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Wang X, Zhou R, Zhao S, Niu S. An Integrated Analysis of microRNAs and the Transcriptome Reveals the Molecular Mechanisms Underlying the Regulation of Leaf Development in Xinyang Maojian Green Tea ( Camellia sinensis). PLANTS (BASEL, SWITZERLAND) 2023; 12:3665. [PMID: 37960023 PMCID: PMC10649745 DOI: 10.3390/plants12213665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/03/2023] [Accepted: 10/22/2023] [Indexed: 11/15/2023]
Abstract
Xinyang Maojian (XYMJ) tea is one of the world's most popular green teas; the development of new sprouts directly affects the yield and quality of tea products, especially for XYMJ, which has hairy tips. Here, we used transcriptome and small RNA sequencing to identify mRNAs and miRNAs, respectively, involved in regulating leaf development in different plant tissues (bud, leaf, and stem). We identified a total of 381 conserved miRNAs. Given that no genomic data for XYMJ green tea are available, we compared the sequencing data for XYMJ green tea with genomic data from a closely related species (Tieguanyin) and the Camellia sinensis var. sinensis database; we identified a total of 506 and 485 novel miRNAs, respectively. We also identified 11 sequence-identical novel miRNAs in the tissues of XYMJ tea plants. Correlation analyses revealed 97 miRNA-mRNA pairs involved in leaf growth and development; the csn-miR319-2/csnTCP2 and miR159-csnMYB modules were found to be involved in leaf development in XYMJ green tea. Quantitative real-time PCR was used to validate the expression levels of the miRNAs and mRNAs. The miRNAs and target genes identified in this study might shed new light on the molecular mechanisms underlying the regulation of leaf development in tea plants.
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Affiliation(s)
- Xianyou Wang
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang 453003, China
| | - Ruijin Zhou
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang 453003, China
| | - Shanshan Zhao
- School of Food Science, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Shengyang Niu
- School of Food Science, Henan Institute of Science and Technology, Xinxiang 453003, China
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2
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Vashisht I, Dhaka N, Jain R, Sood A, Sharma N, Sharma MK, Sharma R. Non-coding RNAs-mediated environmental surveillance determines male fertility in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108030. [PMID: 37708711 DOI: 10.1016/j.plaphy.2023.108030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/16/2023]
Abstract
Plants are continuously exposed to environmental stresses leading to significant yield losses. With the changing climatic conditions, the intensity and duration of these stresses are expected to increase, posing a severe threat to crop productivity worldwide. Male gametogenesis is one of the most sensitive developmental stages. Exposure to environmental stresses during this stage leads to male sterility and yield loss. Elucidating the underlying molecular mechanism of environment-affected male sterility is essential to address this challenge. High-throughput RNA sequencing studies, loss-of-function phenotypes of sRNA biogenesis genes and functional genomics studies with non-coding RNAs have started to unveil the roles of small RNAs, long non-coding RNAs and the complex regulatory interactions between them in regulating male fertility under different growth regimes. Here, we discuss the current understanding of the non-coding RNA-mediated environmental stress surveillance and regulation of male fertility in plants. The candidate ncRNAs emerging from these studies can be leveraged to generate environment-sensitive male sterile lines for hybrid breeding or mitigate the impact of climate change on male fertility, as the situation demands.
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Affiliation(s)
- Ira Vashisht
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Namrata Dhaka
- Department of Biotechnology, Central University of Haryana, Mahendergarh, Haryana, 123031, India
| | - Rubi Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India; Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Rajasthan, 333031, India
| | - Akanksha Sood
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Rajasthan, 333031, India
| | - Niharika Sharma
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW, 2800, Australia
| | - Manoj K Sharma
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rita Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Rajasthan, 333031, India.
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Ahmed F, Bappy MNI, Islam MS. Identification of conserved miRNAs and their targets in Jatropha curcas: an in silico approach. J Genet Eng Biotechnol 2023; 21:43. [PMID: 37024763 PMCID: PMC10079790 DOI: 10.1186/s43141-023-00495-9] [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: 09/26/2022] [Accepted: 03/18/2023] [Indexed: 04/08/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are small endogenous RNAs with an approximate length of 18-22 nucleotides and involved in the regulation of gene expression in transcriptional or post-transcriptional levels. They were found to be associated with leaf morphogenesis, flowering time, vegetative phase change, and response to environmental cues in plants, where they act as a critical regulatory factor. The nature of high conservancy of plant miRNAs within the plant species made it possible to detect the conserved miRNAs by computational approaches. Expressed Sequence Tags (EST) based comparative genomic approaches provide advantages over wet lab approaches as it is convenient, easy to carry out and less time consuming. EST-based in silico approach can unravel new conserved miRNAs in plants, even when the complete genome sequence is not available. RESULTS To identify the novel miRNAs, a total of 46,865 ESTs from Jatropha curcas were searched for homology to all available 6746 mature miRNAs of plant eudicotyledons. Finally, we ended up with 12 novel miRNAs in Jatropha that range from 18 to 19 nucleotides where their respective precursor miRNAs had 54.11-71.76% (A + U) content. The putative miRNAs belong to 12 individual miRNA family and most of them have higher (A + U) content ranging from 47.36 to 77.77% than their respective miRNA homologs. Many of the target genes by the newly identified miRNAs were associated with plant growth and development, stress response, defense and hormone signaling, and oil synthesis pathways. CONCLUSION These findings have the potential to speed up miRNA identification and expand our understanding of miRNA functions in J. curcas.
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Affiliation(s)
- Foeaz Ahmed
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
- Department of Molecular Biology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Md Nazmul Islam Bappy
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
- Department of Animal and Fish Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Md Shariful Islam
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh.
- Department of Molecular Biology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh.
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Rego ECS, Pinheiro TDM, Fonseca FCDA, Gomes TG, Costa EDC, Bastos LS, Alves GSC, Cotta MG, Amorim EP, Ferreira CF, Togawa RC, Costa MMDC, Grynberg P, Miller RNG. Characterization of microRNAs and Target Genes in Musa acuminata subsp. burmannicoides, var. Calcutta 4 during Interaction with Pseudocercospora musae. PLANTS (BASEL, SWITZERLAND) 2023; 12:1473. [PMID: 37050099 PMCID: PMC10097032 DOI: 10.3390/plants12071473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/20/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
Endogenous microRNAs (miRNAs) are small non-coding RNAs that perform post-transcriptional regulatory roles across diverse cellular processes, including defence responses to biotic stresses. Pseudocercospora musae, the causal agent of Sigatoka leaf spot disease in banana (Musa spp.), is an important fungal pathogen of the plant. Illumina HiSeq 2500 sequencing of small RNA libraries derived from leaf material in Musa acuminata subsp. burmannicoides, var. Calcutta 4 (resistant) after inoculation with fungal conidiospores and equivalent non-inoculated controls revealed 202 conserved miRNAs from 30 miR-families together with 24 predicted novel miRNAs. Conserved members included those from families miRNA156, miRNA166, miRNA171, miRNA396, miRNA167, miRNA172, miRNA160, miRNA164, miRNA168, miRNA159, miRNA169, miRNA393, miRNA535, miRNA482, miRNA2118, and miRNA397, all known to be involved in plant immune responses. Gene ontology (GO) analysis of gene targets indicated molecular activity terms related to defence responses that included nucleotide binding, oxidoreductase activity, and protein kinase activity. Biological process terms associated with defence included response to hormone and response to oxidative stress. DNA binding and transcription factor activity also indicated the involvement of miRNA target genes in the regulation of gene expression during defence responses. sRNA-seq expression data for miRNAs and RNAseq data for target genes were validated using stem-loop quantitative real-time PCR (qRT-PCR). For the 11 conserved miRNAs selected based on family abundance and known involvement in plant defence responses, the data revealed a frequent negative correlation of expression between miRNAs and target host genes. This examination provides novel information on miRNA-mediated host defence responses, applicable in genetic engineering for the control of Sigatoka leaf spot disease.
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Affiliation(s)
| | | | | | - Taísa Godoy Gomes
- Instituto de Ciências Biológicas, Universidade de Brasília, Brasília 70910-900, DF, Brazil
| | - Erica de Castro Costa
- Instituto de Ciências Biológicas, Universidade de Brasília, Brasília 70910-900, DF, Brazil
| | - Lucas Santos Bastos
- Instituto de Ciências Biológicas, Universidade de Brasília, Brasília 70910-900, DF, Brazil
| | | | - Michelle Guitton Cotta
- Instituto de Ciências Biológicas, Universidade de Brasília, Brasília 70910-900, DF, Brazil
| | | | | | - Roberto Coiti Togawa
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP 02372, Brasília 70770-917, DF, Brazil
| | - Marcos Mota Do Carmo Costa
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP 02372, Brasília 70770-917, DF, Brazil
| | - Priscila Grynberg
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP 02372, Brasília 70770-917, DF, Brazil
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Saini S, Khurana S, Saini D, Rajput S, Thakur CJ, Singh J, Jaswal A, Kapoor Y, Kumar V, Saini A. In silico analysis of genomic landscape of SARS-CoV-2 and its variant of concerns (Delta and Omicron) reveals changes in the coding potential of miRNAs and their target genes. Gene 2023; 853:147097. [PMID: 36470485 PMCID: PMC9721428 DOI: 10.1016/j.gene.2022.147097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
COVID-19 related morbidities and mortalities are still continued due to the emergence of new variants of SARS-CoV-2. In the last few years, viral miRNAs have been the centre of study to understand the disease pathophysiology. In this work, we aimed to predict the change in coding potential of the viral miRNAs in SARS-CoV-2's VOCs, Delta and Omicron compared to the Reference (Wuhan origin) strain using bioinformatics tools. After ab-intio based screening by the Vmir tool and validation, we retrieved 22, 6, and 6 pre-miRNAs for Reference, Delta, and Omicron. Most of the predicted unique pre-miRNAs of Delta and Omicron were found to be encoded from the terminal and origin of the genomic sequence, respectively. Mature miRNAs identified by MatureBayes from the unique pre-miRNAs were used for target identification using miRDB. A total of 1786, 216, and 143 high-confidence target genes were captured for GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis. The GO and KEGG pathways terms analysis revealed the involvement of Delta miRNAs targeted genes in the pathways such as Human cytomegalovirus infection, Breast cancer, Apoptosis, Neurotrophin signaling, and Axon guidance whereas the Sphingolipid signaling pathway was found for the Omicron. Furthermore, we focussed our analysis on target genes that were validated through GEO's (Gene Expression Omnibus) DEGs (Differentially Expressed Genes) dataset, in which FGL2, TNSF12, OGN, GDF11, and BMP11 target genes were found to be down-regulated by Reference miRNAs and YAE1 and RSU1 by Delta. Few genes were also observed to be validated among in up-regulated gene set of the GEO dataset, in which MMP14, TNFRSF21, SGMS1, and TMEM192 were related to Reference whereas ZEB2 was detected in all three strains. This study thus provides an in-silico based analysis that deciphered the unique pre-miRNAs in Delta and Omicron compared to Reference. However, the findings need future wet lab studies for validation.
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Affiliation(s)
- Sandeep Saini
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India; Department of Biophysics, Panjab University, Sector 25, Chandigarh 160014, India.
| | - Savi Khurana
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Dikshant Saini
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Saru Rajput
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Chander Jyoti Thakur
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Jeevisha Singh
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Akanksha Jaswal
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Yogesh Kapoor
- Department of Engineering and Technology, Shoolini University, Solan, Himachal Pradesh, India
| | - Varinder Kumar
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Avneet Saini
- Department of Biophysics, Panjab University, Sector 25, Chandigarh 160014, India.
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Kapadia C, Datta R, Mahammad SM, Tomar RS, Kheni JK, Ercisli S. Genome-Wide Identification, Quantification, and Validation of Differentially Expressed miRNAs in Eggplant ( Solanum melongena L.) Based on Their Response to Ralstonia solanacearum Infection. ACS OMEGA 2023; 8:2648-2657. [PMID: 36687045 PMCID: PMC9851032 DOI: 10.1021/acsomega.2c07097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/27/2022] [Indexed: 06/13/2023]
Abstract
MicroRNAs (miRNAs), a type of short noncoding RNA molecule (21-23 nucleotides), mediate repressive gene regulation through RNA silencing at the posttranscriptional level and play an important role in the defense response to abiotic and biotic stresses. miRNAs of the plant system have been studied in model crops for their diverse regulatory role while less is known about their significance in other plants whose genome and transcriptome data are scarce in the database, including eggplant (Solanum melongena L.). In the present study, a next-generation sequencing platform was used for the sequencing of miRNA, and real-time quantitative PCR for miRNAs was used to validate the gene expression patterns of miRNAs in Solanum melongena plantlets infected with the bacterial wilt-causing pathogen Ralstonia solanacearum (R. solanacearum). Sequence analyses showed the presence of 375 miRNAs belonging to 29 conserved families. The miR414 is highly conserved miRNA across the plant system while miR5658 and miR5021 were found exclusively in Arabidopsis thaliana surprisingly, these miRNAs were found in eggplants too. The most abundant families were miR5658 and miR414. Ppt-miR414, hvu-miR444b, stu-miR8020, and sly miR5303 were upregulated in Pusa purple long (PPL) (susceptible) at 48 h postinfection, followed by a decline after 96 h postinfection. A similar trend was obtained in ath-miR414, stu-mir5303h, alymiR847-5p, far-miR1134, ath-miR5021, ath-miR5658, osa-miR2873c, lja-miR7530, stu-miR7997c, and gra-miR8741 but at very low levels after infection in the susceptible variety, indicating their negative role in the suppression of host immunity. On the other hand, osa-miR2873c was found to be slightly increased after 96 hpi from 48 hpi. Most of the miRNAs under study showed relatively lower expression in the resistant variety Arka Nidhi after infection than in the susceptible variety. These results shed light on a deeper regulatory role of miRNAs and their targets in regulation of the plant response to bacterial infection. The present experiment and their results suggested that the higher expression of miRNA leads to a decline in host mRNA and thus shows susceptibility.
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Affiliation(s)
- Chintan Kapadia
- Department
of Plant Molecular Biology and Biotechnology, ASPEE College of Horticulture
and Forestry, Navsari Agricultural University, Navsari 396450, India
| | - Rahul Datta
- Department
of Geology and Pedology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemedelska1, 61300 Brno, Czech Republic
| | - Saiyed Mufti Mahammad
- Department
of Plant Molecular Biology and Biotechnology, ASPEE College of Horticulture
and Forestry, Navsari Agricultural University, Navsari 396450, India
| | - Rukam Singh Tomar
- Department
of Biotechnology and Biochemistry, Junagadh
Agricultural University, Junagadh 362 001, India
| | - Jasmin Kumar Kheni
- Department
of Biotechnology and Biochemistry, Junagadh
Agricultural University, Junagadh 362 001, India
| | - Sezai Ercisli
- Department
of Horticulture, Faculty of Agriculture, Ataturk University, 25240 Erzurum, Turkey
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Chaudhary V, Jangra S, Yadav NR. In silico Identification of miRNAs and Their Targets in Cluster Bean for Their Role in Development and Physiological Responses. Front Genet 2022; 13:930113. [PMID: 35846150 PMCID: PMC9280363 DOI: 10.3389/fgene.2022.930113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/08/2022] [Indexed: 11/17/2022] Open
Abstract
Cluster bean popularly known as “guar” is a drought-tolerant, annual legume that has recently emerged as an economically important crop, owing to its high protein and gum content. The guar gum has wide range of applications in food, pharma, and mining industries. India is the leading exporter of various cluster bean-based products all across the globe. Non-coding RNAs (miRNAs) are involved in regulating the expression of the target genes leading to variations in the associated pathways or final protein concentrations. The understanding of miRNAs and their associated targets in cluster bean is yet to be used to its full potential. In the present study, cluster bean EST (Expressed Sequence Tags) database was exploited to identify the miRNA and their predicted targets associated with metabolic and biological processes especially response to diverse biotic and abiotic stimuli using in silico approach. Computational analysis based on cluster bean ESTs led to the identification of 57 miRNAs along with their targets. To the best of our knowledge, this is the first report on identification of miRNAs and their targets using ESTs in cluster bean. The miRNA related to gum metabolism was also identified. Most abundant miRNA families predicted in our study were miR156, miR172, and miR2606. The length of most of the mature miRNAs was found to be 21nt long and the range of minimal folding energy (MFE) was 5.8–177.3 (−kcal/mol) with an average value of 25.4 (−kcal/mol). The identification of cluster bean miRNAs and their targets is predicted to hasten the miRNA discovery, resulting in better knowledge of the role of miRNAs in cluster bean development, physiology, and stress responses.
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Mostafa S, Wang Y, Zeng W, Jin B. Plant Responses to Herbivory, Wounding, and Infection. Int J Mol Sci 2022; 23:ijms23137031. [PMID: 35806046 PMCID: PMC9266417 DOI: 10.3390/ijms23137031] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 12/26/2022] Open
Abstract
Plants have various self-defense mechanisms against biotic attacks, involving both physical and chemical barriers. Physical barriers include spines, trichomes, and cuticle layers, whereas chemical barriers include secondary metabolites (SMs) and volatile organic compounds (VOCs). Complex interactions between plants and herbivores occur. Plant responses to insect herbivory begin with the perception of physical stimuli, chemical compounds (orally secreted by insects and herbivore-induced VOCs) during feeding. Plant cell membranes then generate ion fluxes that create differences in plasma membrane potential (Vm), which provokes the initiation of signal transduction, the activation of various hormones (e.g., jasmonic acid, salicylic acid, and ethylene), and the release of VOCs and SMs. This review of recent studies of plant–herbivore–infection interactions focuses on early and late plant responses, including physical barriers, signal transduction, SM production as well as epigenetic regulation, and phytohormone responses.
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Rostami Azar A, Maroufi A. Identification of Long Non-coding RNA Transcripts in Glycyrrhiza uralensis. IRANIAN JOURNAL OF BIOTECHNOLOGY 2022; 20:e2607. [PMID: 35891954 PMCID: PMC9284242 DOI: 10.30498/ijb.2021.205469.2607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Background: Chinese liquorice (Glycyrrhiza uralensis), an important medicinal plant, contains various valuable secondary metabolites. Secondary metabolites biosynthesis is
very tightly regulated; therefore, elucidation and manipulation of the biosynthetic pathways are of great interest. Recent studies have shown that lncRNAs play important
regulatory roles in many biological processes, thus identification and modification of their expression is essential to metabolic pathways for biosynthesis of secondary metabolites. Objectives: In this study we attempted to identify non-coding RNA transcripts (lncRNAs) that may act as important regulators of diverse biological processes, including stress responses
and developmental programs in Glycyrrhiza uralensis. Materials and Methods: Identification of potential lncRNAs in Chinese liquorice was performed using a bioinformatics pipeline from the available EST dataset of G. uralensis. Results: Bioinformatics analysis revealed that 1365 identical sequences in the range of 200 to 1286 base pair are putative lncRNAs. Only less than one percent of the
predicted lncRNAs display sequence conservation with lncRNAs from other species. Moreover, 13 lncRNAs were detected as the potential precursors of 16 miRNAs.
From this analysis, we also detected possible target genes of 16 known miRNA genes. The majority of the predicted miRNA target genes have important role in response
to plant disease and a couple of them contribute to signalling and metabolic pathways. Conclusion: This study demonstrates the existence of lncRNAs in G. uralensis which has not been found before and provides valuable resources for further understanding and characterizing
of lncRNAs and also a basis for additional investigation to reveal specific roles of lncRNAs in various biological processes and particularly in response to plant diseases.
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Affiliation(s)
- Arash Rostami Azar
- Department of Plant Production and Genetics, University of Kurdistan, Sanandaj, Iran
| | - Asad Maroufi
- Department of Plant Production and Genetics, University of Kurdistan, Sanandaj, Iran.,Research Center for Medicinal Plant Breeding and Development, University of Kurdistan, Sanandaj, Iran
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10
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Interpreting machine learning models to investigate circadian regulation and facilitate exploration of clock function. Proc Natl Acad Sci U S A 2021; 118:2103070118. [PMID: 34353905 PMCID: PMC8364196 DOI: 10.1073/pnas.2103070118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The circadian clock is an internal molecular 24-h timer that is critical to life on Earth. We describe a series of artificial intelligence (AI)– and machine learning (ML)–based approaches that enable more cost-effective analysis and insight into circadian regulation and function. Throughout the manuscript, we illuminate what is inside the ML “black box” via explanation or interpretation of predictive ML models. Using this interpretation of our models, we derive biological insights into why a prediction was made, alongside accurate predictions. Most innovatively, we use only DNA sequence features for accurate circadian gene expression prediction. Using explainable AI, we define possible, responsible regulatory elements as we make these predictions; this critically requires no prior knowledge of regulatory elements. The circadian clock is an important adaptation to life on Earth. Here, we use machine learning to predict complex, temporal, and circadian gene expression patterns in Arabidopsis. Most significantly, we classify circadian genes using DNA sequence features generated de novo from public, genomic resources, facilitating downstream application of our methods with no experimental work or prior knowledge needed. We use local model explanation that is transcript specific to rank DNA sequence features, providing a detailed profile of the potential circadian regulatory mechanisms for each transcript. Furthermore, we can discriminate the temporal phase of transcript expression using the local, explanation-derived, and ranked DNA sequence features, revealing hidden subclasses within the circadian class. Model interpretation/explanation provides the backbone of our methodological advances, giving insight into biological processes and experimental design. Next, we use model interpretation to optimize sampling strategies when we predict circadian transcripts using reduced numbers of transcriptomic timepoints. Finally, we predict the circadian time from a single, transcriptomic timepoint, deriving marker transcripts that are most impactful for accurate prediction; this could facilitate the identification of altered clock function from existing datasets.
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Krishnatreya DB, Agarwala N, Gill SS, Bandyopadhyay T. Understanding the role of miRNAs for improvement of tea quality and stress tolerance. J Biotechnol 2021; 328:34-46. [PMID: 33421509 DOI: 10.1016/j.jbiotec.2020.12.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/04/2020] [Accepted: 12/28/2020] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs) are an emerging class of small non-coding RNAs that exhibit important role in regulation of gene expression, mostly through the mechanism of cleavage and/or inhibition of translation of target mRNAs during or after transcription. Although much has been unravelled about the role of miRNAs in diverse biological processes like maintenance of functional integrity of genes and genome, growth and development, metabolism, and adaptive responses towards biotic and abiotic stresses in plants, not much is known on their specific roles in majority of cash crops - an area of investigation with potentially significant and gainful economic implications. Tea (Camellia sinensis) is globally the second most consumed beverage after water and its cultivation has major agro-economic and social ramifications. In recent years, global tea production has been greatly challenged by many biotic and abiotic stress factors and a deeper understanding of molecular processes regulating stress adaptation in this largely under investigated crop stands to significantly facilitate potential crop improvement strategies towards durable stress tolerance. This review endeavours to highlight recent advances in our understanding of the role of miRNAs in regulating stress tolerance traits in tea plant with additional focus on their role in determining tea quality attributes.
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Affiliation(s)
| | - Niraj Agarwala
- Department of Botany, Gauhati University, Jalukbari, Guwahati, Assam, 781014, India.
| | - Sarvajeet Singh Gill
- Center for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
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12
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Jeyaraj A, Elango T, Li X, Guo G. Utilization of microRNAs and their regulatory functions for improving biotic stress tolerance in tea plant [ Camellia sinensis (L.) O. Kuntze]. RNA Biol 2020; 17:1365-1382. [PMID: 32478595 PMCID: PMC7549669 DOI: 10.1080/15476286.2020.1774987] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/04/2019] [Accepted: 03/20/2019] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs play a central role in responses to biotic stressors through their interactions with their target mRNAs. Tea plant (Camellia sinensis L.), an important beverage crop, is vulnerable to tea geometrid and anthracnose disease that causes considerable crop loss and tea production worldwide. Sustainable production of tea in the current scenario to biotic factors is major challenges. To overcome the problem of biotic stresses, high-throughput sequencing (HTS) with bioinformatics analyses has been used as an effective approach for the identification of stress-responsive miRNAs and their regulatory functions in tea plant. These stress-responsive miRNAs can be utilized for miRNA-mediated gene silencing to enhance stress tolerance in tea plant. Therefore, this review summarizes the current understanding of miRNAs regulatory functions in tea plant responding to Ectropis oblique and Colletotrichum gloeosporioides attacks for future miRNA research. Also, it highlights the utilization of miRNA-mediated gene silencing strategies for developing biotic stress-tolerant tea plant.
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Affiliation(s)
- Anburaj Jeyaraj
- Tea Research Institute, Nanjing Agricultural University, Nanjing, China
- Department of Biotechnology, Karpagam Academy of Higher Education, Tamilnadu, India
| | - Tamilselvi Elango
- Tea Research Institute, Nanjing Agricultural University, Nanjing, China
| | - Xinghui Li
- Tea Research Institute, Nanjing Agricultural University, Nanjing, China
| | - Guiyi Guo
- Henan Key Laboratory of Tea Plant Comprehensive Utilization in South Henan, Xinyang Agriculture and Forestry University, Xinyang, P.R. China
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13
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Identification of miRNA, their targets and miPEPs in peanut (Arachis hypogaea L.). Comput Biol Chem 2019; 83:107100. [DOI: 10.1016/j.compbiolchem.2019.107100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 07/04/2019] [Accepted: 08/06/2019] [Indexed: 01/28/2023]
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14
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Abstract
microRNAs are small non-coding RNA molecules playing a central role in gene regulation. miRBase is the standard reference source for analysis and interpretation of experimental studies. However, the richness and complexity of the annotation is often underappreciated by users. Moreover, even for experienced users, the size of the resource can make it difficult to explore annotation to determine features such as species coverage, the impact of specific characteristics and changes between successive releases. A further consideration is that each new miRBase release contains entries that have had limited review and which may subsequently be removed in a future release to ensure the quality of annotation. To aid the miRBase user, we developed a software tool, miRBaseMiner, for investigating miRBase annotation and generating custom annotation sets. We apply the tool to characterize each release from v9.2 to v22 to examine how annotation has changed across releases and highlight some of the annotation features that users should keep in mind when using for miRBase for data analysis. These include: (1) entries with identical or very similar sequences; (2) entries with multiple annotated genome locations; (3) hairpin precursor entries with extremely low-estimated minimum free energy; (4) entries possessing reverse complementary; (5) entries with 3ʹ poly(A) ends. As each of these factors can impact the identification of dysregulated features and subsequent clinical or biological conclusions, miRBaseMiner is a valuable resource for any user using miRBase as a reference source.
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Affiliation(s)
- Xiangfu Zhong
- Department of Medical Genetics, Oslo University Hospital and University of Oslo , Oslo , Norway
| | - Fatima Heinicke
- Department of Medical Genetics, Oslo University Hospital and University of Oslo , Oslo , Norway
| | - Simon Rayner
- Department of Medical Genetics, Oslo University Hospital and University of Oslo , Oslo , Norway
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15
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Revealing liver specific microRNAs linked with carbohydrate metabolism of farmed carp, Labeo rohita (Hamilton, 1822). Genomics 2019; 112:32-44. [PMID: 31325488 DOI: 10.1016/j.ygeno.2019.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 06/11/2019] [Accepted: 07/16/2019] [Indexed: 12/14/2022]
Abstract
The role of microRNA in gene regulation during developmental biology has been well depicted in several organisms. The present study was performed to investigate miRNAs role in the liver tissues during carbohydrate metabolism and their targets in the farmed carp rohu, Labeo rohita, which is economically important species in aquaculture. Using Illumina-HiSeq technology, a total of 22,612,316; 44,316,046 and 13,338,434 clean reads were obtained from three small-RNA libraries. We have identified 138 conserved and 161 novel miRNAs and studies revealed that miR-22, miR-122, miR-365, miR-200, and miR-146 are involved in carbohydrate metabolism. Further analysis depicted mature miRNA and their predicted target sites in genes that were involved in developmental biology, cellular activities, transportation, etc. This is the first report of the presence of miRNAs in liver tissue of rohu and their comparative profile linked with metabolism serves as a vital resource as a biomarker.
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16
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Pourmazaheri H, Soorni A, Kohnerouz BB, Dehaghi NK, Kalantar E, Omidi M, Naghavi MR. Comparative analysis of the root and leaf transcriptomes in Chelidonium majus L. PLoS One 2019; 14:e0215165. [PMID: 30986259 PMCID: PMC6464174 DOI: 10.1371/journal.pone.0215165] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/27/2019] [Indexed: 12/31/2022] Open
Abstract
Chelidonium majus is a traditional medicinal plant, which commonly known as a rich resource for the major benzylisoquinoline alkaloids (BIAs), including morphine, sanguinarine, and berberine. To understand the biosynthesis of C. majus BIAs, we performed de novo transcriptome sequencing of its leaf and root tissues using Illumina technology. Following comprehensive evaluation of de novo transcriptome assemblies produced with five programs including Trinity, Bridger, BinPacker, IDBA-tran, and Velvet/Oases using a series of k-mer sizes (from 25 to 91), BinPacker was found to produce the best assembly using a k-mer of 25. This study reports the results of differential gene expression (DGE), functional annotation, gene ontology (GO) analysis, classification of transcription factor (TF)s, and SSR and miRNA discovery. Our DGE analysis identified 6,028 transcripts that were up-regulated in the leaf, and 4,722 transcripts that were up-regulated in the root. Further investigations showed that most of the genes involved in the BIA biosynthetic pathway are significantly expressed in the root compared to the leaf. GO analysis showed that the predominant GO domain is "cellular component", while TF analysis found bHLH to be the most highly represented TF family. Our study further identified 10 SSRs, out of a total of 39,841, that showed linkage to five unigenes encoding enzymes in the BIA pathway, and 10 conserved miRNAs that were previously not detected in this plant. The comprehensive transcriptome information presented herein provides a foundation for further explorations on study of the molecular mechanisms of BIA synthesis in C. majus.
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Affiliation(s)
- Helen Pourmazaheri
- Department of Plant Breeding and Biotechnology, College of Agriculture, University of Tabriz, Tabriz, Islamic Republic of Iran
- Department of Pharmacognosy, Faculty of Pharmacy, Alborz University of Medical Sciences, Karaj, Islamic Republic of Iran
| | - Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Bahram Baghban Kohnerouz
- Department of Plant Breeding and Biotechnology, College of Agriculture, University of Tabriz, Tabriz, Islamic Republic of Iran
| | - Nafiseh Khosravi Dehaghi
- Department of Pharmacognosy, Faculty of Pharmacy, Alborz University of Medical Sciences, Karaj, Islamic Republic of Iran
| | - Enayatollah Kalantar
- Department of Microbiology and Immunology, Faculty of Medicine, Alborz University of Medical Science, Karaj, Islamic Republic of Iran
| | - Mansoor Omidi
- Agronomy and Plant Breeding Department, Agricultural & Natural Resources College, University of Tehran, Karaj, Islamic Republic of Iran
| | - Mohammad Reza Naghavi
- Agronomy and Plant Breeding Department, Agricultural & Natural Resources College, University of Tehran, Karaj, Islamic Republic of Iran
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17
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Marakli S. Identification and functional analyses of new sesame miRNAs (Sesamum indicum L.) and their targets. Mol Biol Rep 2018; 45:2145-2155. [PMID: 30209739 DOI: 10.1007/s11033-018-4373-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/06/2018] [Indexed: 12/20/2022]
Abstract
Plant microRNAs (miRNAs) have been commonly investigated during many years. Hundreds of miRNAs have been identified in many different plant species but there is very little information about the function of sesame (Sesamum indicum L.) miRNAs. For this purpose, in silico prediction of novel sesame miRNAs based on BLAST searches of the expressed sequence tag database was performed, using stringent criterias for miRNA annotation. The secondary structures of their precursor sequences, potential target genes of conserved and novel miRNAs were predicted and subjected to Gene Ontology (GO) annotation. mir447 and mir8140 were reported for the first time in sesame. Enrichment analysis of the GO with biological processes, cellular component and molecular functions revealed that these target genes were potentially involved in different metabolic pathways such as transcription factors, metabolism, growth and development, stress-related and even plant hormones. Results are valuable for figure out the gene regulation mechanism in sesame, using in the medicinal aspect of this plant species. Furthermore, these miRNAs and their profiled targets could provide the improvement of regulation and management, and even development of desirable traits in this plant.
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Affiliation(s)
- Sevgi Marakli
- Faculty of Arts and Sciences, Department of Biology, Amasya University, Ipekkoy, 05100, Amasya, Turkey.
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18
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Davoodi Mastakani F, Pagheh G, Rashidi Monfared S, Shams-Bakhsh M. Identification and expression analysis of a microRNA cluster derived from pre-ribosomal RNA in Papaver somniferum L. and Papaver bracteatum L. PLoS One 2018; 13:e0199673. [PMID: 30067748 PMCID: PMC6070170 DOI: 10.1371/journal.pone.0199673] [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: 07/09/2017] [Accepted: 06/12/2018] [Indexed: 11/19/2022] Open
Abstract
Opium poppy (Papaver somniferum L.) is one of the ancient medical crops, which produces several important alkaloids such as morphine, noscapine, sanguinarine and codeine. MicroRNAs are endogenous non-coding RNAs that play important regulatory roles in plant diverse biological processes. Many plant miRNAs are encoded as single transcriptional units, in contrast to animal miRNAs, which are often clustered. Herein, using computational approaches, a total of 22 miRNA precursors were identified, which five of them were located as a clustered in pre-ribosomal RNA. Afterward, the transcript level of the precursor and the mature of clustered miRNAs in two species of the Papaveraceae family, i.e. P. somniferum L. and P. bracteatum L, were quantified by RT-PCR. With respect to obtained results, these clustered miRNAs were expressed differentially in different tissues of these species. Moreover, using target prediction and Gene Ontology (GO)-based on functional classification indicated that these miRNAs might play crucial roles in various biological processes as well as metabolic pathways. In this study, we discovered the clustered miRNA derived from pre-rRNA, which may shed some light on the importance of miRNAs in the plant kingdom.
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Affiliation(s)
- Farshad Davoodi Mastakani
- Department of Agricultural Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Gabriel Pagheh
- Department of Agricultural Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Sajad Rashidi Monfared
- Department of Agricultural Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Masoud Shams-Bakhsh
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
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19
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Hussain K, Mungikar K, Kulkarni A, Kamble A. Identification, characterization and expression analysis of pigeonpea miRNAs in response to Fusarium wilt. Gene 2018; 653:57-64. [DOI: 10.1016/j.gene.2018.02.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/22/2018] [Accepted: 02/07/2018] [Indexed: 11/25/2022]
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20
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Samad AFA, Nazaruddin N, Murad AMA, Jani J, Zainal Z, Ismail I. Deep sequencing and in silico analysis of small RNA library reveals novel miRNA from leaf Persicaria minor transcriptome. 3 Biotech 2018; 8:136. [PMID: 29479512 DOI: 10.1007/s13205-018-1164-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 02/08/2018] [Indexed: 01/25/2023] Open
Abstract
In current era, majority of microRNA (miRNA) are being discovered through computational approaches which are more confined towards model plants. Here, for the first time, we have described the identification and characterization of novel miRNA in a non-model plant, Persicaria minor (P. minor) using computational approach. Unannotated sequences from deep sequencing were analyzed based on previous well-established parameters. Around 24 putative novel miRNAs were identified from 6,417,780 reads of the unannotated sequence which represented 11 unique putative miRNA sequences. PsRobot target prediction tool was deployed to identify the target transcripts of putative novel miRNAs. Most of the predicted target transcripts (mRNAs) were known to be involved in plant development and stress responses. Gene ontology showed that majority of the putative novel miRNA targets involved in cellular component (69.07%), followed by molecular function (30.08%) and biological process (0.85%). Out of 11 unique putative miRNAs, 7 miRNAs were validated through semi-quantitative PCR. These novel miRNAs discoveries in P. minor may develop and update the current public miRNA database.
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Affiliation(s)
- Abdul Fatah A Samad
- 1School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
| | - Nazaruddin Nazaruddin
- 1School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
- 3Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Syiah Kuala, Darussalam, Banda Aceh, 23111 Indonesia
| | - Abdul Munir Abdul Murad
- 1School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
| | - Jaeyres Jani
- BioEasy Sdn. Bhd. and ScienceVision Sdn. Bhd., Setia Alam, Seksyen U13, 40170 Shah Alam, Selangor Malaysia
| | - Zamri Zainal
- 1School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
- 2Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
| | - Ismanizan Ismail
- 1School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
- 2Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
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21
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Jeyaraj A, Zhang X, Hou Y, Shangguan M, Gajjeraman P, Li Y, Wei C. Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences. BMC PLANT BIOLOGY 2017; 17:212. [PMID: 29157210 PMCID: PMC5697157 DOI: 10.1186/s12870-017-1169-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 11/10/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are important for plant growth and responses to environmental stresses via post-transcriptional regulation of gene expression. Tea, which is primarily produced from one bud and two tender leaves of the tea plant (Camellia sinensis), is one of the most popular non-alcoholic beverages worldwide owing to its abundance of secondary metabolites. A large number of miRNAs have been identified in various plants, including non-model species. However, due to the lack of reference genome sequences and/or information of tea plant genome survey scaffold sequences, discovery of miRNAs has been limited in C. sinensis. RESULTS Using small RNA sequencing, combined with our recently obtained genome survey data, we have identified and analyzed 175 conserved and 83 novel miRNAs mainly in one bud and two tender leaves of the tea plant. Among these, 93 conserved and 18 novel miRNAs were validated using miRNA microarray hybridization. In addition, the expression pattern of 11 conserved and 8 novel miRNAs were validated by stem-loop-qRT-PCR. A total of 716 potential target genes of identified miRNAs were predicted. Further, Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that most of the target genes were primarily involved in stress response and enzymes related to phenylpropanoid biosynthesis. The predicted targets of 4 conserved miRNAs were further validated by 5'RLM-RACE. A negative correlation between expression profiles of 3 out of 4 conserved miRNAs (csn-miR160a-5p, csn-miR164a, csn-miR828 and csn-miR858a) and their targets (ARF17, NAC100, WER and MYB12 transcription factor) were observed. CONCLUSION In summary, the present study is one of few such studies on miRNA detection and identification in the tea plant. The predicted target genes of majority of miRNAs encoded enzymes, transcription factors, and functional proteins. The miRNA-target transcription factor gene interactions may provide important clues about the regulatory mechanism of these miRNAs in the tea plant. The data reported in this study will make a huge contribution to knowledge on the potential miRNA regulators of the secondary metabolism pathway and other important biological processes in C. sinensis.
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Affiliation(s)
- Anburaj Jeyaraj
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui Province 230036 People’s Republic of China
| | - Xiao Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui Province 230036 People’s Republic of China
| | - Yan Hou
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui Province 230036 People’s Republic of China
| | - Mingzhu Shangguan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui Province 230036 People’s Republic of China
| | - Prabu Gajjeraman
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui Province 230036 People’s Republic of China
- Department of Biotechnology, Karpagam University, Coimbatore, India
| | - Yeyun Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui Province 230036 People’s Republic of China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui Province 230036 People’s Republic of China
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Jeyaraj A, Liu S, Zhang X, Zhang R, Shangguan M, Wei C. Genome-wide identification of microRNAs responsive to Ectropis oblique feeding in tea plant (Camellia sinensis L.). Sci Rep 2017; 7:13634. [PMID: 29051614 PMCID: PMC5648755 DOI: 10.1038/s41598-017-13692-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/29/2017] [Indexed: 12/02/2022] Open
Abstract
The tea plant (Camellia sinensis L.) is vulnerable to the geometrid Ectropis oblique; although microRNAs (miRNAs) are important for plant growth, development and stress response, the function of miRNAs in the response of C. sinensis to stress from E. oblique is unclear. To identify E. oblique stress-responsive miRNAs and their target genes in tea plant, three small RNA libraries were constructed from leaves subjected to mechanical wounding (MW), geometrid attack (GA) and from healthy control (CK) leaves. Using high-throughput sequencing, 130 known miRNAs and 512 novel miRNAs were identified; of these, differential expression under GA stress was observed for 36 known and 139 novel miRNAs. Furthermore, 169 GA-responsive and 173 MW-responsive miRNAs were detected by miRNA microarray. The expression patterns of six GA-responsive miRNAs were validated by qRT-PCR. Several target genes for these miRNAs encode various transcription factors, including ethylene-responsive transcription factors and squamosa promoter-binding-like proteins, which suggests that these miRNAs may regulate stress-responsive transcriptional processes in tea plant. The present findings provide novel insights into miRNA-mediated regulatory mechanisms underlying the response to GA stress, and also offer valuable information for development of pest resistance using RNA interference-based strategies in tea plants.
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Affiliation(s)
- Anburaj Jeyaraj
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China
| | - Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China
| | - Xiao Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China
| | - Ran Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China
| | - Mingzhu Shangguan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China.
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Ram MK, Mukherjee K, Pandey DM. Identification of Groundnut miRNA and their targets. CANADIAN JOURNAL OF BIOTECHNOLOGY 2017. [DOI: 10.24870/cjb.2017-a180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Feng JL, Yang ZJ, Chen SP, El-Kassaby YA, Chen H. High throughput sequencing of small RNAs reveals dynamic microRNAs expression of lipid metabolism during Camellia oleifera and C. meiocarpa seed natural drying. BMC Genomics 2017; 18:546. [PMID: 28728593 PMCID: PMC5520325 DOI: 10.1186/s12864-017-3923-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 07/04/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Camellia species are ancient oilseed plants with a history of cultivation over two thousand years. Prior to oil extraction, natural seed drying is often practiced, a process affecting fatty acid quality and quantity. MicroRNAs (miRNA) of lipid metabolism associated with camellia seed natural drying are unexplored. To obtain insight into the function of miRNAs in lipid metabolism during natural drying, Illumina sequencing of C. oleifera and C. meiocarpa small-RNA was conducted. RESULTS A total of 274 candidate miRNAs were identified and 3733 target unigenes were annotated by performing a BLASTX. Through integrated GO and KEGG function annotation, 23 miRNA regulating 131 target genes were identified as lipid metabolism, regulating fatty acid biosynthesis, accumulation and catabolism. We observed one, two, and four miRNAs of lipid metabolism which were specially expressed in C. Meiocarpa, C. oleifera, and the two species collectively, respectively. At 30% moisture contents, C. meiocarpa and C. oleifer produced nine and eight significant differentially expressed miRNAs, respectively, with high fatty acid synthesis and accumulation activities. Across the two species, 12 significant differentially expressed miRNAs were identified at the 50% moisture content. CONCLUSIONS Sequencing of small-RNA revealed the presence of 23 miRNAs regulating lipid metabolism in camellia seed during natural drying and permitted comparative miRNA profiles between C. Meiocarpa and C. oleifera. Furthermore, this study successfully identified the best drying environment at which the quantity and quality of lipid in camellia seed are at its maximum.
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Affiliation(s)
- Jin-Ling Feng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhi-Jian Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shi-Pin Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
| | - Hui Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Hazra A, Dasgupta N, Sengupta C, Das S. Extrapolative microRNA precursor based SSR mining from tea EST database in respect to agronomic traits. BMC Res Notes 2017; 10:261. [PMID: 28683768 PMCID: PMC5501407 DOI: 10.1186/s13104-017-2577-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/28/2017] [Indexed: 11/10/2022] Open
Abstract
Tea (Camellia sinensis, (L.) Kuntze) is considered as most popular drink across the world and it is widely consumed beverage for its several health-benefit characteristics. These positive traits primarily rely on its regulatory networks of different metabolic pathways. Development of microsatellite markers from the conserved genomic regions are being worthwhile for reviewing the genetic diversity of closely related species or self-pollinated species. Although several SSR markers have been reported, in tea, the trait-specific Simple Sequence Repeat (SSR) markers, leading to be useful in marker assisted breeding technique, are yet to be identified. Micro RNAs are short, non-coding RNA molecules, involved in post transcriptional mode of gene regulation and thus effects on related phenotype. Present study deals with identification of the microsatellite motifs within the reported and predicted miRNA precursors that are effectively followed by designing of primers from SSR flanking regions in order to PCR validation. In addition to the earlier reports, two new miRNAs are predicting here from tea expressed tag sequence database. Furthermore, 18 SSR motifs are found to be in 13 of all 33 predicted miRNAs. Trinucleotide motifs are most abundant among all followed by dinucleotides. Since, miRNA based SSR markers are evidenced to have significant role on genetic fingerprinting study, these outcomes would pave the way in developing novel markers for tagging tea specific agronomic traits as well as substantiating non-conventional breeding program.
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Affiliation(s)
- Anjan Hazra
- Agricultural and Ecological Research Unit, Indian Statistical Institute, 203, Barrackpore Trunk Road, Kolkata, 700 108, India.,Department of Botany, University of Kalyani, Nadia, Kalyani, 741235, India
| | - Nirjhar Dasgupta
- Agricultural and Ecological Research Unit, Indian Statistical Institute, 203, Barrackpore Trunk Road, Kolkata, 700 108, India
| | - Chandan Sengupta
- Department of Botany, University of Kalyani, Nadia, Kalyani, 741235, India
| | - Sauren Das
- Agricultural and Ecological Research Unit, Indian Statistical Institute, 203, Barrackpore Trunk Road, Kolkata, 700 108, India.
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Hou YH, Jeyaraj A, Zhang X, Wei CL. Absolute quantification of microRNAs in green tea (Camellia sinensis) by stem-loop quantitative real-time PCR. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:2975-2981. [PMID: 27861949 DOI: 10.1002/jsfa.8137] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 10/03/2016] [Accepted: 11/07/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND There are some studies to show that food-derived plant microRNAs (miRNAs) may be detected in mammals. The research evidence has provoked a considerable debate whether plant-derived miRNAs exert the same regulatory functions as endogenous animal miRNAs. To test the hypothesis, methods of highly sensitive absolute quantification miRNAs have been developed. However, absolute miRNA quantification of green tea has not yet been reported. This study is the first to build an absolute quantification method to detect miRNAs level in green tea using stem-loop quantitative real-time PCR (qRT-PCR). RESULTS Two miRNAs, csn-miR164 (a conserved miRNA) and csn-miRn329 (a tea-specific miRNA), were selected as examples for the detection and absolute quantification of miRNAs in green tea samples using stem-loop qRT-PCR. The content of csn-miR164 was significantly higher in the Yuexi Cuilan (YX) samples than in the Shucheng Orchid (SC) samples. The content of csn-miRn329 was found to be high at the start of processing in leaf tissues in both the withering and soaking experiments, after which it gradually decreased with time. CONCLUSION To the best of our knowledge, this is the first report to absolutely quantify the miRNAs present in green tea. This method will help to further investigate the possibility that tea-derived miRNAs may play an important role on defending against various diseases in humans. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Ying-Hui Hou
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China
| | - Anburaj Jeyaraj
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China
| | - Xiao Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China
| | - Chao-Ling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, P.R. China
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Li Q, Deng C, Xia Y, Kong L, Zhang H, Zhang S, Wang J. Identification of novel miRNAs and miRNA expression profiling in embryogenic tissues of Picea balfouriana treated by 6-benzylaminopurine. PLoS One 2017; 12:e0176112. [PMID: 28486552 PMCID: PMC5423612 DOI: 10.1371/journal.pone.0176112] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 04/05/2017] [Indexed: 11/18/2022] Open
Abstract
Here, we compared miRNA expression profiles in embryonic cell cultures of the conifer Picea balfouriana following application of the synthetic cytokinin 6-benzylaminopurine (6-BAP). We used next-generation sequencing to analyze three libraries of small RNAs from the treated embryogenic cell cultures and generated 24,000,000 raw reads from each of the libraries. Over 70 differentially regulated micro RNA (miRNA) families (≥2 fold change in expression) were identified between pairs of treatments. A quantitative analysis showed that miR3633 and miR1026 were upregulated in tissues with the highest embryogenic ability. These two miRNAs were predicted to target genes encoding receptor-like protein kinase and GAMYB transcription factors, respectively. In one library, miR1160, miR5638, miR1315, and miR5225 were downregulated. These four miRNAs were predicted to target genes encoding APETALA2, calmodulin-binding protein, and calcium-dependent protein kinase transcription factors. The expression patterns of the miRNAs and their targets were negatively correlated. Approximately 181 potentially novel P. balfouriana miRNAs were predicted from the three libraries, and seven were validated during the quantitative analysis. This study is the first report of differential miRNA regulation in tissues treated with 6-BAP during somatic embryogenesis. The differentially expressed miRNAs will be of value for investigating the mechanisms of embryogenic processes that are responsive to 6-BAP in P. balfouriana.
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Affiliation(s)
- Qingfen Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Cheng Deng
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Yan Xia
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Lisheng Kong
- Department of Biology, Centre for Forest Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Hanguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Shougong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- * E-mail:
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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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Kulkarni AP, Mittal SPK. Sequence data mining in search of hookworm (Necator americanus) microRNAs. Gene 2016; 590:317-23. [PMID: 27259664 DOI: 10.1016/j.gene.2016.05.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/29/2016] [Indexed: 01/06/2023]
Abstract
The new world hookworm, Necator americanus is a soil-transmitted nematode responsible for Necatoriasis (a type of helminthiasis) in hosts such as humans, dogs, and cats. N. americanus genome and transcriptome has been sequenced and a draft assembly analysis has been published highlighting protein coding genes and possible drug target proteins. Hookworm microRNA identification, annotations and their public release is yet to be attempted. The same is evident from lack of hookworm miRNA information in related popular public nucleotide sequence repositories such as miRBase, GenBank, WormBase etc. Therefore, in the present study we addressed these issues using EST and assembled transcript sequence information of hookworm. Using computational approaches, we identified three miRNAs precursor sequences and their mature forms. We also identified their potential targets from hookworm ESTs and transcripts, and from human transcriptome. Overall, the results indicate presence of nematode specific miRNA homologs in N. americanus and shades light on their putative targets in worm itself and the human host.
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Affiliation(s)
- Abhijeet P Kulkarni
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, Maharashtra, India.
| | - Smriti P K Mittal
- Department of Zoology, Savitribai Phule Pune University, Pune 411007, Maharashtra, India
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Selection and Verification of Candidate Reference Genes for Mature MicroRNA Expression by Quantitative RT-PCR in the Tea Plant (Camellia sinensis). Genes (Basel) 2016; 7:genes7060025. [PMID: 27240406 PMCID: PMC4929424 DOI: 10.3390/genes7060025] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 04/11/2016] [Accepted: 05/24/2016] [Indexed: 12/15/2022] Open
Abstract
Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is a rapid and sensitive method for analyzing microRNA (miRNA) expression. However, accurate qRT-PCR results depend on the selection of reliable reference genes as internal positive controls. To date, few studies have identified reliable reference genes for differential expression analysis of miRNAs among tissues, and among experimental conditions in plants. In this study, three miRNAs and four non-coding small RNAs (ncRNA) were selected as reference candidates, and the stability of their expression was evaluated among different tissues and under different experimental conditions in the tea plant (Camellia sinensis) using the geNorm and NormFinder programs. It was shown that miR159a was the best single reference gene in the bud to the fifth leaf, 5S rRNA was the most suitable gene in different organs, miR6149 was the most stable gene when the leaves were attacked by Ectropis oblique and U4, miR5368n and miR159a were the best genes when the leaves were treated by methyl jasmonate (MeJA), salicylic acid (SA) and abscisic acid (ABA), respectively. Our results provide suitable reference genes for future investigations on miRNA functions in tea plants.
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Mukhopadhyay M, Mondal TK, Chand PK. Biotechnological advances in tea (Camellia sinensis [L.] O. Kuntze): a review. PLANT CELL REPORTS 2016; 35:255-87. [PMID: 26563347 DOI: 10.1007/s00299-015-1884-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/10/2015] [Accepted: 10/13/2015] [Indexed: 05/28/2023]
Abstract
This article presents a comprehensive review on the success and limitations of biotechnological approaches aimed at genetic improvement of tea with a purpose to explore possibilities to address challenging areas. Tea is a woody perennial tree with a life span of more than 100 years. Conventional breeding of tea is slow and limited primarily to selection which leads to narrowing down of its genetic base. Harnessing the benefits of wild relatives has been negligible due to low cross-compatibility, genetic drag and undesirable alleles for low yield. Additionally, being a recalcitrant species, in vitro propagation of tea is constrained too. Nevertheless, maneuvering with tissue/cell culture techniques, a considerable success has been achieved in the area of micropropagation, somatic embryogenesis as well as genetic transformation. Besides, use of molecular markers, "expressomics" (transcriptomics, proteomics, metabolomics), map-based cloning towards construction of physical maps, generation of expressed sequenced tags (ESTs) have facilitated the identification of QTLs and discovery of genes associated with abiotic or biotic stress tolerance and agronomic traits. Furthermore, the complete genome (or at least gene space) sequence of tea is expected to be accessible in the near future which will strengthen combinational approaches for improvement of tea. This review presents a comprehensive account of the success and limitations of the biotechnological tools and techniques hitherto applied to tea and its wild relatives. Expectedly, this will form a basis for making further advances aimed at genetic improvement of tea in particular and of economically important woody perennials in general.
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Affiliation(s)
- Mainaak Mukhopadhyay
- Department of Botany, University of Kalyani, Kalyani, 741235, Nadia, West Bengal, India.
| | - Tapan K Mondal
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012, India.
| | - Pradeep K Chand
- Plant Cell and Tissue Culture Facility, Post-Graduate Department of Botany, Utkal University, Vani Vihar, Bhubaneswar, 751004, Odisha, India.
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32
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New insights of medicinal plant therapeutic activity-The miRNA transfer. Biomed Pharmacother 2015; 74:228-32. [PMID: 26349990 DOI: 10.1016/j.biopha.2015.08.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 08/04/2015] [Indexed: 01/21/2023] Open
Abstract
MicroRNA (miRNA) has become the spotlight of the biomedical research around the world and is considered to be a major post-transcriptional gene regulator. This small, endogenous RNA (21-25 nucleotides long) plays an important role by targeting specific mRNAs in plants, animals and humans. Herbal medicine has been used for thousands of years, however little is known about its molecular mechanism of action. Since the discovery of plant miRNA in human tissue and sera after ingestion, the connection between the two kingdoms is presented under a new perspective. Forward pharmacology, such as miRNA therapeutics could be the next best step toward identifying novel therapeutic options involving medicinal plants. Besides reporting the latest findings regarding the cross-kingdom transfer of miRNA and its therapeutic application, this review can inform further investigations that could lead to a modern definition of herbal medicine.
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Zheng C, Zhao L, Wang Y, Shen J, Zhang Y, Jia S, Li Y, Ding Z. Integrated RNA-Seq and sRNA-Seq Analysis Identifies Chilling and Freezing Responsive Key Molecular Players and Pathways in Tea Plant (Camellia sinensis). PLoS One 2015; 10:e0125031. [PMID: 25901577 PMCID: PMC4406609 DOI: 10.1371/journal.pone.0125031] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 03/19/2015] [Indexed: 12/17/2022] Open
Abstract
Tea [Camellia sinensis (L) O. Kuntze, Theaceae] is one of the most popular non-alcoholic beverages worldwide. Cold stress is one of the most severe abiotic stresses that limit tea plants’ growth, survival and geographical distribution. However, the genetic regulatory network and signaling pathways involved in cold stress responses in tea plants remain unearthed. Using RNA-Seq, DGE and sRNA-Seq technologies, we performed an integrative analysis of miRNA and mRNA expression profiling and their regulatory network of tea plants under chilling (4℃) and freezing (-5℃) stress. Differentially expressed (DE) miRNA and mRNA profiles were obtained based on fold change analysis, miRNAs and target mRNAs were found to show both coherent and incoherent relationships in the regulatory network. Furthermore, we compared several key pathways (e.g., ‘Photosynthesis’), GO terms (e.g., ‘response to karrikin’) and transcriptional factors (TFs, e.g., DREB1b/CBF1) which were identified as involved in the early chilling and/or freezing response of tea plants. Intriguingly, we found that karrikins, a new group of plant growth regulators, and β-primeverosidase (BPR), a key enzyme functionally relevant with the formation of tea aroma might play an important role in both early chilling and freezing response of tea plants. Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) analysis further confirmed the results from RNA-Seq and sRNA-Seq analysis. This is the first study to simultaneously profile the expression patterns of both miRNAs and mRNAs on a genome-wide scale to elucidate the molecular mechanisms of early responses of tea plants to cold stress. In addition to gaining a deeper insight into the cold resistant characteristics of tea plants, we provide a good case study to analyse mRNA/miRNA expression and profiling of non-model plant species using next-generation sequencing technology.
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Affiliation(s)
- Chao Zheng
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
- Key Laboratory of Genetic Improvement and Breeding for Horticultural Plants, Qingdao, Shandong, China
| | - Lei Zhao
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
- Key Laboratory of Genetic Improvement and Breeding for Horticultural Plants, Qingdao, Shandong, China
| | - Yu Wang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
- Key Laboratory of Genetic Improvement and Breeding for Horticultural Plants, Qingdao, Shandong, China
| | - Jiazhi Shen
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
- Key Laboratory of Genetic Improvement and Breeding for Horticultural Plants, Qingdao, Shandong, China
| | - Yinfei Zhang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
- Key Laboratory of Genetic Improvement and Breeding for Horticultural Plants, Qingdao, Shandong, China
| | - Sisi Jia
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
- Key Laboratory of Genetic Improvement and Breeding for Horticultural Plants, Qingdao, Shandong, China
| | - Yusheng Li
- Fruit and Tea Technology Extension Station, Jinan, Shandong, China
| | - Zhaotang Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
- Key Laboratory of Genetic Improvement and Breeding for Horticultural Plants, Qingdao, Shandong, China
- * E-mail:
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Zhang Y, Zhu X, Chen X, Song C, Zou Z, Wang Y, Wang M, Fang W, Li X. Identification and characterization of cold-responsive microRNAs in tea plant (Camellia sinensis) and their targets using high-throughput sequencing and degradome analysis. BMC PLANT BIOLOGY 2014; 14:271. [PMID: 25330732 PMCID: PMC4209041 DOI: 10.1186/s12870-014-0271-x] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 10/03/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are approximately 19 ~ 21 nucleotide noncoding RNAs produced by Dicer-catalyzed excision from stem-loop precursors. Many plant miRNAs have critical functions in development, nutrient homeostasis, abiotic stress responses, and pathogen responses via interaction with specific target mRNAs. Camellia sinensis is one of the most important commercial beverage crops in the world. However, miRNAs associated with cold stress tolerance in C. sinensis remains unexplored. The use of high-throughput sequencing can provide a much deeper understanding of miRNAs. To obtain more insight into the function of miRNAs in cold stress tolerance, Illumina sequencing of C. sinensis sRNA was conducted. RESULT Solexa sequencing technology was used for high-throughput sequencing of the small RNA library from the cold treatment of tea leaves. To align the sequencing data with known plant miRNAs, we characterized 106 conserved C. sinensis miRNAs. In addition, 215 potential candidate miRNAs were found, among, which 98 candidates with star sequences were chosen as novel miRNAs. Both congruously and differentially regulated miRNAs were obtained, and cultivar-specific miRNAs were identified by microarray-based hybridization in response to cold stress. The results were also confirmed by quantitative real-time polymerase chain reaction. To confirm the targets of miRNAs, two degradome libraries from two treatments were constructed. According to degradome sequencing, 455 and 591 genes were identified as cleavage targets of miRNAs from cold treatments and control libraries, respectively, and 283 targets were present in both libraries. Functional analysis of these miRNA targets indicated their involvement in important activities, such as development, regulation of transcription, and stress response. CONCLUSIONS We discovered 31 up-regulated miRNAs and 43 down-regulated miRNAs in 'Yingshuang', and 46 up-regulated miRNA and 45 down-regulated miRNAs in 'Baiye 1' in response to cold stress, respectively. A total of 763 related target genes were detected by degradome sequencing. The RLM-5'RACE procedure was successfully used to map the cleavage sites in six target genes of C. sinensis. These findings reveal important information about the regulatory mechanism of miRNAs in C. sinensis, and promote the understanding of miRNA functions during the cold response. The miRNA genotype-specific expression model might explain the distinct cold sensitivities between tea lines.
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Affiliation(s)
- Yue Zhang
- />Tea Research Institute, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095 Jiangsu Province P. R. China
| | - Xujun Zhu
- />Tea Research Institute, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095 Jiangsu Province P. R. China
| | - Xuan Chen
- />Tea Research Institute, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095 Jiangsu Province P. R. China
| | - Changnian Song
- />College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 P. R. China
| | - Zhongwei Zou
- />Molecular population genetics group, Temasek lifesciences laboratory, 1 Research link, National University of Singapore, Singapore, 117604 Singapore
| | - Yuhua Wang
- />Tea Research Institute, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095 Jiangsu Province P. R. China
| | - Mingle Wang
- />Tea Research Institute, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095 Jiangsu Province P. R. China
| | - Wanping Fang
- />Tea Research Institute, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095 Jiangsu Province P. R. China
| | - Xinghui Li
- />Tea Research Institute, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095 Jiangsu Province P. R. China
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Jeyaraj A, Chandran V, Gajjeraman P. Differential expression of microRNAs in dormant bud of tea [Camellia sinensis (L.) O. Kuntze]. PLANT CELL REPORTS 2014; 33:1053-69. [PMID: 24658841 DOI: 10.1007/s00299-014-1589-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 01/25/2014] [Accepted: 02/10/2014] [Indexed: 05/02/2023]
Abstract
Expression analysis of miRNAs and understanding their target genes function in dormant tea bud might be used to identify molecular network panel and novel approaches for modulating dormancy in tea. Tea [Camellia sinensis (L) O. Kuntze, Theaceae] is an important commercial beverage crop manufactured from the apical bud and two leaves immediately below the bud. The yield and quality of tea depend on the vegetative growth of shoots and bud dormancy. The dormancy of bud is being regulated by many factors, such as mechanical, environmental and molecular mechanisms. MicroRNAs (miRNAs) are a newly identified class of small non-protein coding regulatory RNAs in both plants and animals which regulates gene expression at post-transcriptional level either by cleavage or translational inhibition of targeted mRNA transcripts. With these importances, the expression pattern of tea miRNAs was analyzed in active and dormant bud using stem-loop pulse RT-qPCR method. The results demonstrated the following expression pattern for highly up-regulated miRNAs, cs-miR 414[csmiR 408[cs-miR782[cs-miR169, and down-regulated miRNAs, cs-miR828[cs-miR1864[cs-miR852[csmiR1425 in dormant bud of tea. Furthermore, the role of target transcripts regulated by these miRNAs in relation to bud dormancy was discussed in detail. Therefore, the present study on the miRNA expression in tea will provide basis and considerably broaden the scope of understanding the function of miRNAs within the bud tissues and can serve as an initial point for RNA interference-based controlling strategies of bud dormancy in tea.
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36
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Zhu QW, Luo YP. Identification of miRNAs and their targets in tea (Camellia sinensis). J Zhejiang Univ Sci B 2014; 14:916-23. [PMID: 24101208 DOI: 10.1631/jzus.b1300006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
MicroRNAs (miRNAs) are endogenous small RNAs playing a crucial role in plant growth and development, as well as stress responses. Among them, some are highly evolutionally conserved in the plant kingdom, this provide a powerful strategy for identifying miRNAs in a new species. Tea (Camellia sinensis) is one of the most important commercial beverage crops in the world, but only a limited number of miRNAs have been identified. In the present study, a total of 14 new C. sinensis miRNAs were identified by expressed sequence tag (EST) analysis from 47452 available C. sinensis ESTs. These miRNAs potentially target 51 mRNAs, which can act as transcription factors, and participate in stress response, transmembrane transport, and signal transduction. Analysis of gene ontology (GO), based on these targets, suggested that 37 biological processes were involved, such as oxidation-reduction process, stress response, and transport. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis inferred that the identified miRNAs took part in 13 metabolic networks. Our study will help further understanding of the essential roles of miRNAs in C. sinensis growth and development, and stress response.
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Affiliation(s)
- Quan-wu Zhu
- Institute of Tea Science, Zhejiang University, Hangzhou 310058, China
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37
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Panda D, Dehury B, Sahu J, Barooah M, Sen P, Modi MK. Computational identification and characterization of conserved miRNAs and their target genes in garlic (Allium sativum L.) expressed sequence tags. Gene 2014; 537:333-42. [PMID: 24434367 DOI: 10.1016/j.gene.2014.01.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 12/03/2013] [Accepted: 01/04/2014] [Indexed: 01/22/2023]
Abstract
The endogenous small non-coding functional microRNAs (miRNAs) are short in size, range from ~21 to 24 nucleotides in length, play a pivotal role in gene expression in plants and animals by silencing genes either by destructing or blocking of translation of homologous mRNA. Although various high-throughput, time consuming and expensive techniques like forward genetics and direct cloning are employed to detect miRNAs in plants but comparative genomics complemented with novel bioinformatic tools pave the way for efficient and cost-effective identification of miRNAs through homologous sequence search with previously known miRNAs. In this study, an attempt was made to identify and characterize conserved miRNAs in garlic expressed sequence tags (ESTs) through computational means. For identification of novel miRNAs in garlic, a total 3227 known mature miRNAs of plant kingdom Viridiplantae were searched for homology against 21,637 EST sequences resulting in identification of 6 potential miRNA candidates belonging to 6 different miRNA families. The psRNATarget server predicted 33 potential target genes and their probable functions for the six identified miRNA families in garlic. Most of the garlic miRNA target genes seem to encode transcription factors as well as genes involved in stress response, metabolism, plant growth and development. The results from the present study will shed more light on the understanding of molecular mechanisms of miRNA in garlic which may aid in the development of novel and precise techniques to understand some post-transcriptional gene silencing mechanism in response to stress tolerance.
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Affiliation(s)
- Debashis Panda
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India
| | - Budheswar Dehury
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India
| | - Jagajjit Sahu
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India
| | - Madhumita Barooah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India
| | - Priyabrata Sen
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India
| | - Mahendra K Modi
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India.
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Pani A, Mahapatra RK. Computational identification of microRNAs and their targets in Catharanthus roseus expressed sequence tags. GENOMICS DATA 2013; 1:2-6. [PMID: 26484050 PMCID: PMC4608865 DOI: 10.1016/j.gdata.2013.06.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Revised: 06/27/2013] [Accepted: 06/28/2013] [Indexed: 12/21/2022]
Abstract
No study has been performed on identifying microRNAs (miRNAs) and their targets in the medicinal plant, Catharanthus roseus. In the present study, using the comparative genomics approach, we have predicted two potential C. roseus miRNAs. Furthermore, twelve potential mRNA targets were identified in C. roseus genome based on the characteristics that miRNAs exhibit perfect or nearly perfect complementarity with their targeted mRNA sequences. Among them many of the targets were predicted to encode enzymes that regulate the biosynthesis of terpenoid indole alkaloids (TIA). In addition, most of the predicted targets were the gene coding for transcription factors which are mainly involved in cell growth and development, signaling and metabolism. This is the first in silico study to indicate that miRNA target gene encoding enzymes involved in vinblastine and vincristine biosynthesis, which may help to understand the miRNA-mediated regulation of TIA alkaloid biosynthesis in C. roseus.
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Affiliation(s)
- Alok Pani
- School of Biotechnology, Campus-11, KIIT University, Bhubaneswar, Odisha 751024, India
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Pandey B, Gupta OP, Pandey DM, Sharma I, Sharma P. Identification of new stress-induced microRNA and their targets in wheat using computational approach. PLANT SIGNALING & BEHAVIOR 2013; 8:e23932. [PMID: 23511197 PMCID: PMC3906146 DOI: 10.4161/psb.23932] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
MicroRNAs (miRNAs) are a class of short endogenous non-coding small RNA molecules of about 18-22 nucleotides in length. Their main function is to downregulate gene expression in different manners like translational repression, mRNA cleavage and epigenetic modification. Computational predictions have raised the number of miRNAs in wheat significantly using an EST based approach. Hence, a combinatorial approach which is amalgamation of bioinformatics software and perl script was used to identify new miRNA to add to the growing database of wheat miRNA. Identification of miRNAs was initiated by mining the EST (Expressed Sequence Tags) database available at National Center for Biotechnology Information. In this investigation, 4677 mature microRNA sequences belonging to 50 miRNA families from different plant species were used to predict miRNA in wheat. A total of five abiotic stress-responsive new miRNAs were predicted and named Ta-miR5653, Ta-miR855, Ta-miR819k, Ta-miR3708 and Ta-miR5156. In addition, four previously identified miRNA, i.e., Ta-miR1122, miR1117, Ta-miR1134 and Ta-miR1133 were predicted in newly identified EST sequence and 14 potential target genes were subsequently predicted, most of which seems to encode ubiquitin carrier protein, serine/threonine protein kinase, 40S ribosomal protein, F-box/kelch-repeat protein, BTB/POZ domain-containing protein, transcription factors which are involved in growth, development, metabolism and stress response. Our result has increased the number of miRNAs in wheat, which should be useful for further investigation into the biological functions and evolution of miRNAs in wheat and other plant species.
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Affiliation(s)
- Bharati Pandey
- Plant Biotechnology; Directorate of Wheat Research; Karnal, India
- Department of Biotechnology; Birla Institute of Technology; Mesra, India
| | - Om Prakash Gupta
- Quality and Basic Science; Directorate of Wheat Research; Karnal, India
| | - Dev Mani Pandey
- Department of Biotechnology; Birla Institute of Technology; Mesra, India
| | - Indu Sharma
- Plant Biotechnology; Directorate of Wheat Research; Karnal, India
| | - Pradeep Sharma
- Plant Biotechnology; Directorate of Wheat Research; Karnal, India
- Correspondence to: Pradeep Sharma,
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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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Zhou X, Jin P, Qin S, Chen L, Ma F. Systematic investigation of Amphioxus (Branchiostoma floridae) microRNAs. Gene 2012; 508:110-6. [DOI: 10.1016/j.gene.2012.06.065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 06/20/2012] [Indexed: 01/17/2023]
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Sun YH, Shi R, Zhang XH, Chiang VL, Sederoff RR. MicroRNAs in trees. PLANT MOLECULAR BIOLOGY 2012; 80:37-53. [PMID: 22161564 DOI: 10.1007/s11103-011-9864-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Accepted: 10/26/2011] [Indexed: 05/31/2023]
Abstract
MicroRNAs (miRNAs) are 20-24 nucleotide long molecules processed from a specific class of RNA polymerase II transcripts that mainly regulate the stability of mRNAs containing a complementary sequence by targeted degradation in plants. Many features of tree biology are regulated by miRNAs affecting development, metabolism, adaptation and evolution. MiRNAs may be modified and harnessed for controlled suppression of specific genes to learn about gene function, or for practical applications through genetic engineering. Modified (artificial) miRNAs act as dominant suppressors and are particularly useful in tree genetics because they bypass the generations of inbreeding needed for fixation of recessive mutations. The purpose of this review is to summarize the current status of information on miRNAs in trees and to guide future studies on the role of miRNAs in the biology of woody perennials and to illustrate their utility in directed genetic modification of trees.
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Affiliation(s)
- Ying-Hsuan Sun
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
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Pani A, Mahapatra RK, Behera N, Naik PK. Computational identification of sweet wormwood (Artemisia annua) microRNA and their mRNA targets. GENOMICS PROTEOMICS & BIOINFORMATICS 2012; 9:200-10. [PMID: 22289476 PMCID: PMC5054163 DOI: 10.1016/s1672-0229(11)60023-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 10/28/2011] [Indexed: 11/18/2022]
Abstract
Despite its efficacy against malaria, the relatively low yield (0.01%-0.8%) of artemisinin in Artemisia annua is a serious limitation to the commercialization of the drug. A better understanding of the biosynthetic pathway of artemisinin and its regulation by both exogenous and endogenous factors is essential to improve artemisinin yield. Increasing evidence has shown that microRNAs (miRNAs) play multiple roles in various biological processes. In this study, we used previously known miRNAs from Arabidopsis and rice against expressed sequence tag (EST) database of A. annua to search for potential miRNAs and their targets in A. annua. A total of six potential miRNAs were predicted, which belong to the miR414 and miR1310 families. Furthermore, eight potential target genes were identified in this species. Among them, seven genes encode proteins that play important roles in artemisinin biosynthesis, including HMG-CoA reductase (HMGR), amorpha-4,11-diene synthase (ADS), farnesyl pyrophosphate synthase (FPS) and cytochrome P450. In addition, a gene coding for putative AINTEGUMENTA, which is involved in signal transduction and development, was also predicted as one of the targets. This is the first in silico study to indicate that miRNAs target genes encoding enzymes involved in artemisinin biosynthesis, which may help to understand the miRNA-mediated regulation of artemisinin biosynthesis in A. annua.
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Affiliation(s)
- Alok Pani
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT) University, Bhubaneswar, Odisha 751024, India
| | - Rajani Kanta Mahapatra
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT) University, Bhubaneswar, Odisha 751024, India
- School of Life Sciences, Sambalpur University, Burla, Odisha 768019, India
- Corresponding author.
| | - Niranjan Behera
- School of Life Sciences, Sambalpur University, Burla, Odisha 768019, India
| | - Pradeep Kumar Naik
- Department of Biotechnology & Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh 173215, India
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Monobe M, Ogino A, Ema K, Tokuda Y, Maeda-Yamamoto M. A crude extract from immature green tea (Camellia sinensis) leaves promotes Toll-like receptor 7-mediated interferon-α production in human macrophage-like cells. Cytotechnology 2011; 64:145-8. [PMID: 22124541 DOI: 10.1007/s10616-011-9412-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2011] [Accepted: 11/12/2011] [Indexed: 11/29/2022] Open
Abstract
Toll-like receptor 7 (TLR7) senses viral single-stranded RNA (ssRNA), induces the production of type I interferons (IFNs), IFN-α and -β, in macrophages such as dendritic cells (DCs), and its immune system protects the host from virus infection. Here, we found that a crude extract from immature green tea leaves (iTPS) containing a macromolecule with ssRNA fragments, induces IFN-α production in human macrophage-like cells. In addition IFN-α production was inhibited by treatment with TLR7 inhibitors or a phagocytosis inhibitor.
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Affiliation(s)
- Manami Monobe
- NARO Institute of Vegetable and Tea Science (NIVTS), 2769 Kanaya-Shishidoi, Shimada, Shizuoka, 428-8501, Japan,
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Characterization of novel small RNAs from tea (Camellia sinensis L.). Mol Biol Rep 2011; 39:3977-86. [DOI: 10.1007/s11033-011-1178-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 07/02/2011] [Indexed: 11/26/2022]
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Das A, Mondal TK. Computational Identification of Conserved microRNAs and Their Targets in Tea (Camellia sinensis). ACTA ACUST UNITED AC 2010. [DOI: 10.4236/ajps.2010.12010] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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