lesser explored pulse crops, and examines the prospects of genomics assisted integrated breeding to enhance and stabilize crop yields.
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Affiliation(s)
- Abhishek Bohra
- Indian Institute of Pulses Research (IIPR), Kanpur 208024, India.
| | - Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
| | - P B Kavi Kishor
- Department of Genetics, Osmania University, Hyderabad 500007, India
| | | | - Narendra P Singh
- Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
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23
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Brandt R, Cabedo M, Xie Y, Wenkel S. Homeodomain leucine-zipper proteins and their role in synchronizing growth and development with the environment. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:518-26. [PMID: 24528801 DOI: 10.1111/jipb.12185] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 01/25/2014] [Indexed: 05/21/2023]
Abstract
The Arabidopsis (Arabidopsis thaliana L.) genome encodes for four distinct classes of homeodomain leucine-zipper (HD-ZIP) transcription factors (HD-ZIPI to HD-ZIPIV), which are all organized in multi-gene families. HD-ZIP transcription factors act as sequence-specific DNA-binding proteins that are able to control the expression level of target genes. While HD-ZIPI and HD-ZIPII proteins are mainly associated with environmental responses, HD-ZIPIII and HD-ZIPIV are primarily known to act as patterning factors. Recent studies have challenged this view. It appears that several of the different HD-ZIP families interact genetically to align both morphogenesis and environmental responses, most likely by modulating phytohormone-signaling networks.
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Affiliation(s)
- Ronny Brandt
- Center for Plant Molecular Biology, University of Tübingen, Germany; Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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24
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Naya L, Paul S, Valdés-López O, Mendoza-Soto AB, Nova-Franco B, Sosa-Valencia G, Reyes JL, Hernández G. Regulation of copper homeostasis and biotic interactions by microRNA 398b in common bean. PLoS One 2014; 9:e84416. [PMID: 24400089 PMCID: PMC3882225 DOI: 10.1371/journal.pone.0084416] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 11/19/2013] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs are recognized as important post-transcriptional regulators in plants. Information about the roles of miRNAs in common bean (Phaseolus vulgaris L.), an agronomically important legume, is yet scant. The objective of this work was to functionally characterize the conserved miRNA: miR398b and its target Cu/Zn Superoxide Dismutase 1 (CSD1) in common bean. We experimentally validated a novel miR398 target: the stress up-regulated Nodulin 19 (Nod19). Expression analysis of miR398b and target genes -CSD1 and Nod19- in bean roots, nodules and leaves, indicated their role in copper (Cu) homeostasis. In bean plants under Cu toxicity miR398b was decreased and Nod19 and CSD1, that participates in reactive oxygen species (ROS) detoxification, were up-regulated. The opposite regulation was observed in Cu deficient bean plants; lower levels of CSD1 would allow Cu delivery to essential Cu-containing proteins. Composite common bean plants with transgenic roots over-expressing miR398 showed ca. 20-fold higher mature miR398b and almost negligible target transcript levels as well as increased anthocyanin content and expression of Cu-stress responsive genes, when subjected to Cu deficiency. The down-regulation of miR398b with the consequent up-regulation of its targets was observed in common bean roots during the oxidative burst resulting from short-time exposure to high Cu. A similar response occurred at early stage of bean roots inoculated with Rhizobium tropici, where an increase in ROS was observed. In addition, the miR398b down-regulation and an increase in CSD1 and Nod19 were observed in bean leaves challenged with Sclerotinia scleortiorum fungal pathogen. Transient over-expression of miR398b in Nicotiana benthamiana leaves infected with S. sclerotiorum resulted in enhanced fungal lesions. We conclude that the miR398b-mediated up-regulation of CSD and Nod19 is relevant for common bean plants to cope with oxidative stress generated in abiotic and biotic stresses.
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Affiliation(s)
- Loreto Naya
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos. México
| | - Sujay Paul
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos. México
| | - Oswaldo Valdés-López
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos. México
- Laboratorio de Bioquímica, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México. Tlalnepantla, Estado de México. México
| | - Ana B. Mendoza-Soto
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos. México
| | - Bárbara Nova-Franco
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos. México
| | - Guadalupe Sosa-Valencia
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos. México
| | - José L. Reyes
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos. México
| | - Georgina Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos. México
- * E-mail:
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