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Pei LL, Zhang LL, Liu X, Jiang J. Role of microRNA miR171 in plant development. PeerJ 2023; 11:e15632. [PMID: 37456878 PMCID: PMC10340099 DOI: 10.7717/peerj.15632] [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: 12/15/2022] [Accepted: 06/02/2023] [Indexed: 07/18/2023] Open
Abstract
MicroRNAs (miRNAs) are endogenous non-coding small RNA with 19-24 nucleotides (nts) in length, which play an essential role in regulating gene expression at the post-transcriptional level. As one of the first miRNAs found in plants, miR171 is a typical class of conserved miRNAs. The miR171 sequences among different species are highly similar, and the vast majority of them have both "GAGCCG" and "CAAUAU" fragments. In addition to being involved in plant growth and development, hormone signaling and stress response, miR171 also plays multiple and important roles in plants through interactions with microbe and other small-RNAs. The miRNA functions by regulating the expression of target genes. Most of miR171's target genes are in the GRAS gene family, but also include some NSP, miRNAs, lncRNAs, and other genes. This review is intended to summarize recent updates on miR171 regarding its function in plant life and hopefully provide new ideas for understanding miR171 function and regulatory mechanisms.
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Affiliation(s)
- Ling Ling Pei
- College of Horticulture, Shenyang Agricultural University, Shenyang, Shenhe District, China
| | - Ling Ling Zhang
- College of Horticulture, Shenyang Agriculture University, Shenyang, Shenhe District, China
| | - Xin Liu
- Horticulture Department, Shenyang Agricultural University, Shenyang, Shenhe District, China
| | - Jing Jiang
- Horticulture Department, Shenyang Agricultural University, Shenyang, Shenhe District, China
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Li M, Si X, Liu Y, Liu Y, Cheng X, Dai Z, Yu X, Ali M, Lu G. Transcriptomic analysis of ncRNA and mRNA interactions during leaf senescence in tomato. Int J Biol Macromol 2022; 222:2556-2570. [DOI: 10.1016/j.ijbiomac.2022.10.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/27/2022] [Accepted: 10/02/2022] [Indexed: 11/05/2022]
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Çakır Ö, Arıkan B, Karpuz B, Turgut-Kara N. Expression analysis of miRNAs and their targets related to salt stress in Solanum lycopersicum H-2274. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2020.1870871] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Özgür Çakır
- Department of Molecular Biology and Genetics, Science Faculty, İstanbul University, Istanbul, Turkey
| | - Burcu Arıkan
- Department of Molecular Biology and Genetics, Science Faculty, İstanbul University, Istanbul, Turkey
| | - Burcu Karpuz
- Programme of Molecular Biology and Genetics, Institute of Science, Istanbul University, Istanbul, Turkey
| | - Neslihan Turgut-Kara
- Department of Molecular Biology and Genetics, Science Faculty, İstanbul University, Istanbul, Turkey
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Ma L, Mu J, Grierson D, Wang Y, Gao L, Zhao X, Zhu B, Luo Y, Shi K, Wang Q, Zuo J. Noncoding RNAs: functional regulatory factors in tomato fruit ripening. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1753-1762. [PMID: 32211918 DOI: 10.1007/s00122-020-03582-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/12/2020] [Indexed: 06/10/2023]
Abstract
Tomato has emerged as the model system for investigations into the regulation of fleshy-fruit ripening and senescence, and the ripening process involving the coordinated regulation at the gene/chromatin/epigenetic, transcriptional, post-transcriptional and protein levels. Noncoding RNAs play important roles in fruit ripening as important transcriptional and post-transcriptional regulatory factors. In this review, we systematically summarize the recent advances in the regulation of tomato fruit ripening involved in ethylene biosynthesis and signal transduction, fruit pigment accumulation, fruit flavor and aroma, fruit texture by noncoding RNAs and their coordinate regulatory network model were set up and also suggest future directions for the functional regulations of noncoding RNAs on tomato fruit ripening.
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Affiliation(s)
- Lili Ma
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
| | - Jianlou Mu
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
| | - Donald Grierson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Yunxiang Wang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, China
| | - Lipu Gao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xiaoyan Zhao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Benzhong Zhu
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yunbo Luo
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Kai Shi
- Department of Horticulture, Zhejiang University, Hangzhou, 310058, China.
| | - Qing Wang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Jinhua Zuo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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Zuo J, Wang Q, Han C, Ju Z, Cao D, Zhu B, Luo Y, Gao L. SRNAome and degradome sequencing analysis reveals specific regulation of sRNA in response to chilling injury in tomato fruit. PHYSIOLOGIA PLANTARUM 2017; 160:142-154. [PMID: 27595790 DOI: 10.1111/ppl.12509] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 05/12/2016] [Accepted: 07/18/2016] [Indexed: 05/15/2023]
Abstract
Plant genomes encode diverse small RNA classes that function in distinct gene-silencing pathways. To elucidate the intricate regulation of microRNAs (miRNAs) and endogenous small-interfering RNAs (siRNAs) in response to chilling injury in tomato fruit, the deep sequencing and bioinformatic methods were combined to decipher the small RNAs landscape in the control and chilling-injured groups. Except for the known miRNAs and ta-siRNAs, 85 novel miRNAs and 5 ta-siRNAs members belonging to 3 TAS families (TAS5, TAS9 and TAS10) were identified, 34 putative phased small RNAs and 740 cis/trans-natural antisense small-interfering RNAs (nat-siRNAs) were also found in our results which enriched the tomato small RNAs repository. A large number of genes targeted by those miRNAs and siRNAs were predicted to be involved in the chilling injury responsive process and five of them were verified via degradome sequencing. Based on the above results, a regulatory model that comprehensively reveals the relationships between the small RNAs and their targets was set up. This work provides a foundation for further study of the regulation of miRNAs and siRNAs in the plant in response to chilling injury.
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Affiliation(s)
- Jinhua Zuo
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing, 100097, China
| | - Qing Wang
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing, 100097, China
| | - Cong Han
- Laboratory of Postharvest Physiology and Technology of Fruits and Vegetables, Department of Food Science, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zheng Ju
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Dongyan Cao
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Benzhong Zhu
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yunbo Luo
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Lipu Gao
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing, 100097, China
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In Silico Identification and Validation of Potential microRNAs in Kinnow Mandarin (Citrus reticulata Blanco). Interdiscip Sci 2017; 10:762-770. [PMID: 28534166 DOI: 10.1007/s12539-017-0235-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 04/28/2017] [Accepted: 05/02/2017] [Indexed: 10/19/2022]
Abstract
MicroRNAs (miRNAs) are a large family of 19-25 nucleotides, regulatory, non-coding RNA molecules that control gene expression by cleaving or inhibiting the translation of target gene transcripts in animals and plants. Despite the important functions of miRNAs related to regulation of plant growth and development processes, metabolism, and abiotic and biotic stresses, little is known about the disease-related miRNA. Here, we present a new pipeline for miRNA analysis using expressed sequence tags (ESTs)-based bioinformatics approach in Kinnow mandarin, a commercially important citrus fruit crop. For this, 56,041 raw EST sequences of Citrus reticulata Blanco were retrieved from EST database in NCBI through step-by-step filtering and processing methods and 130 miRNAs were predicted. Upon blast with Citrus sinensis transcriptome data, these produced potential targets related to disease resistance proteins, pectin lyase-like superfamily proteins, lateral organ boundaries (LOB) domain-containing proteins 11, and protein phosphatase 2C family proteins, protein kinases, dehydrogenases, and methyltransferases. Majority of the predicted miRNAs were of 22, 23, and 24 nucleotides in length. To validate these computationally predicted miRNA, poly(A)-tailed Reverse Transcription-PCR was applied to detect the expression of seven miRNA which showed disease-related potential targets, in citrus greening diseased leaf tissues in comparison to the healthy tissues of Kinnow mandarin. Our study provides information on regulatory roles of these potential miRNAs for the citrus greening disease development, miRNA targets, and would be helpful for future research of miRNA function in citrus.
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Cheng HY, Wang Y, Tao X, Fan YF, Dai Y, Yang H, Ma XR. Genomic profiling of exogenous abscisic acid-responsive microRNAs in tomato (Solanum lycopersicum). BMC Genomics 2016; 17:423. [PMID: 27260799 PMCID: PMC4891822 DOI: 10.1186/s12864-016-2591-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/18/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Plant microRNAs (miRNAs) are involved in various biological pathways and stress responses as negative regulators at the posttranscriptional level. Abscisic acid (ABA) is a key signaling molecule that mediates plant stress response by activating many stress-related genes. Although some miRNAs in plants are previously identified to respond to ABA, a comprehensive profile of ABA-responsive miRNAs has not yet been elucidated. RESULTS Here, we identified miRNAs responding to exogenous application of ABA, and their predicted target genes in the model plant organism tomato (Solanum lycopersicum). Deep sequencing of small RNAs from ABA-treated and untreated tomatoes revealed that miRNAs can be up- or down-regulated upon treatment with ABA. A total of 1067 miRNAs were detected (including 365 known and 702 candidate novel miRNAs), of those, 416 miRNAs which had an abundance over two TPM (transcripts per million) were selected for differential expression analysis. We identified 269 (180 known and 89 novel) miRNAs that respond to exogenous ABA treatment with a change in expression level of |log2FC|≥0.25. 136 of these miRNAs (90 known and 46 novel) were expressed at significantly different levels |log2FC|≥1 between treatments. Furthermore, stem-loop RT-PCR was applied to validate the RNA-seq data. Target prediction and analysis of the corresponding ABA-responsive transcriptome data uncovered that differentially expressed miRNAs are involved in condition stress and pathogen resistance, growth and development. Among them, approximately 90 miRNAs were predicted to target transcription factors and pathogen resistance genes. Some miRNAs had functional overlap in biotic and abiotic stress. Most of these miRNAs were down-regulated following exposure to exogenous ABA, while their related target genes were inversely up-regulated, which is consistent with their negative regulatory role in gene expression. CONCLUSIONS Exogenous ABA application influences the composition and expression level of tomato miRNAs. ABA mainly down-regulates miRNAs that their target genes involve in abiotic stress adaption and disease resistance. ABA might increase expression of stress-related genes via miRNA-mediated posttranscriptional regulation, and our results indicate that ABA treatment has the potential to improve both abiotic stress tolerance and pathogen resistance. This study presents a comprehensive profile of ABA-regulated miRNAs in the tomato, and provides a robust database for further investigation of ABA regulatory mechanisms.
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Affiliation(s)
- Hai-Yang Cheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, No 9, Section 4, Renmin South Road, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, No 9, Section 4, Renmin South Road, Chengdu, 610041, China
| | - Xiang Tao
- Chengdu Institute of Biology, Chinese Academy of Sciences, No 9, Section 4, Renmin South Road, Chengdu, 610041, China
| | - Yan-Fen Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, No 9, Section 4, Renmin South Road, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ya Dai
- Chengdu Institute of Biology, Chinese Academy of Sciences, No 9, Section 4, Renmin South Road, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Yang
- Chengdu Institute of Biology, Chinese Academy of Sciences, No 9, Section 4, Renmin South Road, Chengdu, 610041, China
| | - Xin-Rong Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, No 9, Section 4, Renmin South Road, Chengdu, 610041, China.
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Geng H, Sui Z, Zhang S, Du Q, Ren Y, Liu Y, Kong F, Zhong J, Ma Q. Identification of microRNAs in the Toxigenic Dinoflagellate Alexandrium catenella by High-Throughput Illumina Sequencing and Bioinformatic Analysis. PLoS One 2015; 10:e0138709. [PMID: 26398216 PMCID: PMC4580472 DOI: 10.1371/journal.pone.0138709] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 09/02/2015] [Indexed: 12/19/2022] Open
Abstract
Micro-ribonucleic acids (miRNAs) are a large group of endogenous, tiny, non-coding RNAs consisting of 19–25 nucleotides that regulate gene expression at either the transcriptional or post-transcriptional level by mediating gene silencing in eukaryotes. They are considered to be important regulators that affect growth, development, and response to various stresses in plants. Alexandrium catenella is an important marine toxic phytoplankton species that can cause harmful algal blooms (HABs). To date, identification and function analysis of miRNAs in A. catenella remain largely unexamined. In this study, high-throughput sequencing was performed on A. catenella to identify and quantitatively profile the repertoire of small RNAs from two different growth phases. A total of 38,092,056 and 32,969,156 raw reads were obtained from the two small RNA libraries, respectively. In total, 88 mature miRNAs belonging to 32 miRNA families were identified. Significant differences were found in the member number, expression level of various families, and expression abundance of each member within a family. A total of 15 potentially novel miRNAs were identified. Comparative profiling showed that 12 known miRNAs exhibited differential expression between the lag phase and the logarithmic phase. Real-time quantitative RT-PCR (qPCR) was performed to confirm the expression of two differentially expressed miRNAs that were one up-regulated novel miRNA (aca-miR-3p-456915), and one down-regulated conserved miRNA (tae-miR159a). The expression trend of the qPCR assay was generally consistent with the deep sequencing result. Target predictions of the 12 differentially expressed miRNAs resulted in 1813target genes. Gene ontology (GO) analysis and the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG) annotations revealed that some miRNAs were associated with growth and developmental processes of the alga. These results provide insights into the roles that miRNAs play in the growth of A. catenella, and they provide the basis for further studies of the molecular mechanisms that underlie bloom growth in red tides species.
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Affiliation(s)
- Huili Geng
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Zhenghong Sui
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China
- * E-mail:
| | - Shu Zhang
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qingwei Du
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yuanyuan Ren
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yuan Liu
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Fanna Kong
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Jie Zhong
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qingxia Ma
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China
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Wang W, Luan Y. The advance of tomato disease-related microRNAs. PLANT CELL REPORTS 2015; 34:1089-97. [PMID: 25773761 DOI: 10.1007/s00299-015-1782-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 02/25/2015] [Accepted: 03/03/2015] [Indexed: 05/21/2023]
Abstract
Tomato is a model plant for studying plant-pathogen interactions. As regulatory factors, microRNAs (miRNAs) have been widely identified and play crucial roles in tomato-pathogen interactions, including host defense and pathogen counter-defense. Here, the review summarizes the discoveries and highlights of miRNAs in tomato diseases. Roles of artificial miRNAs in disease resistance are further discussed. Hence, a better understanding of the contribution of miRNAs in tomato disease will shed light on strategies in enhancing tomato-pathogen resistance.
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Affiliation(s)
- Weichen Wang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
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Luan Y, Cui J, Zhai J, Li J, Han L, Meng J. High-throughput sequencing reveals differential expression of miRNAs in tomato inoculated with Phytophthora infestans. PLANTA 2015; 241:1405-16. [PMID: 25697288 DOI: 10.1007/s00425-015-2267-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 02/10/2015] [Indexed: 05/21/2023]
Abstract
The characterization and compare expression profiling of the miRNA transcriptome lay a solid foundation for unraveling the complex miRNA-mediated regulatory network in tomato resistance mechanisms against LB. MicroRNAs (miRNAs) are a class of small endogenous non-coding RNAs with 20-24 nt. They have been identified in many plants with their diverse regulatory roles in biotic stresses. The knowledge, that miRNAs regulate late blight (LB), caused by Phytophthora infestans, is rather limited. In this study, we used miRNA-Seq to investigate the miRNA expression difference between the tomatoes treated with and without P. infestans. A total of 42,714,516 raw reads were generated from two small RNA libraries by high-throughput sequencing. Finally, 207 known miRNAs and 67 new miRNAs were obtained. The differential expression profile of miRNAs in tomato was further analyzed with twofold change (P value ≤0.01). A total of 70 miRNAs were manifested to change significantly in samples treated with P. infestans, including 50 down-regulated miRNAs and 20 up-regulated miRNAs. Moreover, a total of 73 target genes were acquired for 28 differentially expressed miRNAs by psRNATarget analysis. By enrichment pathway analysis of target genes, plant-pathogen interaction was the most highly relevant pathway which played an important role in disease defense. In addition, 30 miRNAs were selected for qRT-PCR to validate their expression patterns. The expression patterns for targets of miR6027, miR5300, miR476b, miR159a, miR164a and miRn13 were selectively examined, and the results showed that there was a negative correlation on the expression patterns between miRNAs and their targets. The targets have previously been reported to be related with plant immune and involved in plant-pathogen interaction pathway in this study, suggesting these miRNAs might act as regulators in process of tomato resistance against P. infestans. These discoveries will provide us useful information to explain tomato resistance mechanisms against LB.
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Affiliation(s)
- Yushi Luan
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
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Sun XH, Zhao LP, Zou Q, Wang ZB. Identification of microRNA genes and their mRNA targets in Festuca arundinacea. Appl Biochem Biotechnol 2014; 172:3875-87. [PMID: 24577674 DOI: 10.1007/s12010-014-0805-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 02/12/2014] [Indexed: 01/26/2023]
Abstract
MicroRNAs (miRNAs) have emerged as a novel class of endogenous, small, non-coding RNAs of 22 nucleotides (nts) in length, which plays important roles in post-transcriptional degradation of target mRNA or inhibition of protein synthesis through binding the specific sites of target mRNA. Growing evidences have shown that miRNAs play an important role in various biological processes, including growth and development, signal transduction, apoptosis, proliferation, stress responses, maintenance of genome stability, and so on. In our study, we used bioinformatic tools to predict miRNA and the corresponding target genes of Festuca arundinacea. We used known miRNAs of other plants from miRBase to search against expressed sequence tags (EST) databases and genome survey sequences (GSS) of F. arundinacea. A total of 8 potential miRNAs were predicted. Phylogenetic analysis of the predicted miRNAs revealed that miRNA398c of F. arundinacea species was evolutionary highly conserved with Populus trichocarpa. The 8 potential miRNAs corresponding to 20 target genes were found. Most of the miRNA target genes were predicted to encode transcription factors that regulate cell growth and development, signaling, metabolism, and other biology processes. By bioinformatics methods, we can effectively predict novel miRNAs and its target genes and add information to F. arundinacea miRNA database. Moreover, it shows a path for the prediction and analysis of miRNAs to those species whose genomes are not available through bioinformatics tools.
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Affiliation(s)
- Xi Hong Sun
- Animal Science and Technology College, Henan University of Science and Technology, Luoyang City, 471003, Henan Province, People's Republic of China
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Li Z, Zhou X. Small RNA biology: from fundamental studies to applications. SCIENCE CHINA. LIFE SCIENCES 2013; 56:1059-1062. [PMID: 23943246 DOI: 10.1007/s11427-013-4535-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 07/22/2013] [Indexed: 06/02/2023]
Affiliation(s)
- Zhenghe Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
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Zhang S, Yue Y, Sheng L, Wu Y, Fan G, Li A, Hu X, ShangGuan M, Wei C. PASmiR: a literature-curated database for miRNA molecular regulation in plant response to abiotic stress. BMC PLANT BIOLOGY 2013; 13:33. [PMID: 23448274 PMCID: PMC3599438 DOI: 10.1186/1471-2229-13-33] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Accepted: 02/21/2013] [Indexed: 05/03/2023]
Abstract
BACKGROUND Over 200 published studies of more than 30 plant species have reported a role for miRNAs in regulating responses to abiotic stresses. However, data from these individual reports has not been collected into a single database. The lack of a curated database of stress-related miRNAs limits research in this field, and thus a cohesive database system should necessarily be constructed for data deposit and further application. DESCRIPTION PASmiR, a literature-curated and web-accessible database, was developed to provide detailed, searchable descriptions of miRNA molecular regulation in different plant abiotic stresses. PASmiR currently includes data from ~200 published studies, representing 1038 regulatory relationships between 682 miRNAs and 35 abiotic stresses in 33 plant species. PASmiR's interface allows users to retrieve miRNA-stress regulatory entries by keyword search using plant species, abiotic stress, and miRNA identifier. Each entry upon keyword query contains detailed regulation information for a specific miRNA, including species name, miRNA identifier, stress name, miRNA expression pattern, detection method for miRNA expression, a reference literature, and target gene(s) of the miRNA extracted from the corresponding reference or miRBase. Users can also contribute novel regulatory entries by using a web-based submission page. The PASmiR database is freely accessible from the two URLs of http://hi.ustc.edu.cn:8080/PASmiR, and http://pcsb.ahau.edu.cn:8080/PASmiR. CONCLUSION The PASmiR database provides a solid platform for collection, standardization, and searching of miRNA-abiotic stress regulation data in plants. As such this database will be a comprehensive repository for miRNA regulatory mechanisms involved in plant response to abiotic stresses for the plant stress physiology community.
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Affiliation(s)
- Shihua Zhang
- School of life sciences, Anhui Agricultural University, Hefei 230036, China
- Key laboratory of Tea Biochemistry and Biotechnology, Ministry of Education, Ministry of Agriculture, Anhui Agricultural University, Hefei 230036, China
| | - Yi Yue
- College of information and computer science, Anhui Agricultural University, Hefei 230036, China
| | - Liang Sheng
- Key laboratory of Tea Biochemistry and Biotechnology, Ministry of Education, Ministry of Agriculture, Anhui Agricultural University, Hefei 230036, China
| | - Yunzhi Wu
- College of information and computer science, Anhui Agricultural University, Hefei 230036, China
| | - Guohua Fan
- College of information and computer science, Anhui Agricultural University, Hefei 230036, China
| | - Ao Li
- Department of Electronic Science and Technology, University of Science and Technology of China, Hefei, China
| | - Xiaoyi Hu
- Key laboratory of Tea Biochemistry and Biotechnology, Ministry of Education, Ministry of Agriculture, Anhui Agricultural University, Hefei 230036, China
| | - Mingzhu ShangGuan
- Key laboratory of Tea Biochemistry and Biotechnology, Ministry of Education, Ministry of Agriculture, Anhui Agricultural University, Hefei 230036, China
| | - Chaoling Wei
- Key laboratory of Tea Biochemistry and Biotechnology, Ministry of Education, Ministry of Agriculture, Anhui Agricultural University, Hefei 230036, China
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Korir NK, Li X, Xin S, Wang C, Changnian S, Kayesh E, Fang J. Characterization and expression profiling of selected microRNAs in tomato (Solanum lycopersicon) 'Jiangshu14'. Mol Biol Rep 2013; 40:3503-21. [PMID: 23408149 DOI: 10.1007/s11033-012-2425-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Accepted: 12/18/2012] [Indexed: 01/22/2023]
Abstract
Presence of selected tomato (Solanum lycopersicon) microRNAs (sly-miRNAs) was validated and their expression profiles established in roots, stems, leaves, flowers and fruits of tomato variety Jiangshu14 by quantitative RT-PCR (qRT-PCR). In addition conservation characteristics these sly-miRNAs were analyzed and target genes predicted bioinformatically. Results indicate that some of these miRNAs are specific to tomato while most are conserved in other plant species. Predicted sly-miRNA targets genes were shown to be targeted by either by a single or more miRNAs and are involved in diverse processes in tomato plant growth and development. All the 36 miRNAs were present in the cDNA of mixed tissues and qRT-PCR revealed that some of these sly-miRNAs are ubiquitous in tomato while others have tissue-specific expression. The experimental validation and expression profiling as well target gene prediction of these miRNAs in tomato as done in this study can add to the knowledge on the important roles played by these sly-miRNAs in the growth and development, environmental stress tolerance as well as pest and disease resistance in tomatoes and related species. In addition these findings broaden the knowledge of small RNA-mediated regulation in S. lycopersicon. It is recommended that experimental validation of the target genes be done so as to give a much more comprehensive information package on these miRNAs in tomato and specifically in the selected variety.
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Affiliation(s)
- Nicholas Kibet Korir
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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Gong Z, Zhang S, Zhang W, Huang H, Li Q, Deng H, Ma J, Zhou M, Xiang J, Wu M, Li X, Xiong W, Li X, Li Y, Zeng Z, Li G. Long non-coding RNAs in cancer. SCIENCE CHINA-LIFE SCIENCES 2012; 55:1120-4. [PMID: 23233227 DOI: 10.1007/s11427-012-4413-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Accepted: 11/10/2012] [Indexed: 12/28/2022]
Affiliation(s)
- Zhaojian Gong
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, the Third Xiangya Hospital, Central South University, Changsha 410013, China
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The role and clinical implications of microRNAs in hepatocellular carcinoma. SCIENCE CHINA-LIFE SCIENCES 2012; 55:906-19. [PMID: 23108868 DOI: 10.1007/s11427-012-4384-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 09/11/2012] [Indexed: 12/12/2022]
Abstract
Hepatocellular carcinoma (HCC) is common and one of the most aggressive of all human cancers. Recent studies have indicated that miRNAs, a class of small noncoding RNAs that regulate gene expression post-transcriptionally, directly contribute to HCC by targeting many critical regulatory genes. Several miRNAs are involved in hepatitis B or hepatitis C virus replication and virus-induced changes, whereas others participate in multiple intracellular signaling pathways that modulate apoptosis, cell cycle checkpoints, and growth-factor-stimulated responses. When disturbed, these pathways appear to result in malignant transformation and ultimately HCC development. Recently, miRNAs circulating in the blood have acted as possible early diagnostic markers for HCC. These miRNA also could serve as indicators with respect to drug efficacy and be prognostic in HCC patients. Such biomarkers would assist stratification of HCC patients and help direct personalized therapy. Here, we summarize recent advances regarding the role of miRNAs in HCC development and progression. Our expectation is that these and ongoing studies will contribute to the understanding of the multiple roles of these small noncoding RNAs in liver tumorigenesis.
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Recent progress in microRNA study: Benefits from technique advance. SCIENCE CHINA-LIFE SCIENCES 2012; 55:649-50. [DOI: 10.1007/s11427-012-4342-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 06/23/2012] [Indexed: 01/08/2023]
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