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Yu C, Huang Z, Xu Y, Zhang B, Li Y. Deep sequencing of microRNAs reveals circadian-dependent microRNA expression in the eyestalks of the Chinese mitten crab Eriocheir sinensis. Sci Rep 2023; 13:5253. [PMID: 37002260 PMCID: PMC10066325 DOI: 10.1038/s41598-023-32277-1] [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: 11/30/2022] [Accepted: 03/24/2023] [Indexed: 04/03/2023] Open
Abstract
MicroRNAs (miRNAs) are small endogenous non-coding RNAs. In crustaceans, miRNAs might be involved in the regulation of circadian rhythms. Many physiological functions of crustaceans including immunity and hormone secretion exhibit circadian rhythms, but it remains unclear whether specific miRNAs contribute to the alteration of crustacean physiological processes under circadian rhythms. This study investigated the mechanisms of miRNA regulation of circadian rhythms in the Chinese mitten crab (Eriocheir sinensis), one of China's most important aquaculture species. We obtained eyestalks from crab specimens at four time points (6:00; 12:00; 18:00; 24:00) during a 24-h period. We identified 725 mature miRNAs, with 23 known miRNAs differentially expressed depending on the time of day. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that the putative target genes for differentially expressed miRNAs were significantly enriched in the immune response and endocrine-related pathways. Numerous putative target genes are involved in the circadian-related pathways and enriched on circadian-control genes. These results suggest that the expression of miRNAs regulates some specific physiological functions in E. sinensis under circadian cycles. We also profiled various putative target genes enriched under the circadian-related pathway. This study performed miRNA expression in the eyestalks of E. sinensis during a 24-h daily cycle, providing insights into the molecular mechanism underlying crustacean circadian rhythms and suggesting miRNAs' role in studying crustacean physiology should not be overlooked.
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Affiliation(s)
- Changyue Yu
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhiwei Huang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yingkai Xu
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Baoli Zhang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yingdong Li
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
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2
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Jain N, Shiv A, Sinha N, Singh PK, Prasad P, Balyan HS, Gupta PK. Leaf rust responsive miRNA and their target genes in wheat. Funct Integr Genomics 2022; 23:14. [PMID: 36550370 DOI: 10.1007/s10142-022-00928-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022]
Abstract
Small RNA sequencing (sRNA-seq) and degradome analysis were used for the identification of miRNAs and their target host genes in a pair of near-isogenic lines (NILs), which differed for the presence of leaf rust resistance gene Lr28. The study led to identification of (i) 506 known and 346 novel miRNAs; and (ii) 5054 target genes including 4557 in silico predicted and 497 degradome-based genes using 105 differentially expressed (DE) miRNAs. A subset of 128 targets (67 in silico + 61 degradome-based) was differentially expressed in RNA-seq data that was generated by us earlier using the same pair of NILs; among these 128 targets, 58 target genes exhibited an inverse relationship with the DE miRNAs (expression of miRNAs and activation/suppression of target genes). Eight miRNAs which belonged to the conserved miRNA families and were known to be induced in response to fungal diseases in plants included the following: miR156, miR158, miR159, miR168, miR169, miR172, miR319, miR396. The target genes belonged to the following classes of genes known to be involved in downstream disease resistance pathways; peroxidases, sugar transporters, auxin response signaling, oxidation-reduction, etc. It was also noticed that although a majority of miRNAs and target genes followed the above classical inverse relationship, there were also examples, where no such relationship was observed. Among the target genes, there were also 51 genes that were not only regulated by miRNAs, but were also differentially methylated at sequences including the following segments: promotors, introns, TSS, exons. The results of the present study suggest a complex interplay among miRNA genes, target genes, and various epigenetic controls, which regulate the expression of genes involved in downstream pathways for disease resistance.
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Affiliation(s)
- Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Aalok Shiv
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Nivedita Sinha
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - P K Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Pramod Prasad
- Regional Station, ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, 171002, India
| | - H S Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India.
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Moraga C, Sanchez E, Ferrarini MG, Gutierrez RA, Vidal EA, Sagot MF. BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data. Gigascience 2022; 11:giac093. [PMID: 36283679 PMCID: PMC9596168 DOI: 10.1093/gigascience/giac093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/08/2021] [Accepted: 09/15/2022] [Indexed: 11/04/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that are key players in the regulation of gene expression. In the past decade, with the increasing accessibility of high-throughput sequencing technologies, different methods have been developed to identify miRNAs, most of which rely on preexisting reference genomes. However, when a reference genome is absent or is not of high quality, such identification becomes more difficult. In this context, we developed BrumiR, an algorithm that is able to discover miRNAs directly and exclusively from small RNA (sRNA) sequencing (sRNA-seq) data. We benchmarked BrumiR with datasets encompassing animal and plant species using real and simulated sRNA-seq experiments. The results demonstrate that BrumiR reaches the highest recall for miRNA discovery, while at the same time being much faster and more efficient than the state-of-the-art tools evaluated. The latter allows BrumiR to analyze a large number of sRNA-seq experiments, from plants or animal species. Moreover, BrumiR detects additional information regarding other expressed sequences (sRNAs, isomiRs, etc.), thus maximizing the biological insight gained from sRNA-seq experiments. Additionally, when a reference genome is available, BrumiR provides a new mapping tool (BrumiR2reference) that performs an a posteriori exhaustive search to identify the precursor sequences. Finally, we also provide a machine learning classifier based on a random forest model that evaluates the sequence-derived features to further refine the prediction obtained from the BrumiR-core. The code of BrumiR and all the algorithms that compose the BrumiR toolkit are freely available at https://github.com/camoragaq/BrumiR.
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Affiliation(s)
- Carol Moraga
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
- Inria Lyon Centre, ERABLE team, 56 Bd Niels Bohr, 69100 Villeurbanne, France
- Universidad de O'Higgins, Instituto de Ciencias de la Ingeniería, 2820000 Rancagua, Chile
| | - Evelyn Sanchez
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingenieria y Tecnologia, Universidad Mayor, 8580745 Santiago, Chile
- Agencia Nacional de Investigación y Desarrollo–Millennium Science Initiative Program, Millennium Institute for Integrative Biology iBio, 7500565 Santiago, Chile
| | - Mariana Galvão Ferrarini
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
- Inria Lyon Centre, ERABLE team, 56 Bd Niels Bohr, 69100 Villeurbanne, France
- Université de Lyon, INSA-Lyon, INRA, BF2i, UMR0203, Villeurbanne F-69621, France
| | - Rodrigo A Gutierrez
- Agencia Nacional de Investigación y Desarrollo–Millennium Science Initiative Program, Millennium Institute for Integrative Biology iBio, 7500565 Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile , 8331010 Santiago, Chile
- Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation, Instituto de Ecología y Biodiversidad, 8370415 Santiago, Chile
| | - Elena A Vidal
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingenieria y Tecnologia, Universidad Mayor, 8580745 Santiago, Chile
- Agencia Nacional de Investigación y Desarrollo–Millennium Science Initiative Program, Millennium Institute for Integrative Biology iBio, 7500565 Santiago, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Ingenieria y Tecnologia, Universidad Mayor, 8580745 Santiago, Chile
| | - Marie-France Sagot
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
- Inria Lyon Centre, ERABLE team, 56 Bd Niels Bohr, 69100 Villeurbanne, France
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Luo J, Zhao S, Ren Q, Wang Q, Chen Z, Cui J, Jing Y, Liu P, Yan R, Song X, Liu G, Li X. Dynamic Analysis of microRNAs from Different Life Stages of Rhipicephalus microplus (Acari: Ixodidae) by High-Throughput Sequencing. Pathogens 2022; 11:pathogens11101148. [PMID: 36297205 PMCID: PMC9611014 DOI: 10.3390/pathogens11101148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022] Open
Abstract
MicroRNAs (miRNAs), which are small, noncoding RNA molecules, play an important regulatory role in gene expression at the posttranscriptional level. Relatively limited knowledge exists on miRNAs in Rhipicephalus microplus ticks in China; however, understanding the physiology of miRNA functions and expression at different developmental stages is important. In this study, three small RNA libraries were constructed for R. microplus eggs, larvae, and female adults; miRNAs were detected during these developmental stages by high-throughput sequencing, with 18,162,337, 8,090,736, and 11,807,326 clean reads, respectively. A total of 5132 known miRNAs and 31 novel miRNAs were identified. A total of 1736 differentially expressed miRNAs were significantly different at a p-value of <0.01; in female adults, 467 microRNAs were upregulated and 376 miRNAs downregulated compared to larval tick controls. Using larvae as controls, 218 upregulated and 203 downregulated miRNAs were detected in eggs; in eggs, 108 miRNAs were upregulated and 364 downregulated compared to female adults controls. To verify the reliability of the sequencing data, RT−qPCR was applied to compare expression levels of novel miRNAs. Some differentially expressed miRNAs are involved in developmental physiology, signal transduction, and cell-extracellular communications based on GO annotation and KEGG pathway analyses. Here, we provide a dynamic analysis of miRNAs in R. microplus and their potential targets, which has significance for understanding the biology of ticks and lays the foundation for improved understanding of miRNA functioning in the regulation of R. microplus development. These results can assist future miRNA studies in other tick species that have great significance for human and animal health.
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Affiliation(s)
- Jin Luo
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou 730046, China
| | - Shuaiyang Zhao
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou 730046, China
| | - Qiaoyun Ren
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou 730046, China
| | - Qilin Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou 730046, China
| | - Zeyu Chen
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou 730046, China
| | - Jingjing Cui
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou 730046, China
| | - Yujiao Jing
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou 730046, China
| | - Peiwen Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou 730046, China
| | - Ruofeng Yan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaokai Song
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Guangyuan Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou 730046, China
- Correspondence: (G.L.); (X.L.)
| | - Xiangrui Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (G.L.); (X.L.)
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Integrated Approaches to Identify miRNA Biomarkers Associated with Cognitive Dysfunction in Multiple Sclerosis Using Text Mining, Gene Expression, Pathways, and GWAS. Diagnostics (Basel) 2022; 12:diagnostics12081914. [PMID: 36010264 PMCID: PMC9406323 DOI: 10.3390/diagnostics12081914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/03/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
Multiple sclerosis (MS), a chronic autoimmune disorder, affects the central nervous system of many young adults. More than half of MS patients develop cognition problems. Although several genomic and transcriptomic studies are currently reported in MS cognitive impairment, a comprehensive repository dealing with all the experimental data is still underdeveloped. In this study, we combined text mining, gene regulation, pathway analysis, and genome-wide association studies (GWAS) to identify miRNA biomarkers to explore the cognitive dysfunction in MS, and to understand the genomic etiology of the disease. We first identified the dysregulated miRNAs associated with MS and cognitive dysfunction using PubTator (text mining), HMDD (experimental associations), miR2Disease, and PhenomiR database (differentially expressed miRNAs). Our results suggest that miRNAs such as hsa-mir-148b-3p, hsa-mir-7b-5p, and hsa-mir-7a-5p are commonly associated with MS and cognitive dysfunction. Next, we retrieved GWAS signals from GWAS Catalog, and analyzed the enrichment analysis of association signals in genes/miRNAs and their association networks. Then, we identified susceptible genetic loci, rs17119 (chromosome 6; p = 1 × 10−10), rs1843938 (chromosome 7; p = 1 × 10−10), and rs11637611 (chromosome 15; p = 1.00 × 10−15), associated with significant genetic risk. Lastly, we conducted a pathway analysis for the susceptible genetic variants and identified novel risk pathways. The ECM receptor signaling pathway (p = 3.98 × 10−8) and PI3K/Akt signaling pathway (p = 5.98 × 10−5) were found to be associated with differentially expressed miRNA biomarkers.
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Srikakulam N, Guria A, Karanthamalai J, Murugesan V, Krishnan V, Sundaramoorthy K, Saha S, Singh R, Victorathisayam T, Rajapriya V, Sridevi G, Pandi G. An Insight Into Pentatricopeptide-Mediated Chloroplast Necrosis via microRNA395a During Rhizoctonia solani Infection. Front Genet 2022; 13:869465. [PMID: 35706449 PMCID: PMC9189367 DOI: 10.3389/fgene.2022.869465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Sheath blight (ShB) disease, caused by Rhizoctonia solani, is one of the major biotic stress-oriented diseases that adversely affect the rice productivity worldwide. However, the regulatory mechanisms are not understood yet comprehensively. In the current study, we had investigated the potential roles of miRNAs in economically important indica rice variety Pusa Basmati-1 upon R. solani infection by carrying out in-depth, high-throughput small RNA sequencing with a total data size of 435 million paired-end raw reads from rice leaf RNA samples collected at different time points. Detailed data analysis revealed a total of 468 known mature miRNAs and 747 putative novel miRNAs across all the libraries. Target prediction and Gene Ontology functional analysis of these miRNAs were found to be unraveling various cellular, molecular, and biological functions by targeting various plant defense-related genes. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to validate the miRNAs and their putative target genes. Out of the selected miRNA-specific putative target genes, miR395a binding and its cleavage site on pentatricopeptide were determined by 5’ RACE-PCR. It might be possible that R. solani instigated chloroplast degradation by modulating the pentatricopeptide which led to increased susceptibility to fungal infection.
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Jha N, Mangukia N, Gadhavi H, Patel M, Bhavsar M, Rawal R, Patel S. Small RNA sequencing and identification of papaya (Carica papaya L.) miRNAs with potential cross-kingdom human gene targets. Mol Genet Genomics 2022; 297:981-997. [PMID: 35570207 PMCID: PMC9107959 DOI: 10.1007/s00438-022-01904-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 04/23/2022] [Indexed: 12/11/2022]
Abstract
Several studies have demonstrated potential role of plant-derived miRNAs in cross-kingdom species relationships by transferring into non-plant host cells to regulate certain host cellular functions. How nutrient-rich plants regulate host cellular functions, which in turn alleviate physiological and disease conditions in the host remains to be explored in detail. This computational study explores the potential targets, putative role, and functional implications of miRNAs derived from Carica papaya L., one of the most cultivated tropical crops in the world and a rich source of phytochemicals and enzymes, in human diet. Using the next-generation sequencing, -Illumina HiSeq2500, ~ 30 million small RNA sequence reads were generated from C. papaya young leaves, resulting in the identification of a total of 1798 known and 49 novel miRNAs. Selected novel C. papaya miRNAs were predicted to regulate certain human targets, and subsequent annotation of gene functions indicated a probable role in various biological processes and pathways, such as MAPK, WNT, and GPCR signaling pathways, and platelet activation. These presumptive target gene in humans were predominantly linked to various diseases, including cancer, diabetes, mental illness, and platelet disorder. The computational finding of this study provides insights into how C. papaya-derived miRNAs may regulate certain conditions of human disease and provide a new perspective on human health. However, the therapeutic potential of C. papaya miRNA can be further explored through experimental studies.
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Affiliation(s)
- Neha Jha
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Naman Mangukia
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
- BioInnovations, Bhayander (West), Mumbai, 401101, Maharashtra, India
| | - Harshida Gadhavi
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Maulik Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
- Advait Theragnostics Pvt. Ltd., Ahmedabad, Gujarat, India
| | - Mansi Bhavsar
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Rakesh Rawal
- Department of Biochemistry and Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Saumya Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India.
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Wang N, Lysenkov V, Orte K, Kairisto V, Aakko J, Khan S, Elo LL. Tool evaluation for the detection of variably sized indels from next generation whole genome and targeted sequencing data. PLoS Comput Biol 2022; 18:e1009269. [PMID: 35176018 PMCID: PMC8916674 DOI: 10.1371/journal.pcbi.1009269] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 03/11/2022] [Accepted: 01/30/2022] [Indexed: 11/18/2022] Open
Abstract
Insertions and deletions (indels) in human genomes are associated with a wide range of phenotypes, including various clinical disorders. High-throughput, next generation sequencing (NGS) technologies enable the detection of short genetic variants, such as single nucleotide variants (SNVs) and indels. However, the variant calling accuracy for indels remains considerably lower than for SNVs. Here we present a comparative study of the performance of variant calling tools for indel calling, evaluated with a wide repertoire of NGS datasets. While there is no single optimal tool to suit all circumstances, our results demonstrate that the choice of variant calling tool greatly impacts the precision and recall of indel calling. Furthermore, to reliably detect indels, it is essential to choose NGS technologies that offer a long read length and high coverage coupled with specific variant calling tools.
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Affiliation(s)
- Ning Wang
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Vladislav Lysenkov
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Katri Orte
- Department of Pathology, Laboratory Division, Turku University Hospital, Turku, Finland
- Department of Genomics, Laboratory Division, Turku University Hospital, Turku, Finland
| | - Veli Kairisto
- Department of Genomics, Laboratory Division, Turku University Hospital, Turku, Finland
| | - Juhani Aakko
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Sofia Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- * E-mail: (SK); (LLE)
| | - Laura L. Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Institute of Biomedicine, University of Turku, Finland
- * E-mail: (SK); (LLE)
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9
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Wang W, Li JP, Liu JL. The Novel microRNA Rno-miR-686-3p Is Associated with the Ischaemic Penumbra. Eur Neurol 2022; 85:224-234. [PMID: 35100587 DOI: 10.1159/000521491] [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: 07/21/2021] [Accepted: 12/03/2021] [Indexed: 11/19/2022]
Abstract
INTRODUCTION We explored microRNA (miRNA) profiles correlated with the penumbra in three different phases of ischaemic stroke, using a permanent middle cerebral artery occlusion (p-MCAO) rat model. MATERIALS AND METHODS A 2-mm coronal section was cut from the optic chiasma in the caudal direction, and the penumbra was located in the area between a longitudinal line approximately 2 mm from the midline and a transverse diagonal line at the "2-o'clock" position. Total RNA was extracted from tissue specimens and peripheral blood samples, followed by deep sequencing analysis. RESULTS We identified nine novel miRNA candidates in tissues and evaluated their expression levels using real-time quantitative polymerase chain reaction. In situ hybridization was conducted to assess miRNA localization in the brain. Of these nine candidates, we identified and characterized a novel miRNA, rno-miR-686-3p, which was localized in cell nuclei of the cortex, and associated with the penumbra. rno-miR-686-3p was downregulated at 1 (p = 0.042), 3 (p = 0.032), and 4 h (p = 0.007) post-p-MCAO in the penumbra. A total of 297 potential target genes were predicted. Moreover, functional annotation clustering and pathway enrichment analysis predicted that rno-miR-686-3p participates in transcriptional regulation and the Wnt and cyclic adenosine monophosphate (cAMP) signalling pathways. CONCLUSION rno-miR-686-3p is a novel miRNA associated with the ischaemic penumbra that is implicated in transcriptional regulation and modulation of the Wnt and cAMP signalling pathways. Furthermore, it may serve as a possible new biomarker with potential value for detecting the existence of the penumbra.
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Affiliation(s)
- Wei Wang
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University in Nanning, Guangxi, China,
| | - Jin-Pin Li
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University in Nanning, Guangxi, China
| | - Jing-Li Liu
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University in Nanning, Guangxi, China
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10
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Hu Q, Zang X, Ding Y, Gu T, Shi J, Li Z, Cai G, Liu D, Wu Z, Hong L. Porcine uterine luminal fluid-derived extracellular vesicles improve conceptus-endometrial interaction during implantation. Theriogenology 2022; 178:8-17. [PMID: 34735978 DOI: 10.1016/j.theriogenology.2021.10.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/18/2021] [Accepted: 10/18/2021] [Indexed: 12/13/2022]
Abstract
Successful implantation of porcine conceptus requires synergistic interaction with various signal molecules in the maternal uterus. Extracellular vesicles (EVs) in uterine luminal fluid (ULF) of mice play important roles in conceptus development. However, studies have not explored the roles of extracellular vesicles (EV) in ULF of pigs. The aim of this study was to identify characteristics, origin, and roles of ULF-derived EVs on day 9 of the estrous cycle and on day 9,12 and 15 of pregnancy in pigs. Western blot, BCA assay and HE staining analysis showed increase in EVs concentration in ULF began from day 12 of pregnancy. Immunofluorescence staining and transmission electron microscopy analysis showed that EVs were mainly derived from endometrial epithelial cells. Fluorescent labeling, CCK-8 and transwell migration assays showed that these EVs were delivered to the trophoblast or parthenogenetic activation embryos to regulate proliferation and migration of trophoblast cells. A total of 305 miRNAs were identified using small RNA sequencing analysis. Functional enrichment analysis showed that miRNAs in these EVs potentially play vital regulatory functions in EV transportation or conceptus implantation. QRT-PCR analysis was used to further verify the RNA-seq data. The findings of this study provide information on the functions of porcine ULF-derived EVs and provide a reference dataset for future translational studies on porcine ULF-derived EVs.
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Affiliation(s)
- Qun Hu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Xupeng Zang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Yue Ding
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Ting Gu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Junsong Shi
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Wens Breeding Swine Technology Co. Ltd., Yunfu, China
| | - Zicong Li
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, China
| | - Gengyuan Cai
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Dewu Liu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Zhenfang Wu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, China.
| | - Linjun Hong
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China.
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11
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Shan S, Wang SN, Song X, Khashaveh A, Lu ZY, Dhiloo KH, Li RJ, Gao XW, Zhang YJ. Characterization and target gene analysis of microRNAs in the antennae of the parasitoid wasp Microplitis mediator. INSECT SCIENCE 2021; 28:1033-1048. [PMID: 32496619 DOI: 10.1111/1744-7917.12832] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/14/2020] [Accepted: 05/26/2020] [Indexed: 06/11/2023]
Abstract
MicroRNAs (miRNAs), a class of non-coding single-strand RNA molecules encoded by endogenous genes, are about 21-24 nucleotides long and are involved in the post-transcriptional regulation of gene expression in plants and animals. Generally, the types and quantities of miRNAs in the different tissues of an organism are diverse, and these divergences may be related to their specific functions. Here we have identified 296 known miRNAs and 46 novel miRNAs in the antennae of the parasitoid wasp Microplitis mediator by high-throughput sequencing. Thirty-three miRNAs were predicted to target olfactory-associated genes, including odorant binding proteins (OBPs), chemosensory proteins, odorant receptors (ORs), ionotropic receptors (IRs) and gustatory receptors. Among these, 17 miRNAs were significantly highly expressed in the antennae, four miRNAs were highly expressed both in the antennae and head or wings, while the remaining 12 miRNAs were mainly expressed in the head, thorax, abdomen, legs and wings. Notably, miR-9a-5p and miR-2525-3p were highly expressed in male antennae, whereas miR-1000-5p and novel-miR-13 were enriched in female antennae. The 17 miRNAs highly expressed in antennae are likely to be associated with olfaction, and were predicted to target one OBP (targeted by miR-3751-3p), one IR (targeted by miR-7-5p) and 14 ORs (targeted by 15 miRNAs including miR-6-3p, miR-9a-5p, miR-9b-5p, miR-29-5p, miR-71-5p, miR-275-3p, miR-1000-5p, miR-1000-3p, miR-2525-3p, miR-6012-3p, miR-9719-3p, novel-miR-10, novel-miR-13, novel-miR-14 and novel-miR-28). These candidate olfactory-associated miRNAs are all likely to be involved in chemoreception through the regulation of chemosensory gene expression in the antennae of M. mediator.
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Affiliation(s)
- Shuang Shan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shan-Ning Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Plant and Environment Protection, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Xuan Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Adel Khashaveh
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zi-Yun Lu
- IPM Center of Hebei Province, Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture, Plant Protection Institute, Hebei Academy of Agricultural and Forestry Sciences, Baoding, Hebei, China
| | - Khalid Hussain Dhiloo
- Department of Entomology, Faculty of Crop Protection, Sindh Agriculture University, Tandojam, Pakistan
| | - Rui-Jun Li
- College of Plant Protection, Agricultural University of Hebei, Baoding, Hebei, China
| | - Xi-Wu Gao
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Yong-Jun Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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12
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Luo J, Ren Q, Liu W, Qiu X, Zhang G, Tan Y, Cao R, Yin H, Luo J, Li X, Liu G. MicroRNA-1 Expression and Function in Hyalomma Anatolicum anatolicum (Acari: Ixodidae) Ticks. Front Physiol 2021; 12:596289. [PMID: 33897444 PMCID: PMC8061306 DOI: 10.3389/fphys.2021.596289] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/15/2021] [Indexed: 01/07/2023] Open
Abstract
MicroRNAs act as mRNA post-transcriptional regulators, playing important roles in cell differentiation, transcriptional regulation, growth, and development. In this study, microRNA expression profiles of Hyalomma anatolicum anatolicum ticks at different developmental stages were detected by high-throughput sequencing and functionally assessed. In total, 2,585,169, 1,252,678, 1,558,217, and 1,155,283 unique reads were obtained from eggs, larvae, nymphs, and adults, respectively, with 42, 46, 45, and 41 conserved microRNAs in these stages, respectively. Using eggs as a control, 48, 43, and 39 microRNAs were upregulated, and 3, 10, and 9 were downregulated in larvae, nymphs, and adults, respectively. MicroRNA-1 (miR-1) was expressed in high abundance throughout Ha. anatolicum development, with an average of nearly one million transcripts, and it is highly conserved among tick species. Quantitative real-time PCR (qPCR) showed that miR-1 expression gradually increased with tick development, reaching the highest level at engorgement. Differential tissue expression was detected, with significantly higher levels in the salivary glands and epidermis than in the midgut. Inhibition assays showed no significant change in body weight or spawning time or amount between experimental and control groups, but there was a significant difference (p < 0.01) in engorgement time. With miR-1 inhibition, ticks displayed obvious deformities during later development. To more fully explain the microRNA mechanism of action, the miR-1 cluster was analyzed according to the target gene; members that jointly act on Hsp60 include miR-5, miR-994, miR-969, and miR-1011. Therefore, microRNAs are critical for normal tick development, and the primary structure of the mature sequence of miR-1 is highly conserved. Nonetheless, different developmental stages and tissues show different expression patterns, with a certain role in prolonging feeding. miR-1, together with other cluster members, regulates mRNA function and may be used as a molecular marker for species origin, evolution analysis, and internal reference gene selection.
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Affiliation(s)
- Jin Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Qiaoyun Ren
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Wenge Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiaofei Qiu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Gaofeng Zhang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yangchun Tan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Runlai Cao
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiangrui Li
- Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Guangyuan Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
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13
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Li Q, Liu G, Bao Y, Wu Y, You Q. Evaluation and application of tools for the identification of known microRNAs in plants. APPLICATIONS IN PLANT SCIENCES 2021; 9:e11414. [PMID: 33854848 PMCID: PMC8027368 DOI: 10.1002/aps3.11414] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/07/2021] [Indexed: 06/12/2023]
Abstract
MicroRNAs (miRNAs), endogenous non-coding RNA regulators, post-transcriptionally inhibit the expression of their target genes. Several tools have been developed for predicting annotated known miRNAs, but there is no consensus about how to select the most suitable method for any given species. In this study, eight miRNA prediction tools (mirnovo, miRPlant, miRDeep-P2, miRExpress, miRkwood, miRDeep2, miR-PREFeR, and sRNAbench) were selected for evaluation. High-throughput small RNA sequencing data from four plant species (including C3 and C4 species, and both monocots and dicots, i.e., Arabidopsis thaliana, Oryza sativa, Triticum aestivum, and Zea mays) were used for the analysis. The sensitivity, accuracy, area under the curve, consistency, duration, and RAM usage of the known miRNA predictions were evaluated for each tool. The miRNA annotations were obtained using miRBase and sRNAanno. Algorithms, such as random forest, BLAST, and receiver operating characteristic curves, were used to evaluate accuracy. Of the tools evaluated, sRNAbench was found to be the most accurate, miRDeep-P2 was the most sensitive, miRDeep-P2 was the fastest, and miRkwood had the highest memory usage. Due to its large genome size, only three tools were able to successfully predict known miRNAs in wheat (Triticum aestivum). Our results enable us to recommend the tool best suited to a variety of researcher needs, which we hope will reduce confusion and enhance future work.
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Affiliation(s)
- Qinglian Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Co‐Innovation Center for Modern Production Technology of Grain CropsCollege of AgricultureYangzhou UniversityYangzhou225009China
- Jiangsu Xuzhou Sweet Potato Research CenterXuzhou221131China
| | - Guanqing Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Co‐Innovation Center for Modern Production Technology of Grain CropsCollege of AgricultureYangzhou UniversityYangzhou225009China
| | - Yu Bao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Co‐Innovation Center for Modern Production Technology of Grain CropsCollege of AgricultureYangzhou UniversityYangzhou225009China
| | - Yuechao Wu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Co‐Innovation Center for Modern Production Technology of Grain CropsCollege of AgricultureYangzhou UniversityYangzhou225009China
| | - Qi You
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Co‐Innovation Center for Modern Production Technology of Grain CropsCollege of AgricultureYangzhou UniversityYangzhou225009China
- State Key Laboratory of Cotton BiologyAnyangHenan455000China
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14
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Xia Z, Wang Z, Kav NNV, Ding C, Liang Y. Characterization of microRNA-like RNAs associated with sclerotial development in Sclerotinia sclerotiorum. Fungal Genet Biol 2020; 144:103471. [PMID: 32971275 DOI: 10.1016/j.fgb.2020.103471] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 09/03/2020] [Accepted: 09/08/2020] [Indexed: 12/29/2022]
Abstract
Sclerotinia sclerotiorum is a model necrotrophic pathogen causing great economic losses worldwide. Sclerotia are dormant structures that play significant biological and ecological roles in the life and disease cycles of S. sclerotiorum and other species of sclerotia-forming fungi. microRNA-like RNAs (milRNAs) as non-coding small RNAs play regulatory roles in fungal development and pathogenicity. Therefore, milRNAs associated with sclerotial development in S. sclerotiorum were investigated in this study. A total of 275 milRNAs with induced expression during sclerotia development were identified, in which 51 were differentially expressed. The target genes of all milRNAs were predicted. The putative functions of the targets regulated by milRNAs were annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The expression levels of six selected milRNAs that coordinated with their corresponding targets were validated by qRT-PCR. Among these six milRNAs, Ssc-milR-240 was potentially associated with sclerotial development by epigenetic regulation of its target histone acetyltransferase. This study will facilitate the better understanding of the milRNA regulation associated with sclerotial development in S. sclerotiorum and even other sclerotia-forming fungi. This work will provide novel insights into the molecular regulations of fungal morphogenesis and the candidate targets of milRNAs used for the sustainable management of plant diseases caused by S. sclerotiorum.
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Affiliation(s)
- Zihao Xia
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China; Liaoning Key Laboratory of Plant Pathology, Shenyang Agricultural University, Shenyang 110866, China
| | - Zehao Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China; Liaoning Key Laboratory of Plant Pathology, Shenyang Agricultural University, Shenyang 110866, China
| | - Nat N V Kav
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G2P5, Canada
| | - Chengsong Ding
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China; Liaoning Key Laboratory of Plant Pathology, Shenyang Agricultural University, Shenyang 110866, China
| | - Yue Liang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China; Liaoning Key Laboratory of Plant Pathology, Shenyang Agricultural University, Shenyang 110866, China.
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15
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Li Y, Liu X, Yin Z, You Y, Zou Y, Liu M, He Y, Zhang H, Zheng X, Zhang Z, Wang P. MicroRNA-like milR236, regulated by transcription factor MoMsn2, targets histone acetyltransferase MoHat1 to play a role in appressorium formation and virulence of the rice blast fungus Magnaporthe oryzae. Fungal Genet Biol 2020; 137:103349. [PMID: 32006681 DOI: 10.1016/j.fgb.2020.103349] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 01/28/2020] [Indexed: 12/25/2022]
Abstract
MicroRNAs (miRNAs) play important roles in various cellular growth and developmental processes through post-transcriptional gene regulation via mRNA cleavage and degradation and the inhibition of protein translation. To explore if miRNAs play a role in appressoria formation and virulence that are also governed by the regulators of G-protein signaling (RGS) proteins in the rice blast fungus Magnaporthe oryzae, we have compared small RNA (sRNA) production between several ΔMorgs mutant and the wild-type strains. We have identified sRNA236 as a microRNA-like milR236 that targets the encoding sequence of MoHat1, a histone acetyltransferase type B catalytic subunit involved in appressorium function and virulence. We have also found that milR236 overexpression induces delayed appressorium formation and virulence attenuation, similar to those displayed by the ΔMohat1 mutant strain. Moreover, we have shown that the transcription factor MoMsn2 binds to the promoter sequence of milR236 to further suppress MoHAT1 transcription and MoHat1-regulated appressorium formation and virulence. In summary, by identifying a novel regulatory role of sRNA in the blast fungus, our studies reveal a new paradigm in the multifaceted regulatory pathways that govern the appressorium formation and virulence of M. oryzae.
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Affiliation(s)
- Ying Li
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - Xinyu Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - Ziyi Yin
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - Yimei You
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - Yibin Zou
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - Muxing Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - Yanglan He
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - Haifeng Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - Xiaobo Zheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - Zhengguang Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China.
| | - Ping Wang
- Departments of Microbiology, Immunology, and Parasitology, and Pediatrics Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
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16
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Ylioja CM, Rolf MM, Mamedova LK, Bradford BJ. Associations between body condition score at parturition and microRNA profile in colostrum of dairy cows as evaluated by paired mapping programs. J Dairy Sci 2019; 102:11609-11621. [PMID: 31548065 DOI: 10.3168/jds.2019-16675] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 08/03/2019] [Indexed: 12/18/2022]
Abstract
MicroRNA (miRNA) are abundant in milk, and likely have regulatory activity involving lactation and immunity. The objective of this study was to determine the miRNA profile in colostrum of overconditioned cows compared with cows of more moderate body condition score (BCS) at calving. Multiparous cows with either high (≥4.0 on a scale of 1 to 5; n = 7) or moderate BCS (2.75 to 3.50; n = 9) in the week before parturition were selected from a commercial dairy herd. Blood and colostrum were sampled within 24 h after calving. Blood serum was analyzed for free fatty acid (FFA) concentration. MicroRNA was isolated from colostrum samples after removing milk fat and cells. MicroRNA were sequenced, and reads were mapped to the bovine genome and to the existing database of miRNA at miRBase.org. Two programs, Oasis 2.0 and miRDeep2, were employed in parallel for read alignment, and analysis of miRNA count data was performed using DESeq2. Identification of differentially expressed miRNA from DESeq2 was not affected by the differences in miRNA detected by the 2 mapping programs. Most abundant miRNA included miR-30a, miR-148a, miR-181a, let-7f, miR-26a, miR-21, miR-22, and miR-92a. Large-scale shifts in miRNA profile were not observed; however, colostrum of cows with high BCS contained less miR-486, which has been linked with altered glucose metabolism. Colostrum from cows with elevated serum FFA contained less miR-885, which may be connected to hepatic function during the transition period. Potential functions of abundant miRNA suggest involvement in development and maintenance of cellular function in the mammary gland, with the additional possibility of influencing neonatal tissue and immune system development.
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Affiliation(s)
- C M Ylioja
- Department of Animal Sciences and Industry, Kansas State University, Manhattan 66506
| | - M M Rolf
- Department of Animal Sciences and Industry, Kansas State University, Manhattan 66506
| | - L K Mamedova
- Department of Animal Sciences and Industry, Kansas State University, Manhattan 66506
| | - B J Bradford
- Department of Animal Sciences and Industry, Kansas State University, Manhattan 66506.
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17
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Bertucci A, Pierron F, Ye T, Gonzalez P, Couture P, Baudrimont M. Identification and expression of microRNAs in european eels Anguilla anguilla from two natural sites with different pollution levels. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 250:274-283. [PMID: 30999204 DOI: 10.1016/j.envpol.2019.04.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 03/25/2019] [Accepted: 04/06/2019] [Indexed: 06/09/2023]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNA that control multiple biological processes through negative post-transcriptional regulation of gene expression. Recently a role of miRNAs in the response of aquatic organisms to environmental toxicants emerged. Toxicant-induced changes in miRNA expression might then represent novel biomarkers to evaluate the health status of these organisms. In this study, we aimed to identify the miRNA repertoire in the liver of the European eel Anguilla anguilla and to compare their differential expression between a polluted site located in the Gironde Estuary and a pristine site in Arcachon Bay (France). A total of 299 mature miRNAs were identified. In polluted water, 19 miRNAs were up-regulated and 22 were down-regulated. We predicted that these differentially expressed miRNAs could target 490 genes that were involved in ribosome biogenesis, response to hormones, response to chemical and chromatin modification. Moreover, we observed only few examples (29) of negative correlation between the expression levels of miRNAs and their targets suggesting that, in the system studied, miRNAs might not only regulate gene expression directly by degrading mRNA but also by inhibiting protein translation or by regulating other epigenetic processes. This study is the first example of in situ investigation of the role of miRNAs in the response of a fish species to water quality. Our findings provide new insights into the involvement of epigenetic mechanisms in the response of animals chronically exposed to pollution and pave the way for the utilization of miRNAs in aquatic ecotoxicology.
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Affiliation(s)
| | - Fabien Pierron
- Univ. Bordeaux, UMR EPOC CNRS 5805, 33615, Pessac, France
| | - Tao Ye
- IGBMC - CNRS UMR 7104 - Inserm U 964, 1 BP 10142, 67404, Illkirch Cedex, France
| | | | - Patrice Couture
- Institut National de La Recherche Scientifique (INRS), Centre Eau Terre Environnement, 490 rue De La Couronne, Québec, QC, G1K 9A9, Canada
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18
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Genome-Wide Identification of Putative MicroRNAs in Cassava ( Manihot esculenta Crantz) and Their Functional Landscape in Cellular Regulation. BIOMED RESEARCH INTERNATIONAL 2019; 2019:2019846. [PMID: 31321230 PMCID: PMC6607727 DOI: 10.1155/2019/2019846] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 05/14/2019] [Accepted: 05/22/2019] [Indexed: 11/18/2022]
Abstract
MicroRNAs are small noncoding RNAs, involved in the regulation of many cellular processes in plants. Hundreds of miRNAs have been identified in cassava by various techniques, yet these identifications were constrained by a lack of miRNA templates and the narrow range of conditions in transcriptome study. In this research, we conducted genome-wide analysis identification, whereby miRNAs from cassava genome were thoroughly screened using bioinformatics approach independent of predefined templates and studied conditions. Our work provided a catalog of putative mature miRNAs and explored the landscape of miRNAome in cassava. These putative miRNAs were validated using statistical analysis as well as available cassava expression data. We showed that the crowded locations of cassava miRNAs are consistent with other plants and animals and hypothesized to have the same evolutionary origin. At least 10 conserved miRNAs were identified in cassava based on the comparative study of miRNA conservation. Finally, investigation of miRNAs and target gene relationships enabled us to envisage the complexities of cellular regulatory systems modulated at posttranscriptional level.
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19
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The lifestyle transition of Arthrobotrys oligospora is mediated by microRNA-like RNAs. SCIENCE CHINA-LIFE SCIENCES 2019; 63:543-551. [PMID: 31016536 DOI: 10.1007/s11427-018-9437-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 12/27/2018] [Accepted: 04/15/2019] [Indexed: 01/19/2023]
Abstract
The lifestyle transition of fungi, defined as switching from taking organic material as nutrients to pathogens, is a fundamental phenomenon in nature. However, the mechanisms of such transition remain largely unknown. Here we show microRNA-like RNAs (milRNAs) play a key role in fungal lifestyle transition for the first time. We identified milRNAs by small RNA sequencing in Arthrobotrys oligospora, a known nematode-trapping fungus. Among them, 7 highly expressed milRNAs were confirmed by northern-blot analysis. Knocking out two milRNAs significantly decreased A. oligospora's ability to switch lifestyles. We further identified that two of these milRNAs were associated with argonaute protein QDE-2 by RNA-immunoprecipitation (RIP) analysis. Three of the predicted target genes of milRNAs were found in immunoprecipitation (IP) products of QDE-2. Disruption of argonaute gene qde-2 also led to serious defects in lifestyle transition. Interestingly, knocking out individual milRNAs or qde-2 lead to diverse responses under different conditions, and qde-2 itself may be targeted by the milRNAs. Collectively, it indicates the lifestyle transition of fungi is mediated by milRNAs through RNA interference (RNAi) machinery, revealing the wide existence of miRNAs in fungi kingdom and providing new insights into understanding the adaptation of fungi from scavengers to predators and the mechanisms underlying fungal infections.
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Luo J, Ren Q, Chen Z, Liu W, Qu Z, Xiao R, Chen R, Lin H, Wu Z, Luo J, Yin H, Wang H, Liu G. Comparative analysis of microRNA profiles between wild and cultured Haemaphysalis longicornis (Acari, Ixodidae) ticks. ACTA ACUST UNITED AC 2019; 26:18. [PMID: 30916642 PMCID: PMC6436478 DOI: 10.1051/parasite/2019018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/11/2019] [Indexed: 12/25/2022]
Abstract
The miRNA profiles of a Haemaphysalis longicornis wild-type (HLWS) and of a Haemaphysalis longicornis cultured population (HLCS) were sequenced using the Illumina Hiseq 4000 platform combined with bioinformatics analysis and real-time polymerase chain reaction (RT-PCR). A total of 15.63 and 15.48 million raw reads were acquired for HLWS and HLCS, respectively. The data identified 1517 and 1327 known conserved miRNAs, respectively, of which 342 were differentially expressed between the two libraries. Thirty-six novel candidate miRNAs were predicted. To explain the functions of these novel miRNAs, Gene Ontology (GO) analysis was performed. Target gene function prediction identified a significant set of genes related to salivary gland development, pathogen-host interaction and regulation of the defence response to pathogens expressed by wild H. longicornis ticks. Cellular component biogenesis, the immune system process, and responses to stimuli were represented at high percentages in the two tick libraries. GO enrichment analysis showed that the percentages of most predicted functions of the target genes of miRNA were similar, as were certain specific categories of functional enhancements, and that these genes had different numbers and specific functions (e.g., auxiliary transport protein and electron carrier functions). This study provides novel findings showing that miRNA regulation affects the expression of immune genes, indicating a considerable influence of environment-induced stressful stimulation on immune homeostasis. Differences in the living environments of ticks can lead to differences in miRNAs between ticks and provide a basis and a convenient means to screen for genes encoding immune factors in ticks.
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Affiliation(s)
- Jin Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China
| | - Qiaoyun Ren
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China
| | - Ze Chen
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China
| | - Wenge Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China
| | - Zhiqiang Qu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China
| | - Ronghai Xiao
- Inspection and Comprehensive Technology Center of Ruili Entry Exit Inspection and Quarantine Bureau, Yunnan 678600, PR China
| | - Ronggui Chen
- Ili Center of Animal Disease Control and Diagnosis, Ili 835000, PR China
| | - Hanliang Lin
- Xinjiang Animal Health Supervision Station, Urumqi, Xinjiang 830063, PR China
| | - Zegong Wu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China - Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, PR China
| | - Hui Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China - Centre for Ecology and Hydrology, Natural Environment Research Council (NERC), Wallingford, Oxon OX10 8BB, UK - Department of Engineering, Institute of Biomedical Engineering, University of Oxford, Oxford OX3 7DQ, UK
| | - Guangyuan Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China
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21
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Shao Y, Tang J, Chen S, Wu Y, Wang K, Ma B, Zhou Q, Chen A, Wang Y. milR4 and milR16 Mediated Fruiting Body Development in the Medicinal Fungus Cordyceps militaris. Front Microbiol 2019; 10:83. [PMID: 30761116 PMCID: PMC6362416 DOI: 10.3389/fmicb.2019.00083] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 01/16/2019] [Indexed: 11/13/2022] Open
Abstract
Cordyceps militaris readily performs sexual reproduction, thus providing a remarkably rich model for understanding the processes involved in sexual development. It could regulate expression of human genes by diet-derived miRNA-like RNAs (milRNAs). However, the study of miRNAs in C. militaris has been limited. In the present study, genes encoding Dicers, Argonautes, and RNA-dependent RNA polymerases were identified. Illumina deep sequencing was performed to characterize the milRNAs in C. militaris at asexual and sexual development stages. Total 38 milRNAs were identified and five milRNAs were validated by northern blot and qRT-PCR, out of which, 19 were specific for sexual development. Importantly, the fungi could not form fruiting bodies after disruption of milR4, while the perithecium was formed in advance after over-expression of milR4. Abnormal pale yellow fruiting body primordium, covered with abnormal primordium, was formed in the strain with miR16 disruption. Although no milR4 or milR16 target genes were identified, differential expression of many different genes involved in mycelium growth and sexual development (mating process, mating signaling, and fruiting body development) among these mutants were found. Overall, milRNAs play vital roles in sexual development in C. militaris.
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Affiliation(s)
- Ying Shao
- Jiangsu Key Laboratory of Food Resource Development and Quality Safe, Xuzhou University of Technology, Xuzhou, China
| | - Jin Tang
- Jiangsu Xuzhou Technician Institute, Xuzhou, China
| | - Shanglong Chen
- Jiangsu Key Laboratory of Food Resource Development and Quality Safe, Xuzhou University of Technology, Xuzhou, China
| | - Yonghua Wu
- Jiangsu Key Laboratory of Food Resource Development and Quality Safe, Xuzhou University of Technology, Xuzhou, China
| | - Kun Wang
- Jiangsu KONEN Biological Engineering Co., Ltd., Nanjing, China
| | - Bin Ma
- Jiangsu KONEN Biological Engineering Co., Ltd., Nanjing, China
| | - Qiumei Zhou
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Anhui Chen
- Jiangsu Key Laboratory of Food Resource Development and Quality Safe, Xuzhou University of Technology, Xuzhou, China
| | - Yulong Wang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China.,Key Laboratory of Crop Quality Improvement of Anhui Province/Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
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22
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Molecular signatures of cytotoxic effects in human embryonic kidney 293 cells treated with single and mixture of ochratoxin A and citrinin. Food Chem Toxicol 2018; 123:374-384. [PMID: 30428381 DOI: 10.1016/j.fct.2018.11.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 10/26/2018] [Accepted: 11/07/2018] [Indexed: 01/04/2023]
Abstract
Ochratoxin A (OTA) and citrinin (CTN) are important mycotoxins, which often coexist in food and feed stuff. In this study, individual and combinative cytotoxicity of OTA and CTN were tested in human embryonic kidney (HEK) 293 cells via MTT assay, and synergistic cytotoxic effects were found following co-treatment with OTA and CTN, manifested by significant accumulation of HEK293 cells in S and G2/M stages. Transcriptomic and sRNA sequencing were performed to explore molecular signatures mediating individual or combinative cytotoxicity. A total of 378 miRNAs were identified, among which 66 miRNAs targeting thousands of genes were differentially expressed in response to different treatments, and 120 differentially expressed genes (DEGs) were regulated by either individual or combinative treatments. Correlations between two representative miRNAs (hsa-miR-1-3p and hsa-miR-122-5p), and their target genes, programmed cell death 10 (PDCD10) and cyclin G1 (CCNG1), associated with apoptotic signaling and cell cycle were analyzed by luciferase assay system. Further, their expression patterns were validated by quantitative real-time PCR and western blot analysis, suggesting that both miRNA-target interactions might account for the mycotoxin-induced cell death. Taken together, these findings provide molecular evidences for synergistic cytotoxic effects of exposure to single and mixture of OTA and CTN in HEK293 cells.
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23
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Soula A, Valere M, López-González MJ, Ury-Thiery V, Groppi A, Landry M, Nikolski M, Favereaux A. Small RNA-Seq reveals novel miRNAs shaping the transcriptomic identity of rat brain structures. Life Sci Alliance 2018; 1:e201800018. [PMID: 30456375 PMCID: PMC6238413 DOI: 10.26508/lsa.201800018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 12/19/2022] Open
Abstract
Small RNA-Seq of the rat central nervous system reveals known and novel miRNAs specifically regulated in brain structures and correlated with the expression of their predicted target genes, suggesting a critical role in the transcriptomic identity of brain structures. In the central nervous system (CNS), miRNAs are involved in key functions, such as neurogenesis and synaptic plasticity. Moreover, they are essential to define specific transcriptomes in tissues and cells. However, few studies were performed to determine the miRNome of the different structures of the rat CNS, although a major model in neuroscience. Here, we determined by small RNA-Seq, the miRNome of the olfactory bulb, the hippocampus, the cortex, the striatum, and the spinal cord and showed the expression of 365 known miRNAs and 90 novel miRNAs. Differential expression analysis showed that several miRNAs were specifically enriched/depleted in these CNS structures. Transcriptome analysis by mRNA-Seq and correlation based on miRNA target predictions suggest that the specifically enriched/depleted miRNAs have a strong impact on the transcriptomic identity of the CNS structures. Altogether, these results suggest the critical role played by these enriched/depleted miRNAs, in particular the novel miRNAs, in the functional identities of CNS structures.
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Affiliation(s)
- Anaïs Soula
- University of Bordeaux, Bordeaux, France.,Centre Nationale de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 5297, Interdisciplinary Institute of Neuroscience, Bordeaux, France
| | - Mélissa Valere
- University of Bordeaux, Bordeaux, France.,Centre Nationale de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 5297, Interdisciplinary Institute of Neuroscience, Bordeaux, France
| | - María-José López-González
- University of Bordeaux, Bordeaux, France.,Centre Nationale de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 5297, Interdisciplinary Institute of Neuroscience, Bordeaux, France
| | - Vicky Ury-Thiery
- University of Bordeaux, Bordeaux, France.,Centre Nationale de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 5297, Interdisciplinary Institute of Neuroscience, Bordeaux, France
| | - Alexis Groppi
- Centre de Bioinformatique de Bordeaux, University of Bordeaux, Bordeaux, France
| | - Marc Landry
- University of Bordeaux, Bordeaux, France.,Centre Nationale de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 5297, Interdisciplinary Institute of Neuroscience, Bordeaux, France
| | - Macha Nikolski
- Centre de Bioinformatique de Bordeaux, University of Bordeaux, Bordeaux, France.,CNRS/Laboratoire Bordelais de Recherche en Informatique, University of Bordeaux, Talence, France
| | - Alexandre Favereaux
- University of Bordeaux, Bordeaux, France.,Centre Nationale de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 5297, Interdisciplinary Institute of Neuroscience, Bordeaux, France
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24
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Luo X, Cao D, Zhang J, Chen L, Xia X, Li H, Zhao D, Zhang F, Xue H, Chen L, Li Y, Cao S. Integrated microRNA and mRNA expression profiling reveals a complex network regulating pomegranate (Punica granatum L.) seed hardness. Sci Rep 2018; 8:9292. [PMID: 29915181 PMCID: PMC6006261 DOI: 10.1038/s41598-018-27664-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 06/05/2018] [Indexed: 12/31/2022] Open
Abstract
The breeding of new soft-seeded pomegranate cultivars provides new products for the market and increases farmers' incomes, yet the genetic architecture mediating seed hardness is largely unknown. Here, the seed hardness and hundred-seed weights of 26 cultivars were determined in 2 successive years. We conducted miRNA and mRNA sequencing to analyse the seeds of two varieties of Punica granatum: soft-seeded Tunisia and hard-seeded Sanbai, at 60 and 120 d after flowering. Seed hardness was strongly positively correlated with hundred-seed weight. We detected 25 and 12 differentially expressed miRNA-mRNA pairs with negative regulatory relationships between the two genotypes at 60 and 120 d after flowering, respectively. These miRNA-mRNA pairs mainly regulated seed hardness by altering cell wall structure. Transcription factors including NAC1, WRKY and MYC, which are involved in seed hardness, were targeted by differentially expressed mdm-miR164e and mdm-miR172b. Thus, seed hardness is the result of a complex biological process regulated by a miRNA-mRNA network in pomegranate. These results will help us understand the complexity of seed hardness and help to elucidate the miRNA-mediated molecular mechanisms that contribute to seed hardness in pomegranate.
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Affiliation(s)
- Xiang Luo
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Da Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Jianfeng Zhang
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, P.R. China
| | - Li Chen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Xiaocong Xia
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Haoxian Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Diguang Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Fuhong Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Hui Xue
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Lina Chen
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Yongzhou Li
- College of Horticultural Science, Henan Agricultural University, Zhengzhou, 450002, P.R. China
| | - Shangyin Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China.
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25
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Tyagi A, Nigam D, S. V. AM, Solanke AU, Singh NK, Sharma TR, Gaikwad K. Genome-wide discovery of tissue-specific miRNAs in clusterbean (Cyamopsis tetragonoloba) indicates their association with galactomannan biosynthesis. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1241-1257. [PMID: 29193664 PMCID: PMC5978871 DOI: 10.1111/pbi.12866] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 11/15/2017] [Accepted: 11/22/2017] [Indexed: 05/13/2023]
Abstract
Owing to the presence of 80% soluble dietary fibre, high protein content and high value gum, clusterbean (Cyamopsis tetragonoloba) has recently emerged as an economically important legume. The developing clusterbean seeds accumulate 90% galactomannans in the endosperm and, therefore, can be used as a model crop to understand galactomannan biosynthesis and its regulation. miRNAs are tiny master regulators of their corresponding target genes, resulting in variations in the amounts of their metabolic end products. To understand the role of these regulators in galactomannan biosynthesis regulation, small RNA libraries were prepared and sequenced from five tissues of clusterbean genotype RGC-936, and miRanalyzer and DSAP programs were used to identify conserved miRNAs and novel small RNAs. A total of 187 known and 171 novel miRNAs were found to be differentially expressed, of which 10 miRNAs were validated. A complicated network topology and 35% sharing of the target mRNAs between known and novel miRNAs suggest random evolution of novel miRNAs. The gene ontology (GO) annotation of potential target genes revealed the genes coding for signalling and carbohydrate metabolism (50.10%), kinases and other enzymes (20.75%), transcription factors (10.20%), transporters (8.35%) and other targets (10.6%). Two novel unigenes were annotated as ManS (mannosyltransferase/mannan synthase) and UGE (UDP- D-glucose 4-epimerase) and validated as targets for three novel miRNAs, that is Ct-miR3130, Ct-miR3135 and Ct-miR3157. Our findings reveal that these novel miRNAs could play an important role in the regulation of the galactomannan pathway in C. tetragonoloba and possibly other galactomannan-producing species.
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Affiliation(s)
- Anshika Tyagi
- ICAR‐National Research Centre on Plant BiotechnologyNew DelhiIndia
| | - Deepti Nigam
- ICAR‐National Research Centre on Plant BiotechnologyNew DelhiIndia
| | | | | | | | - Tilak R. Sharma
- ICAR‐National Research Centre on Plant BiotechnologyNew DelhiIndia
- Present address:
National Agri‐Food Biotechnology InstituteMohaliIndia
| | - Kishor Gaikwad
- ICAR‐National Research Centre on Plant BiotechnologyNew DelhiIndia
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Wang H, Zhong J, Chai Z, Zhu J, Xin J. Comparative expression profile of microRNAs and piRNAs in three ruminant species testes using next-generation sequencing. Reprod Domest Anim 2018; 53:963-970. [PMID: 29752750 DOI: 10.1111/rda.13195] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 03/24/2018] [Indexed: 01/05/2023]
Abstract
microRNA (miRNA) and piwi-interacting RNA (piRNA) are two classes small non-coding regulatory RNAs that play crucial roles in multiple biological processes such as spermatogenesis. However, there are no published studies on conjoint analysis of miRNA and piRNA profiles among cattle, yak and their interspecies (the dzo) using sequencing technology. Next-generation sequencing technology was used to profile miRNAs and piRNAs among those three ruminants to elucidate their functions. A total of 119, 14 and six differentially expressed miRNAs were obtained in cattle vs. dzo, cattle vs. yak and yak vs. dzo comparison groups, while there were 873, 1,065 and 1,158 differentially expressed piRNAs in those three comparison groups. The expression of three miRNAs was validated in the three ruminants, and the results suggested that the miRNA expression profiles data could represent actual miRNA expression levels. Moreover, the putative targets of differentially expressed miRNAs were predicted by their own genome, it is worth to note that both the cattle and yak genome were used for dzo, then the targets were subjected to GO enrichment and KEGG pathway analysis, revealing the likely roles for these differentially expressed miRNAs in spermatogenesis. In conclusion, this study provided a useful resource for further elucidation of the miRNAs and piRNAs regulatory roles in spermatogenesis. It may also facilitate the development of therapeutic strategies for dzo reproduction research.
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Affiliation(s)
- H Wang
- Key Laboratory of Animal Genetics and Breeding, State Ethnic Affairs Commission and Ministry of Education, Southwest Minzu University, Chengdu, China
| | - J Zhong
- Key Laboratory of Animal Genetics and Breeding, State Ethnic Affairs Commission and Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Z Chai
- Key Laboratory of Animal Genetics and Breeding, State Ethnic Affairs Commission and Ministry of Education, Southwest Minzu University, Chengdu, China
| | - J Zhu
- Key Laboratory of Animal Genetics and Breeding, State Ethnic Affairs Commission and Ministry of Education, Southwest Minzu University, Chengdu, China
| | - J Xin
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
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27
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Chen D, Zhang Z, Chen B, Ji D, Hao Y, Zhou P, Wei Z, Cao Y. Altered microRNA and Piwi-interacting RNA profiles in cumulus cells from patients with diminished ovarian reserve. Biol Reprod 2018. [PMID: 28651359 DOI: 10.1093/biolre/iox062] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Diminished ovarian reserve (DOR) is defined as decreased number or quality of follicles and oocytes in a woman at childbearing age. It is estimated that up to 10% of women in the general population may suffer from DOR. This study aims to comprehensively characterize microRNA (miRNA) and Piwi-interacting RNA (piRNA) expression profiles in cumulus cells of DOR patients. Cumulus cells were collected from 20 women of similar chronological age who received assisted reproductive technology treatment: 10 with DOR and 10 with normal ovarian reserve (NOR). The small RNAs were extracted from each sample and reverse transcribed. Deep sequencing and bioinformatic analysis were performed to identify the small noncoding RNA profiles. The rRNAs were the most abundant small RNA class in cumulus cells derived from human MII oocytes, following were miRNAs and tRNAs. Twenty-six piRNAs, 79 annotated miRNAs, and 5 novel miRNAs were identified differentially expressed. In DOR group, the chromosomal strand bias patterns of piRNAs on chromosome 1, 3, 5, and X were distinct from its counterpart in NOR group. The involved biological pathways from the putative target genes of differentially expressed miRNAs were enriched by using GO analysis and KEGG pathway annotations, and mTOR pathway and meiosis-associated biological processes were enriched. This study provided additional information on the dysfunctions of cumulus cells in patients with diminished ovarian reserve. Future investigations will involve the characterization of specific functional roles of noncoding small RNA in ovarian reserve regulation.
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Affiliation(s)
- Dawei Chen
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Bio-preservation and Artificial Organs, Hefei, China
| | - Zhiguo Zhang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Bio-preservation and Artificial Organs, Hefei, China
| | - Beili Chen
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Bio-preservation and Artificial Organs, Hefei, China
| | - Dongmei Ji
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Bio-preservation and Artificial Organs, Hefei, China
| | - Yan Hao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Bio-preservation and Artificial Organs, Hefei, China
| | - Ping Zhou
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Bio-preservation and Artificial Organs, Hefei, China
| | - Zhaolian Wei
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Bio-preservation and Artificial Organs, Hefei, China
| | - Yunxia Cao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Bio-preservation and Artificial Organs, Hefei, China
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28
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Liu Y, Chen Z, Xu K, Wang Z, Wu C, Sun Z, Ji N, Huang M, Zhang M. Next generation sequencing for miRNA profile of spleen CD4 + T cells in the murine model of acute asthma. Epigenomics 2018; 10:1071-1083. [PMID: 29737865 DOI: 10.2217/epi-2018-0043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To explore the miRNAs profile of CD4+ T lymphocytes in asthma via next generation sequencing. METHODS In the murine model of acute asthma, spleen CD4+ T lymphocytes were sorted, in which small RNAs were extracted and sequenced. Novel miRNAs were measured with real time quantitative reverse transcription polymerase chain reaction (qRT-PCR). RESULTS A total of 127 miRNAs were found to exhibit at least twofold change. In the 262 predicted novel miRNAs, 14 novel miRNAs were measured in qRT-PCR in the sorted CD4+ T cells or in the differentiated Th1/Th2 cells and novel miR-11 (xxx-m0228-3p) was significantly decreased in the sorted CD4+ T cells from the murine model of asthma and in the Th2 cells. CONCLUSION Aberrant miRNAs profile in the CD4+ T lymphocytes from acute asthma was documented.
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Affiliation(s)
- Ye Liu
- Department of Geriatrics, Jiangsu Province Geriatric Hospital, Nanjing 210024, PR China
| | - Zhongqi Chen
- Department of Respiratory & Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Kun Xu
- Department of Respiratory Medicine, The Affiliated Wuxi No.2 People's Hospital of Nanjing Medical University, Wuxi 214002, PR China
| | - Zhengxia Wang
- Department of Respiratory & Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Chaojie Wu
- Department of Respiratory & Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Zhixiao Sun
- Department of Respiratory & Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Ningfei Ji
- Department of Geriatrics, Jiangsu Province Geriatric Hospital, Nanjing 210024, PR China.,Department of Respiratory & Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Mao Huang
- Department of Respiratory & Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Mingshun Zhang
- Department of Immunology, Nanjing Medical University, Nanjing 211166, PR China
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29
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Zeng W, Wang J, Wang Y, Lin J, Fu Y, Xie J, Jiang D, Chen T, Liu H, Cheng J. Dicer-Like Proteins Regulate Sexual Development via the Biogenesis of Perithecium-Specific MicroRNAs in a Plant Pathogenic Fungus Fusarium graminearum. Front Microbiol 2018; 9:818. [PMID: 29755439 PMCID: PMC5932338 DOI: 10.3389/fmicb.2018.00818] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 04/10/2018] [Indexed: 11/23/2022] Open
Abstract
Ascospores act as the primary inoculum of Fusarium graminearum, which causes the destructive disease Fusarium head blight (FHB), or scab. MicroRNAs (miRNAs) have been reported in the F. graminearum vegetative stage, and Fgdcl2 is involved in microRNA-like RNA (milRNA) biogenesis but has no major impact on vegetative growth, abiotic stress or pathogenesis. In the present study, we found that ascospore discharge was decreased in the Fgdcl1 deletion mutant, and completely blocked in the double-deletion mutant of Fgdcl1 and Fgdcl2. Besides, more immature asci were observed in the double-deletion mutant. Interestingly, the up-regulated differentially expressed genes (DEGs) common to ΔFgdcl1 and ΔFgdcl1/2 were related to ion transmembrane transporter and membrane components. The combination of small RNA and transcriptome sequencing with bioinformatics analysis predicted 143 novel milRNAs in wild-type perithecia, and 138 of these milRNAs partly or absolutely depended on Fgdcl1, while only 5 novel milRNAs were still obtained in the Fgdcl1 and Fgdcl2 double-deletion mutant. Furthermore, 117 potential target genes were predicted. Overall, Fgdcl1 and Fgdcl2 genes were partly functionally redundant in ascospore discharge and perithecium-specific milRNA generation in F. graminearum, and these perithecium-specific milRNAs play potential roles in sexual development.
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Affiliation(s)
- Wenping Zeng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jie Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ying Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jing Lin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanping Fu
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiatao Xie
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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30
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Bisgin H, Gong B, Wang Y, Tong W. Evaluation of Bioinformatics Approaches for Next-Generation Sequencing Analysis of microRNAs with a Toxicogenomics Study Design. Front Genet 2018; 9:22. [PMID: 29467792 PMCID: PMC5808213 DOI: 10.3389/fgene.2018.00022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/17/2018] [Indexed: 12/18/2022] Open
Abstract
MicroRNAs (miRNAs) are key post-transcriptional regulators that affect protein translation by targeting mRNAs. Their role in disease etiology and toxicity are well recognized. Given the rapid advancement of next-generation sequencing techniques, miRNA profiling has been increasingly conducted with RNA-seq, namely miRNA-seq. Analysis of miRNA-seq data requires several steps: (1) mapping the reads to miRBase, (2) considering mismatches during the hairpin alignment (windowing), and (3) counting the reads (quantification). The choice made in each step with respect to the parameter settings could affect miRNA quantification, differentially expressed miRNAs (DEMs) detection and novel miRNA identification. Furthermore, these parameters do not act in isolation and their joint effects impact miRNA-seq results and interpretation. In toxicogenomics, the variation associated with parameter setting should not overpower the treatment effect (such as the dose/time-dependent effect). In this study, four commonly used miRNA-seq analysis tools (i.e., miRDeep2, miRExpress, miRNAkey, sRNAbench) were comparatively evaluated with a standard toxicogenomics study design. We tested 30 different parameter settings on miRNA-seq data generated from thioacetamide-treated rat liver samples for three dose levels across four time points, followed by four normalization options. Because both miRExpress and miRNAkey yielded larger variation than that of the treatment effects across multiple parameter settings, our analyses mainly focused on the side-by-side comparison between miRDeep2 and sRNAbench. While the number of miRNAs detected by miRDeep2 was almost the subset of those detected by sRNAbench, the number of DEMs identified by both tools was comparable under the same parameter settings and normalization method. Change in the number of nucleotides out of the mature sequence in the hairpin alignment (window option) yielded the largest variation for miRNA quantification and DEMs detection. However, such a variation is relatively small compared to the treatment effect when the study focused on DEMs that are more critical to interpret the toxicological effect. While the normalization methods introduced a large variation in DEMs, toxic behavior of thioacetamide showed consistency in the trend of time-dose responses. Overall, miRDeep2 was found to be preferable over other choices when the window option allowed up to three nucleotides from both ends.
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Affiliation(s)
- Halil Bisgin
- Department of Computer Science, Engineering, and Physics, University of Michigan-Flint, Flint, MI, United States
| | - Binsheng Gong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research (FDA), Jefferson, AR, United States
| | - Yuping Wang
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research (FDA), Jefferson, AR, United States
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research (FDA), Jefferson, AR, United States
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31
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Wu X, Kim TK, Baxter D, Scherler K, Gordon A, Fong O, Etheridge A, Galas DJ, Wang K. sRNAnalyzer-a flexible and customizable small RNA sequencing data analysis pipeline. Nucleic Acids Res 2017; 45:12140-12151. [PMID: 29069500 PMCID: PMC5716150 DOI: 10.1093/nar/gkx999] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 10/11/2017] [Indexed: 12/11/2022] Open
Abstract
Although many tools have been developed to analyze small RNA sequencing (sRNA-Seq) data, it remains challenging to accurately analyze the small RNA population, mainly due to multiple sequence ID assignment caused by short read length. Additional issues in small RNA analysis include low consistency of microRNA (miRNA) measurement results across different platforms, miRNA mapping associated with miRNA sequence variation (isomiR) and RNA editing, and the origin of those unmapped reads after screening against all endogenous reference sequence databases. To address these issues, we built a comprehensive and customizable sRNA-Seq data analysis pipeline—sRNAnalyzer, which enables: (i) comprehensive miRNA profiling strategies to better handle isomiRs and summarization based on each nucleotide position to detect potential SNPs in miRNAs, (ii) different sequence mapping result assignment approaches to simulate results from microarray/qRT-PCR platforms and a local probabilistic model to assign mapping results to the most-likely IDs, (iii) comprehensive ribosomal RNA filtering for accurate mapping of exogenous RNAs and summarization based on taxonomy annotation. We evaluated our pipeline on both artificial samples (including synthetic miRNA and Escherichia coli cultures) and biological samples (human tissue and plasma). sRNAnalyzer is implemented in Perl and available at: http://srnanalyzer.systemsbiology.net/.
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Affiliation(s)
- Xiaogang Wu
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Taek-Kyun Kim
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - David Baxter
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Aaron Gordon
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Olivia Fong
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | - Alton Etheridge
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | - David J Galas
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | - Kai Wang
- Institute for Systems Biology, Seattle, WA 98109, USA
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32
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Small RNAome sequencing delineates the small RNA landscape of pluripotent adult stem cells in the planarian Schmidtea mediterranea. GENOMICS DATA 2017; 14:114-125. [PMID: 29124009 PMCID: PMC5671611 DOI: 10.1016/j.gdata.2017.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 10/15/2017] [Accepted: 10/17/2017] [Indexed: 12/22/2022]
Abstract
Small noncoding RNAs play a pivotal role in the regulation of gene expression, and are key regulators of animal development. Freshwater planarian exhibits an extraordinary ability to regenerate any missing body parts, representing an emerging model for studying mechanism underlying stem cell regulation and tissue regeneration. Here, we utilized next-generation sequencing (NGS) to identify small RNAs that are expressed in planarian adult stem cells, and are implicated in tissue regeneration. We profiled microRNAs (miRNAs), piwi-interacting RNA (piRNAs), small rDNA-derived RNAs (srRNAs) and endogenous interfering RNAs (endo-siRNAs) population from size 18–30 nt, measured the expression of 244 conserved miRNAs, and identified 41 novel miRNAs and 64 novel endo-siRNAs. Expression profiling analyses revealed that most piRNAs and srRNAs are up-regulated during regeneration, and that the most abundantly expressed srRNAs are from 5.8s and 28s rRNA. Furthermore, a target prediction method was adopted to investigate the anti-correlation of small RNAs and mRNA expression. We built up a gene regulatory network based on the genes that are targeted by dynamically changed small RNAs. These results expand the known small RNA repertoire in planarian, and provide valuable insights and a rich resource for understanding the small RNAs landscape in stem cell-mediated regeneration.
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33
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Andreassen R, Høyheim B. miRNAs associated with immune response in teleost fish. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 75:77-85. [PMID: 28254620 DOI: 10.1016/j.dci.2017.02.023] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 02/25/2017] [Accepted: 02/26/2017] [Indexed: 06/06/2023]
Abstract
MicroRNAs (miRNAs) have been identified as important post transcriptional regulators of gene expression. In higher vertebrates, a subset of miRNAs has been identified as important regulators of a number of key genes in immune system gene networks, and this paper review recent studies on miRNAs associated with immune response in teleost fish. Challenge studies conducted in several species have identified differently expressed miRNAs associated with viral or bacterial infection. The results from these studies point out several miRNAs that are likely to have evolutionary conserved functions that are related to immune response in teleost fish. Changed expression levels of mature miRNAs from the five miRNA genes miRNA-462, miRNA-731, miRNA-146, miRNA-181 and miRNA-223 are observed following viral as well as bacterial infection in several teleost fish. Furthermore, significant changes in expression of mature miRNAs from the five genes miRNA-21, miRNA-155, miRNA-1388, miRNA-99 and miRNA-100 are observed in multiple studies of virus infected fish while changes in expression of mature miRNA from the three genes miRNA-122, miRNA-192 and miRNA-451 are observed in several studies of fish with bacterial infections. Interestingly, some of these genes are not present in higher vertebrates. The function of the evolutionary conserved miRNAs responding to infection depends on the target gene(s) they regulate. A few target genes have been identified while a large number of target genes have been predicted by in silico analysis. The results suggest that many of the targets are genes from the host's immune response gene networks. We propose a model with expected temporal changes in miRNA expression if they target immune response activators/effector genes or immune response inhibitors, respectively. The best way to understand the function of a miRNA is to identify its target gene(s), but as the amount of genome resources for teleost fish is limited, with less well characterized genomes and transcriptomes, identifying the true target genes of the miRNAs associated with the immune response is a challenge. Identifying such target genes by applying new methods and approaches will likely be the next important step to understand the function of the miRNAs associated with immune response in teleost fish.
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Affiliation(s)
- Rune Andreassen
- Department of Pharmacy and Biomedical and Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Pilestredet 50, N-0130 Oslo, Norway.
| | - Bjørn Høyheim
- Department of Basic Sciences and Aquatic Medicine, School of Veterinary Medicine, Norwegian University of Life Sciences, Ullevålsveien 72, 0454 Oslo, Norway.
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34
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Comparative analysis of miRNAs of two rapeseed genotypes in response to acetohydroxyacid synthase-inhibiting herbicides by high-throughput sequencing. PLoS One 2017; 12:e0184917. [PMID: 28950015 PMCID: PMC5614533 DOI: 10.1371/journal.pone.0184917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 09/02/2017] [Indexed: 01/07/2023] Open
Abstract
Acetohydroxyacid synthase (AHAS), also called acetolactate synthase, is a key enzyme involved in the first step of the biosynthesis of the branched-chain amino acids valine, isoleucine and leucine. Acetohydroxyacid synthase-inhibiting herbicides (AHAS herbicides) are five chemical families of herbicides that inhibit AHAS enzymes, including imidazolinones (IMI), sulfonylureas (SU), pyrimidinylthiobenzoates, triazolinones and triazolopyrimidines. Five AHAS genes have been identified in rapeseed, but little information is available regarding the role of miRNAs in response to AHAS herbicides. In this study, an AHAS herbicides tolerant genotype and a sensitive genotype were used for miRNA comparative analysis. A total of 20 small RNA libraries were obtained of these two genotypes at three time points (0h, 24 h and 48 h) after spraying SU and IMI herbicides with two replicates. We identified 940 conserved miRNAs and 1515 novel candidate miRNAs in Brassica napus using high-throughput sequencing methods combined with computing analysis. A total of 3284 genes were predicted to be targets of these miRNAs, and their functions were shown using GO, KOG and KEGG annotations. The differentiation expression results of miRNAs showed almost twice as many differentiated miRNAs were found in tolerant genotype M342 (309 miRNAs) after SU herbicide application than in sensitive genotype N131 (164 miRNAs). In additiond 177 and 296 miRNAs defined as differentiated in sensitive genotype and tolerant genotype in response to SU herbicides. The miR398 family was observed to be associated with AHAS herbicide tolerance because their expression increased in the tolerant genotype but decreased in the sensitive genotype. Moreover, 50 novel miRNAs from 39 precursors were predicted. There were 8 conserved miRNAs, 4 novel miRNAs and 3 target genes were validated by quantitative real-time PCR experiment. This study not only provides novel insights into the miRNA content of AHAS herbicides tolerant rapeseed in response to AHAS herbicides, but also demonstrates that miRNAs may be involved in AHAS herbicides tolerance.
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35
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Paicu C, Mohorianu I, Stocks M, Xu P, Coince A, Billmeier M, Dalmay T, Moulton V, Moxon S. miRCat2: accurate prediction of plant and animal microRNAs from next-generation sequencing datasets. Bioinformatics 2017; 33:2446-2454. [PMID: 28407097 PMCID: PMC5870699 DOI: 10.1093/bioinformatics/btx210] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 03/28/2017] [Accepted: 04/10/2017] [Indexed: 01/05/2023] Open
Abstract
MOTIVATION MicroRNAs are a class of ∼21-22 nt small RNAs which are excised from a stable hairpin-like secondary structure. They have important gene regulatory functions and are involved in many pathways including developmental timing, organogenesis and development in eukaryotes. There are several computational tools for miRNA detection from next-generation sequencing datasets. However, many of these tools suffer from high false positive and false negative rates. Here we present a novel miRNA prediction algorithm, miRCat2. miRCat2 incorporates a new entropy-based approach to detect miRNA loci, which is designed to cope with the high sequencing depth of current next-generation sequencing datasets. It has a user-friendly interface and produces graphical representations of the hairpin structure and plots depicting the alignment of sequences on the secondary structure. RESULTS We test miRCat2 on a number of animal and plant datasets and present a comparative analysis with miRCat, miRDeep2, miRPlant and miReap. We also use mutants in the miRNA biogenesis pathway to evaluate the predictions of these tools. Results indicate that miRCat2 has an improved accuracy compared with other methods tested. Moreover, miRCat2 predicts several new miRNAs that are differentially expressed in wild-type versus mutants in the miRNA biogenesis pathway. AVAILABILITY AND IMPLEMENTATION miRCat2 is part of the UEA small RNA Workbench and is freely available from http://srna-workbench.cmp.uea.ac.uk/. CONTACT v.moulton@uea.ac.uk or s.moxon@uea.ac.uk. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Claudia Paicu
- The Earlham Institute, Norwich Research Park, Norwich, UK
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Irina Mohorianu
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Matthew Stocks
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Ping Xu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Aurore Coince
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Martina Billmeier
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
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36
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Using RNA sequencing to identify putative competing endogenous RNAs (ceRNAs) potentially regulating fat metabolism in bovine liver. Sci Rep 2017; 7:6396. [PMID: 28743867 PMCID: PMC5527063 DOI: 10.1038/s41598-017-06634-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 06/14/2017] [Indexed: 12/22/2022] Open
Abstract
RNA sequencing has been extensively used to study specific gene expression patterns to discover potential key genes related to complex traits of interest in animals. Of note, a new regulatory mechanism builds a large-scale regulatory network among transcriptome, where lncRNAs act as competing endogenous RNAs (ceRNAs) to sponge miRNAs to regulate the expression of miRNA target genes post-transcriptionally. In this study, we sequenced the cDNA and sRNA libraries of nine liver samples from three Holstein cows during dry period, early lactation, and peak of lactation with HiSeq platform. As a result, we identified 665 genes, 57 miRNAs and 33 lncRNAs that displayed differential expression patterns across periods. Subsequently, a total of 41ceRNA pairs (lncRNA-mRNA) sharing 11 miRNAs were constructed including 30 differentially expressed genes. Importantly, 12 among them were presented in our large metabolic networks, and predicted to influence the lipid metabolism through insulin, PI3K-Akt, MAPK, AMPK, mTOR, and PPAR signaling pathways, thus, these genes were considered as the most promising candidates for milk fat formation. To our knowledge, this is first investigation to profile the ceRNA regulatory networks of liver transcriptome that could affect milk fat synthesis in bovine, providing a new view of the regulatory mechanism of RNAs.
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37
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Miao Q, Deng P, Saha S, Jenkins JN, Hsu CY, Abdurakhmonov IY, Buriev ZT, Pepper A, Ma DP. Genome-wide identification and characterization of microRNAs differentially expressed in fibers in a cotton phytochrome A1 RNAi line. PLoS One 2017; 12:e0179381. [PMID: 28614407 PMCID: PMC5470697 DOI: 10.1371/journal.pone.0179381] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 05/28/2017] [Indexed: 02/07/2023] Open
Abstract
Cotton fiber is an important commodity throughout the world. Fiber property determines fiber quality and commercial values. Previous studies showed that silencing phytochrome A1 gene (PHYA1) by RNA interference in Upland cotton (Gossypium hirsutum L. cv. Coker 312) had generated PHYA1 RNAi lines with simultaneous improvements in fiber quality (longer, stronger and finer fiber) and other key agronomic traits. Characterization of the altered molecular processes in these RNAi genotypes and its wild-type controls is a great interest to better understand the PHYA1 RNAi phenotypes. In this study, a total of 77 conserved miRNAs belonging to 61 families were examined in a PHYA1 RNAi line and its parental Coker 312 genotype by using multiplex sequencing. Of these miRNAs, seven (miR7503, miR7514, miR399c, miR399d, miR160, miR169b, and miR2950) were found to be differentially expressed in PHYA1 RNAi cotton. The target genes of these differentially expressed miRNAs were involved in the metabolism and signaling pathways of phytohormones, which included Gibberellin, Auxin and Abscisic Acid. The expression of several MYB transcription factors was also affected by miRNAs in RNAi cotton. In addition, 35 novel miRNAs (novel miR1-novel miR35) were identified in fibers for the first time in this study. Target genes of vast majority of these novel miRNAs were also predicted. Of these, nine novel miRNAs (novel-miR1, 2, 16, 19, 26, 27, 28, 31 and 32) were targeted to cytochrome P450-like TATA box binding protein (TBP). The qRT-PCR confirmed expression levels of several differentially regulated miRNAs. Expression patterns of four miRNAs-targets pairs were also examined via RNA deep sequencing. Together, the results imply that the regulation of miRNA expression might confer to the phenotype of the PHYA1 RNAi line(s) with improved fiber quality.
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Affiliation(s)
- Qing Miao
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, United States of America
| | - Peng Deng
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, New York, NY, United States of America
| | - Sukumar Saha
- USDA-ARS, Crop Science Research Laboratory, Mississippi State, MS, United States of America
| | - Johnie N. Jenkins
- USDA-ARS, Crop Science Research Laboratory, Mississippi State, MS, United States of America
| | - Chuan-Yu Hsu
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS, United States of America
| | | | - Zabardast T. Buriev
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan
| | - Alan Pepper
- Department of Biology, Texas A & M University, College Station, TX, United States of America
| | - Din-Pow Ma
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, United States of America
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38
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Li Y, Zeng A, Li G, Guan YN, Yang HT, Shen B, Jing Q. Dynamic regulation of small RNAome during the early stage of cardiac differentiation from pluripotent embryonic stem cells. GENOMICS DATA 2017; 12:136-145. [PMID: 28540181 PMCID: PMC5432660 DOI: 10.1016/j.gdata.2017.05.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 04/09/2017] [Accepted: 05/03/2017] [Indexed: 11/16/2022]
Abstract
Embryonic stem cells (mESCs), having potential to differentiate into three germ-layer cells including cardiomyocytes, shall be a perfect model to help understanding heart development. Here, using small RNA deep sequencing, we studied the small RNAome in the early stage of mouse cardiac differentiation. We found that the expression pattern of most microRNA (miRNA) were highly enriched at the beginning and declined thereafter, some were still insufficiently expressed on day 6, and most miRNAs recovered in the following days. When pluripotent embryonic stem cells are differentiating to cardiomyocytes, targeted genes are concentrated on TGF, WNT and cytoskeletal remodeling pathway. The pathway and network of dynamically changed target genes of the miRNAs at different time points were also investigated. Furthermore, we demonstrated that small rDNA-derived RNAs (srRNAs) were significantly up-regulated during differentiation, especially in stem cells. The pathways of srRNAs targeted genes were also presented. We described the existence and the differential expression of transfer RNA (tRNA), Piwi-interacting RNA (piRNA) and Endogenous siRNAs (endo-siRNAs) in this process. This study reports the genome-wide small RNAome profile, and provides a uniquely comprehensive view of the small RNA regulatory network that governs embryonic stem cell differentiation and cardiac development.
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Affiliation(s)
- Yue Li
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Jiao-Tong University School of Medicine and Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China
- Department of Cardiology, Changhai Hospital, Shanghai 200433, China
- Correspondence to: Y. Li, Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Jiao-Tong University School of Medicine and Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China.Key Laboratory of Stem Cell BiologyInstitute of Health SciencesShanghai Jiao-Tong University School of Medicine and Shanghai Institute for Biological ScienceChinese Academy of SciencesShanghai200031China
| | - An Zeng
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Jiao-Tong University School of Medicine and Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ge Li
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Jiao-Tong University School of Medicine and Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ya-Na Guan
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Jiao-Tong University School of Medicine and Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Huang-Tian Yang
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Jiao-Tong University School of Medicine and Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bairong Shen
- Center for Systems Biology, Soochow University, Suzhou 215006, China
- Corresponding author.
| | - Qing Jing
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Jiao-Tong University School of Medicine and Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China
- Department of Cardiology, Changhai Hospital, Shanghai 200433, China
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39
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Li Y, Wan L, Bi S, Wan X, Li Z, Cao J, Tong Z, Xu H, He F, Li X. Identification of Drought-Responsive MicroRNAs from Roots and Leaves of Alfalfa by High-Throughput Sequencing. Genes (Basel) 2017; 8:genes8040119. [PMID: 28406444 PMCID: PMC5406866 DOI: 10.3390/genes8040119] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 12/13/2022] Open
Abstract
Alfalfa, an important forage legume, is an ideal crop for sustainable agriculture and a potential crop for bioenergy resources. Drought, one of the most common environmental stresses, substantially affects plant growth, development, and productivity. MicroRNAs (miRNAs) are newly discovered gene expression regulators that have been linked to several plant stress responses. To elucidate the role of miRNAs in drought stress regulation of alfalfa, a high-throughput sequencing approach was used to analyze 12 small RNA libraries comprising of four samples, each with three biological replicates. From the 12 libraries, we identified 348 known miRNAs belonging to 80 miRNA families, and 281 novel miRNAs, using Mireap software. Eighteen known miRNAs in roots and 12 known miRNAs in leaves were screened as drought-responsive miRNAs. With the exception of miR319d and miR157a which were upregulated under drought stress, the expression pattern of drought-responsive miRNAs was different between roots and leaves in alfalfa. This is the first study that has identified miR3512, miR3630, miR5213, miR5294, miR5368 and miR6173 as drought-responsive miRNAs. Target transcripts of drought-responsive miRNAs were computationally predicted. All 447 target genes for the known miRNAs were predicted using an online tool. This study provides a significant insight on understanding drought-responsive mechanisms of alfalfa.
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Affiliation(s)
- Yue Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Liqiang Wan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Shuyi Bi
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xiufu Wan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Zhenyi Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Jing Cao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Zongyong Tong
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Hongyu Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Feng He
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xianglin Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Ling J, Luo Z, Liu F, Mao Z, Yang Y, Xie B. Genome-wide analysis of microRNA targeting impacted by SNPs in cucumber genome. BMC Genomics 2017; 18:275. [PMID: 28376783 PMCID: PMC5379521 DOI: 10.1186/s12864-017-3665-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 03/25/2017] [Indexed: 01/08/2023] Open
Abstract
Background microRNAs (miRNAs) are endogenous small RNAs that play important regulatory functions in plant development. Genetic variations in miRNAs sequences or their target-binding sites (microRNA-target interaction sites) can alter miRNA targets in animal and human. Whether these single nucleotide polymorphisms (SNPs) in plant are functional have not yet been determined. Results In this study, we constructed leaf, root, and stem-derived small libraries of cucumber (Cucumis sativus) line 9930 (cultivated China-group cucumber) and C. sativus var. hardwickii (wild India group cucumber). A total of 22 conserved miRNA families, nine less-conserved miRNA families, and 49 cucumber-specific miRNAs were identified in both line 9930 and hardwickii. We employed cucumber resequencing data to perform a genome-wide scan for SNPs in cucumber miRNA-target interaction sites, including miRNA mature sequences and miRNA-target binding sites. As a result, we identified a total of 19 SNPs in mature miRNA sequences and 113 SNPs in miRNA-target binding sites with the potential to affect miRNA-target interactions. Furthermore, we experimentally confirmed that these SNPs produced 14 9930-unique targets mRNAs and 15 hardwickii-unique targets mRNA for cucumber miRNAs. This is the first experimental validation of SNPs in miRNA-target interaction sites affecting miRNA-target binding in plants. Conclusions Our results indicate that SNPs can alter miRNA function and produce unique miRNA targets in cultivated and wild cucumbers. Therefore, miRNA-related SNPs may have played important in events that led to the agronomic differences between domestic and wild cucumber. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3665-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jian Ling
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhongqin Luo
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Feng Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhenchuan Mao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yuhong Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Bingyan Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China.
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Ning P, Zhou Y, Gao L, Sun Y, Zhou W, Liu F, Yao Z, Xie L, Wang J, Gong C. Unraveling the microRNA of Caragana korshinskii along a precipitation gradient on the Loess Plateau, China, using high-throughput sequencing. PLoS One 2017; 12:e0172017. [PMID: 28207805 PMCID: PMC5313209 DOI: 10.1371/journal.pone.0172017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 01/30/2017] [Indexed: 12/02/2022] Open
Abstract
Drought remains one of the main factors that negatively affect plant growth and development. Caragana korshinskii is widely distributed on the Loess Plateau, China, where it mediates soil and water loss and helps prevent desertification. However, little is known about the stress response mechanisms of C. korshinskii in water-starved environments. MicroRNAs (miRNAs) have been implicated in the regulation of plant responses to several types of biotic and abiotic stress. Here, we describe the miRNAs of wild C. korshinskii from Huangling, Yulin, and Dalad Banner, which occur along a precipitation gradient. Using next-generation sequencing technology, we obtained a total of 13 710 681, 15 048 945, and 15 198 442 reads for each location, respectively; after filtering and BLAST analysis, 490 conserved miRNAs and 96 novel miRNAs were characterized from the sRNAome data, with key functions determined using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses. We also designed stem-loop qRT-PCR to validate the expression patterns of 5 conserved miRNAs (miR390, miR398, miR530, miR2119, and miR5559) that obviously responded to water stress in plants grown both under natural and experimental water stress conditions and found that the expression levels of miR2119 and miR5559 were negatively correlated with their predicted target genes. This study is the first to identify miRNAs from wild C. korshinskii and provides a basis for future studies of miRNA-mediated gene regulation of stress responses in C. korshinskii.
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Affiliation(s)
- Pengbo Ning
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi, China
| | - Yulu Zhou
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| | - Lifang Gao
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| | - Yingying Sun
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| | - Wenfei Zhou
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| | - Furong Liu
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhenye Yao
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| | - Lifang Xie
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| | - Junhui Wang
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| | - Chunmei Gong
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
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Bousios A, Gaut BS, Darzentas N. Considerations and complications of mapping small RNA high-throughput data to transposable elements. Mob DNA 2017; 8:3. [PMID: 28228849 PMCID: PMC5311732 DOI: 10.1186/s13100-017-0086-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 01/31/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND High-throughput sequencing (HTS) has revolutionized the way in which epigenetic research is conducted. When coupled with fully-sequenced genomes, millions of small RNA (sRNA) reads are mapped to regions of interest and the results scrutinized for clues about epigenetic mechanisms. However, this approach requires careful consideration in regards to experimental design, especially when one investigates repetitive parts of genomes such as transposable elements (TEs), or when such genomes are large, as is often the case in plants. RESULTS Here, in an attempt to shed light on complications of mapping sRNAs to TEs, we focus on the 2,300 Mb maize genome, 85% of which is derived from TEs, and scrutinize methodological strategies that are commonly employed in TE studies. These include choices for the reference dataset, the normalization of multiply mapping sRNAs, and the selection among sRNA metrics. We further examine how these choices influence the relationship between sRNAs and the critical feature of TE age, and contrast their effect on low copy genomic regions and other popular HTS data. CONCLUSIONS Based on our analyses, we share a series of take-home messages that may help with the design, implementation, and interpretation of high-throughput TE epigenetic studies specifically, but our conclusions may also apply to any work that involves analysis of HTS data.
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Affiliation(s)
- Alexandros Bousios
- School of Life Sciences, University of Sussex, Brighton, East Sussex BN1 9RH UK
| | - Brandon S. Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92697 USA
| | - Nikos Darzentas
- Central European Institute of Technology, Masaryk University, Brno, 62500 Czech Republic
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Jin Q, Xu Y, Mattson N, Li X, Wang B, Zhang X, Jiang H, Liu X, Wang Y, Yao D. Identification of Submergence-Responsive MicroRNAs and Their Targets Reveals Complex MiRNA-Mediated Regulatory Networks in Lotus ( Nelumbo nucifera Gaertn). FRONTIERS IN PLANT SCIENCE 2017; 8:6. [PMID: 28149304 PMCID: PMC5241310 DOI: 10.3389/fpls.2017.00006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/03/2017] [Indexed: 05/25/2023]
Abstract
MicroRNAs (miRNAs) are endogenous non-coding RNAs with important regulatory functions in plant development and stress responses. However, their population abundance in lotus (Nelumbo nucifera Gaertn) has so far been poorly described, particularly in response to stresses. In this work, submergence-related miRNAs and their target genes were systematically identified, compared, and validated at the transcriptome-wide level using high-throughput sequencing data of small RNA, Mrna, and the degradome. A total of 128 known and 20 novel miRNAs were differentially expressed upon submergence. We identified 629 target transcripts for these submergence-responsive miRNAs. Based on the miRNA expression profiles and GO and KEGG annotation of miRNA target genes, we suggest possible molecular responses and physiological changes of lotus in response to submergence. Several metabolic, physiological and morphological adaptations-related miRNAs, i.e., NNU_far-miR159, NNU_gma-miR393h, and NNU_aly-miR319c-3p, were found to play important regulatory roles in lotus response to submergence. This work will contribute to a better understanding of miRNA-regulated adaption responses of lotus to submergence stress.
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Affiliation(s)
- Qijiang Jin
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Yingchun Xu
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Neil Mattson
- Horticulture Section, School of Integrative Plant Science, Cornell UniversityNew York, NY, USA
| | - Xin Li
- Institute of Agricultural Science of Taihu Lake DistrictSuzhou, China
| | - Bei Wang
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Xiao Zhang
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Hongwei Jiang
- Institute of Agricultural Science of Taihu Lake DistrictSuzhou, China
| | - Xiaojing Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of SciencesNanjing, China
| | - Yanjie Wang
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Dongrui Yao
- Institute of Botany, Jiangsu Province and Chinese Academy of SciencesNanjing, China
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Cai X, Liu Q, Zhang X, Ren Y, Lei X, Li S, Chen Q, Deng K, Wang P, Zhang H, Shi D. Identification and analysis of the expression of microRNA from lactating and nonlactating mammary glands of the Chinese swamp buffalo. J Dairy Sci 2017; 100:1971-1986. [PMID: 28109598 DOI: 10.3168/jds.2016-11461] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 11/20/2016] [Indexed: 11/19/2022]
Abstract
To study the role of microRNA (miR) in the lactation physiology of water buffalo, 2 multiparous dairy buffaloes (including an 8-yr-old buffalo that had been lactating for 3 mo, as well as a 10-yr-old nonlactating, nonpregnant buffalo) were used for miR library construction. The profile of differentially expressed miR in lactating and nonlactating mammary gland tissues of these water buffalo were investigated using Illumina-Solexa high-throughput sequencing technology (Illumina, San Diego, CA). The data identified 259 miR families, 359 mature miR, 363 pre-miR, 230 novel buffalo miR, and 5 buffalo-specific miR that were expressed in mammary tissues. Some highly significantly differentially expressed miR were explored, including bbu-miR-497, bbu-miR-30a-5p, bbu-miR-148a, bbu-miR-29a, bbu-miR-125a, bbu-miR-125b, and bbu-miR-103. The expression patterns of 18 miR were confirmed by quantitative real-time PCR in both tissues, and the expression of bbu miR-103 and novel miR-57 constituted the largest differences between lactating and nonlactating tissues. Further functional analysis indicated that the overexpression or suppression of miR-103 in buffalo mammary epithelial cells downregulated or upregulated the expression of pantothenate kinase 3, and also significantly increased the transcription factor steroid regulatory element binding protein, followed by the acceleration of de novo synthesis of fatty acids by upregulation of acetyl coenzyme A carboxylase α expression. The expression levels of 34 predicted target genes of novel-miR-57 in lactating and nonlactating mammary gland tissues were all analyzed by quantitative real-time PCR. Finally, only the expression of docking protein 4 could be upregulated or downregulated selectively by bbu-novel-miR-57 in buffalo mammary epithelial cells and the Bcap-37 cell line. This study provides an overview of the miR expression profile of water buffalo and the interaction between some key miR and their target genes, which may improve understanding of the important roles of miR in buffalo milk fat synthesis.
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Affiliation(s)
- Xiaoyan Cai
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics, Guangxi University, Nanning, China 530004; Guangxi Institute of Animal Science, Nanning, China, 530001
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics, Guangxi University, Nanning, China 530004.
| | - Xiaoxi Zhang
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics, Guangxi University, Nanning, China 530004
| | - Yanping Ren
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics, Guangxi University, Nanning, China 530004
| | - Xiaocan Lei
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics, Guangxi University, Nanning, China 530004
| | - Sheng Li
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics, Guangxi University, Nanning, China 530004
| | - Qiuping Chen
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics, Guangxi University, Nanning, China 530004
| | - Kai Deng
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics, Guangxi University, Nanning, China 530004
| | - Ping Wang
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics, Guangxi University, Nanning, China 530004
| | - Haihang Zhang
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics, Guangxi University, Nanning, China 530004
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Agricultural Bioresources in the Subtropics, Guangxi University, Nanning, China 530004.
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Zendjabil M, Favard S, Tse C, Abbou O, Hainque B. [The microRNAs as biomarkers: What prospects?]. C R Biol 2017; 340:114-131. [PMID: 28081967 DOI: 10.1016/j.crvi.2016.12.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 12/12/2016] [Accepted: 12/15/2016] [Indexed: 12/12/2022]
Abstract
MicroRNAs are nucleic acids of about twenty nucleotides that regulate about a third of the genome at the post-transcriptional level. Thanks to their different forms of transport, microRNAs are stable and can be detected in biological fluids such as blood, urine, cerebrospinal fluid, or saliva. In addition, the profile of circulating microRNAs is a specific part of the cells in which it is secreted and is modified according to the physiological or pathological conditions of these cells. MicroRNAs therefore appear as biomarkers of interest for many diseases. However, these applications face several challenges because there are currently considerable differences between the sample processing procedures, assay methods, and especially the result standardization strategies. This literature review aims to take stock of the current use of microRNAs as biomarkers mainly in biological fluids and address the perspectives that emerge from the fact that their vesicular circulating forms could be used to assess the state of the cells and the tissues that produce them.
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Affiliation(s)
- Mustapha Zendjabil
- Service de biochimie, établissement hospitalier universitaire (EHU) d'Oran, 1(er)-Novembre-1954, BP 4166 Ibn Rochd, Oran, Algérie.
| | - Séverine Favard
- Service de biochimie métabolique, hôpitaux universitaires Pitié-Salpêtrière-Charles-Foix, 47, boulevard de l'Hôpital, 75013 Paris, France
| | - Chantal Tse
- Service de biochimie métabolique, hôpitaux universitaires Pitié-Salpêtrière-Charles-Foix, 47, boulevard de l'Hôpital, 75013 Paris, France
| | - Omar Abbou
- Service de biochimie, établissement hospitalier universitaire (EHU) d'Oran, 1(er)-Novembre-1954, BP 4166 Ibn Rochd, Oran, Algérie
| | - Bernard Hainque
- Service de biochimie métabolique, hôpitaux universitaires Pitié-Salpêtrière-Charles-Foix, 47, boulevard de l'Hôpital, 75013 Paris, France
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Zhang D, Wang Y, Ji Z, Wang Z. Data on differentially expressed microRNAs in the liver between nonalcoholic fatty liver disease and normal Wistar rat using Solexa sequencing. Data Brief 2016; 8:280-5. [PMID: 27331102 PMCID: PMC4906032 DOI: 10.1016/j.dib.2016.05.041] [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: 03/14/2016] [Revised: 05/11/2016] [Accepted: 05/19/2016] [Indexed: 11/23/2022] Open
Abstract
The dataset includes data from the Solexa sequencing reported in our paper: “Identification and differential expression of microRNAs associated with fat deposition in the liver of Wistar rats with nonalcoholic fatty liver disease” [1]. The data collected include small RNAs and microRNAs in liver tissue from high glucose-induced NAFLD Wistar rats, using normal Wistar rats as their negative controls. 6 small RNA libraries were constructed and the expression profiles were compared between the two groups. Here we describe in detail how the data, deposited in the Gene Expression Omnibus (GEO) with the accession number GEO: GSE68411, was generated including the basic analysis.
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Smith A, Calley J, Mathur S, Qian HR, Wu H, Farmen M, Caiment F, Bushel PR, Li J, Fisher C, Kirby P, Koenig E, Hall DG, Watson DE. The Rat microRNA body atlas; Evaluation of the microRNA content of rat organs through deep sequencing and characterization of pancreas enriched miRNAs as biomarkers of pancreatic toxicity in the rat and dog. BMC Genomics 2016; 17:694. [PMID: 27576563 PMCID: PMC5006322 DOI: 10.1186/s12864-016-2956-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 07/20/2016] [Indexed: 02/06/2023] Open
Abstract
Background MicroRNAs (miRNA) are ~19–25 nucleotide long RNA molecules that fine tune gene expression through the inhibition of translation or degradation of the mRNA through incorporation into the RNA induced silencing complex (RISC). MicroRNAs are stable in the serum and plasma, are detectable in a wide variety of body fluids, are conserved across veterinary species and humans and are expressed in a tissue specific manner. They can be detected at low concentrations in circulation in animals and humans, generating interest in the utilization of miRNAs as serum and/or plasma based biomarkers of tissue injury. MicroRNA tissue profiling in rodents has been published, but sample an insufficient number of organs of toxicologic interest using microarray or qPCR technologies for miRNA detection. Here we impart an improved rat microRNA body atlas consisting of 21 and 23 tissues of toxicologic interest from male and female Sprague Dawley rats respectively, using Illumina miRNA sequencing. Several of the authors created a dog miRNA body atlas and we collaborated to test miRNAs conserved in rat and dog pancreas in caerulein toxicity studies utilizing both species. Results A rich data set is presented that more robustly defines the tissue specificity and enrichment profiles of previously published and undiscovered rat miRNAs. We generated 1,927 sequences that mapped to mature miRNAs in rat, mouse and human from miRBase and discovered an additional 1,162 rat miRNAs as compared to the current number of rat miRNAs in miRBase version 21. Tissue specific and enriched miRNAs were identified and a subset of these miRNAs were validated by qPCR for tissue specificity or enrichment. As an example of the power of this approach, we have conducted rat and dog pancreas toxicity studies and examined the levels of some tissue specific and enriched miRNAs conserved between rat and dog in the serum of each species. The studies demonstrate that conserved tissue specific/enriched miRs-216a-5p, 375-3p, 148a-3p, 216b-5p and 141-3p are candidate biomarkers of pancreatic injury in the rat and dog. Conclusions A microRNA body atlas for rat and dog was useful in identifying new candidate miRNA biomarkers of organ toxicity in 2 toxicologically relevant species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2956-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aaron Smith
- Department of Investigative Toxicology, Non Clinical Safety Assessment and Pathology, Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, 46285, IN, USA.
| | - John Calley
- Department of TTX Bioinformatics, Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, 46285, IN, USA
| | - Sachin Mathur
- Department of TTX Bioinformatics, Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, 46285, IN, USA
| | - Hui-Rong Qian
- Department of Discovery and Development Statistics, Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, 46285, IN, USA
| | - Han Wu
- Department of Discovery and Development Statistics, Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, 46285, IN, USA
| | - Mark Farmen
- Department of Discovery and Development Statistics, Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, 46285, IN, USA
| | - Florian Caiment
- Department of Toxicogenomics, Maastricht University, Universiteitsingel, Maastricht, The Netherlands
| | - Pierre R Bushel
- National Institute of Environmental Health Sciences, Biostatistics Branch, Durham, NC, USA
| | - Jianying Li
- Kelly Government Solutions, Research Triangle Park, Durham, NC, 27709, USA
| | - Craig Fisher
- Drug Safety Evaluation, Takeda Pharmaceuticals International Company, Deerfield, USA
| | - Patrick Kirby
- Drug Safety Evaluation, Takeda Pharmaceuticals International Company, Deerfield, USA
| | - Erik Koenig
- Molecular Pathology, Takeda Pharmaceuticals International Company, Deerfield, USA
| | - David G Hall
- Department of Investigative Pathology, Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, 46285, IN, USA
| | - David E Watson
- Department of Investigative Toxicology, Non Clinical Safety Assessment and Pathology, Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, 46285, IN, USA
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Gao F, Nan F, Feng J, Lv J, Liu Q, Xie S. Identification of conserved and novel microRNAs in Porphyridium purpureum via deep sequencing and bioinformatics. BMC Genomics 2016; 17:612. [PMID: 27516065 PMCID: PMC4981961 DOI: 10.1186/s12864-016-2985-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/01/2016] [Indexed: 11/22/2022] Open
Abstract
Background Porphyridium purpureum has been utilized in important industrial and pharmaceutical fields. The identification of microRNAs (miRNAs) in this unique species is of great importance: such identification can help fill gaps in the small RNA (sRNA) studies of this organism and help to elucidate essential biological processes and their regulation mechanisms in this special micro alga. Results In this study, 254 high-confidence miRNAs (203 conserved miRNAs and 51 novel miRNAs) were identified by sRNA deep sequencing (sRNA-seq) combined with bioinformatics. A total of 235 putative miRNA families were predicted, including 192 conserved families and 43 species-specific families. The conservation and diversity of predicted miRNA families were analysed in different plant species. Both the 100 % northern blot validation rate (VR) of four randomly selected miRNAs and the results of stem-loop quantitative real time RT-PCR (qRT-PCR) assays of 25 randomly selected miRNAs demonstrated that the majority of the miRNAs identified in this study are credible. A total of 14,958 and 2184 genes were predicted to be targeted by the 186 conserved and 41 novel miRNAs. Gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that some target genes likely provide valuable references for further understanding of vital functions in P. purpureum. In addition, a cytoscape network will provide some clues for research into the complex biological processes that occur in this unique alga. Conclusions We first identified a large set of conserved and novel miRNAs in P. purpureum. The characteristic and validation analysis on miRNAs demonstrated authenticity of identification data. Functional annotation of target genes and metabolic pathways they involved in illuminated the direction for further utilization and development this micro alga based on its unique properties. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2985-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fan Gao
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Fangru Nan
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Jia Feng
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Junping Lv
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Qi Liu
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Shulian Xie
- School of Life Science, Shanxi University, Taiyuan, 030006, China.
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Ziemann M, Kaspi A, El-Osta A. Evaluation of microRNA alignment techniques. RNA (NEW YORK, N.Y.) 2016; 22:1120-38. [PMID: 27284164 PMCID: PMC4931105 DOI: 10.1261/rna.055509.115] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 05/04/2016] [Indexed: 05/26/2023]
Abstract
Genomic alignment of small RNA (smRNA) sequences such as microRNAs poses considerable challenges due to their short length (∼21 nucleotides [nt]) as well as the large size and complexity of plant and animal genomes. While several tools have been developed for high-throughput mapping of longer mRNA-seq reads (>30 nt), there are few that are specifically designed for mapping of smRNA reads including microRNAs. The accuracy of these mappers has not been systematically determined in the case of smRNA-seq. In addition, it is unknown whether these aligners accurately map smRNA reads containing sequence errors and polymorphisms. By using simulated read sets, we determine the alignment sensitivity and accuracy of 16 short-read mappers and quantify their robustness to mismatches, indels, and nontemplated nucleotide additions. These were explored in the context of a plant genome (Oryza sativa, ∼500 Mbp) and a mammalian genome (Homo sapiens, ∼3.1 Gbp). Analysis of simulated and real smRNA-seq data demonstrates that mapper selection impacts differential expression results and interpretation. These results will inform on best practice for smRNA mapping and enable more accurate smRNA detection and quantification of expression and RNA editing.
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Affiliation(s)
- Mark Ziemann
- Epigenetics in Human Health and Disease Laboratory, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, AustraliaEpigenomics Profiling Facility, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia
| | - Antony Kaspi
- Epigenetics in Human Health and Disease Laboratory, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, AustraliaEpigenomics Profiling Facility, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, AustraliaEpigenomics Profiling Facility, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia
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Lin R, He L, He J, Qin P, Wang Y, Deng Q, Yang X, Li S, Wang S, Wang W, Liu H, Li P, Zheng A. Comprehensive analysis of microRNA-Seq and target mRNAs of rice sheath blight pathogen provides new insights into pathogenic regulatory mechanisms. DNA Res 2016; 23:415-425. [PMID: 27374612 PMCID: PMC5066168 DOI: 10.1093/dnares/dsw024] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/12/2016] [Indexed: 02/03/2023] Open
Abstract
MicroRNAs (miRNAs) are ∼22 nucleotide non-coding RNAs that regulate gene expression by targeting mRNAs for degradation or inhibiting protein translation. To investigate whether miRNAs regulate the pathogenesis in necrotrophic fungus Rhizoctonia solani AG1 IA, which causes significant yield loss in main economically important crops, and to determine the regulatory mechanism occurring during pathogenesis, we constructed hyphal small RNA libraries from six different infection periods of the rice leaf. Through sequencing and analysis, 177 miRNA-like small RNAs (milRNAs) were identified, including 15 candidate pathogenic novel milRNAs predicted by functional annotations of their target mRNAs and expression patterns of milRNAs and mRNAs during infection. Reverse transcription-quantitative polymerase chain reaction results for randomly selected milRNAs demonstrated that our novel comprehensive predictions had a high level of accuracy. In our predicted pathogenic protein-protein interaction network of R. solani, we added the related regulatory milRNAs of these core coding genes into the network, and could understand the relationships among these regulatory factors more clearly at the systems level. Furthermore, the putative pathogenic Rhi-milR-16, which negatively regulates target gene expression, was experimentally validated to have regulatory functions by a dual-luciferase reporter assay. Additionally, 23 candidate rice miRNAs that may involve in plant immunity against R. solani were discovered. This first study on novel pathogenic milRNAs of R. solani AG1 IA and the recognition of target genes involved in pathogenicity, as well as rice miRNAs, participated in defence against R. solani could provide new insights into revealing the pathogenic mechanisms of the severe rice sheath blight disease.
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Affiliation(s)
- Runmao Lin
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Liye He
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Jiayu He
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Peigang Qin
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Yanran Wang
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Qiming Deng
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China.,Key Laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu 611130, China.,Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya'an 625014, China
| | - Xiaoting Yang
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Shuangcheng Li
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China.,Key Laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu 611130, China
| | - Shiquan Wang
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China.,Key Laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu 611130, China
| | - Wenming Wang
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China.,Key Laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu 611130, China
| | - Huainian Liu
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Ping Li
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China.,Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya'an 625014, China
| | - Aiping Zheng
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China.,Key Laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu 611130, China
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