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Enriquez-Felix EE, Pérez-Salazar C, Rico-Ruiz JG, Calheiros de Carvalho A, Cruz-Morales P, Villalobos-Escobedo JM, Herrera-Estrella A. Argonaute and Dicer are essential for communication between Trichoderma atroviride and fungal hosts during mycoparasitism. Microbiol Spectr 2024; 12:e0316523. [PMID: 38441469 PMCID: PMC10986496 DOI: 10.1128/spectrum.03165-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 02/17/2024] [Indexed: 04/06/2024] Open
Abstract
Trichoderma species are known for their mycoparasitic activity against phytopathogenic fungi that cause significant economic losses in agriculture. During mycoparasitism, Trichoderma spp. recognize molecules produced by the host fungus and release secondary metabolites and hydrolytic enzymes to kill and degrade the host's cell wall. Here, we explored the participation of the Trichoderma atroviride RNAi machinery in the interaction with six phytopathogenic fungi of economic importance. We determined that both Argonaute-3 and Dicer-2 play an essential role during mycoparasitism. Using an RNA-Seq approach, we identified that perception, detox, and cell wall degradation depend on the T. atroviride-RNAi when interacting with Alternaria alternata, Rhizoctonia solani AG2, and R. solani AG5. Furthermore, we constructed a gene co-expression network that provides evidence of two gene modules regulated by RNAi, which play crucial roles in essential processes during mycoparasitism. In addition, based on small RNA-seq, we conclude that siRNAs regulate amino acid and carbon metabolism and communication during the Trichoderma-host interaction. Interestingly, our data suggest that siRNAs might regulate allorecognition (het) and transport genes in a cross-species manner. Thus, these results reveal a fine-tuned regulation in T. atroviride dependent on siRNAs that is essential during the biocontrol of phytopathogenic fungi, showing a greater complexity of this process than previously established.IMPORTANCEThere is an increasing need for plant disease control without chemical pesticides to avoid environmental pollution and resistance, and the health risks associated with the application of pesticides are increasing. Employing Trichoderma species in agriculture to control fungal diseases is an alternative plant protection strategy that overcomes these issues without utilizing chemical fungicides. Therefore, understanding the biocontrol mechanisms used by Trichoderma species to antagonize other fungi is critical. Although there has been extensive research about the mechanisms involved in the mycoparasitic capability of Trichoderma species, there are still unsolved questions related to how Trichoderma regulates recognition, attack, and defense mechanisms during interaction with a fungal host. In this work, we report that the Argonaute and Dicer components of the RNAi machinery and the small RNAs they process are essential for gene regulation during mycoparasitism by Trichoderma atroviride.
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Affiliation(s)
- Eli Efrain Enriquez-Felix
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
| | - Camilo Pérez-Salazar
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
| | - José Guillermo Rico-Ruiz
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
| | | | - Pablo Cruz-Morales
- Novo Nordisk Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- The LatAmBio Initiative, Irapuato, Guanajuato, Mexico
| | - José Manuel Villalobos-Escobedo
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
- The LatAmBio Initiative, Irapuato, Guanajuato, Mexico
- Plant and Microbial Biology Department, University of California, Berkeley, Carlifornia, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, Carlifornia, USA
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
- The LatAmBio Initiative, Irapuato, Guanajuato, Mexico
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Yang X, Yan S, Li Y, Li G, Sun S, Li J, Cui Z, Huo J, Sun Y, Wang X, Liu F. Comparison of Transcriptome between Tolerant and Susceptible Rice Cultivar Reveals Positive and Negative Regulators of Response to Rhizoctonia solani in Rice. Int J Mol Sci 2023; 24:14310. [PMID: 37762614 PMCID: PMC10532033 DOI: 10.3390/ijms241814310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Rice (Oryza sativa L.) is one of the world's most crucial food crops, as it currently supports more than half of the world's population. However, the presence of sheath blight (SB) caused by Rhizoctonia solani has become a significant issue for rice agriculture. This disease is responsible for causing severe yield losses each year and is a threat to global food security. The breeding of SB-resistant rice varieties requires a thorough understanding of the molecular mechanisms involved and the exploration of immune genes in rice. To this end, we conducted a screening of rice cultivars for resistance to SB and compared the transcriptome based on RNA-seq between the most tolerant and susceptible cultivars. Our study revealed significant transcriptomic differences between the tolerant cultivar ZhengDao 22 (ZD) and the most susceptible cultivar XinZhi No.1 (XZ) in response to R. solani invasion. Specifically, the tolerant cultivar showed 7066 differentially expressed genes (DEGs), while the susceptible cultivar showed only 60 DEGs. In further analysis, we observed clear differences in gene category between up- and down-regulated expression of genes (uDEGs and dDEGs) based on Gene Ontology (GO) classes in response to infection in the tolerant cultivar ZD, and then identified uDEGs related to cell surface pattern recognition receptors, the Ca2+ ion signaling pathway, and the Mitogen-Activated Protein Kinase (MAPK) cascade that play a positive role against R. solani. In addition, DEGs of the jasmonic acid and ethylene signaling pathways were mainly positively regulated, whereas DEGs of the auxin signaling pathway were mainly negatively regulated. Transcription factors were involved in the immune response as either positive or negative regulators of the response to this pathogen. Furthermore, our results showed that chloroplasts play a crucial role and that reduced photosynthetic capacity is a critical feature of this response. The results of this research have important implications for better characterization of the molecular mechanism of SB resistance and for the development of resistant cultivars through molecular breeding methods.
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Affiliation(s)
- Xiurong Yang
- Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Shuangyong Yan
- Institute of Crop Research, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Yuejiao Li
- Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Guangsheng Li
- Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Shuqin Sun
- Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Junling Li
- Institute of Crop Research, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Zhongqiu Cui
- Institute of Crop Research, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Jianfei Huo
- Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Yue Sun
- Institute of Crop Research, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Xiaojing Wang
- Institute of Crop Research, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Fangzhou Liu
- Institute of Crop Research, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
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Xue J, Zhang H, Zhao Q, Cui S, Yu K, Sun R, Yu Y. Construction of Yeast One-Hybrid Library of Alternaria oxytropis and Screening of Transcription Factors Regulating swnK Gene Expression. J Fungi (Basel) 2023; 9:822. [PMID: 37623593 PMCID: PMC10455089 DOI: 10.3390/jof9080822] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
The indolizidine alkaloid-swainsonine (SW) is the main toxic component of locoweeds and the main cause of locoweed poisoning in grazing animals. The endophytic fungi, Alternaria Section Undifilum spp., are responsible for the biosynthesis of SW in locoweeds. The swnK gene is a multifunctional complex enzyme encoding gene in fungal SW biosynthesis, and its encoding product plays a key role in the multistep catalytic synthesis of SW by fungi using pipecolic acid as a precursor. However, the transcriptional regulation mechanism of the swnK gene is still unclear. To identify the transcriptional regulators involved in the swnK gene in endophytic fungi of locoweeds, we first analyzed the upstream non-coding region of the swnK gene in the A. oxytropis UA003 strain and predicted its high transcriptional activity region combined with dual-luciferase reporter assay. Then, a yeast one-hybrid library of A. oxytropis UA003 strain was constructed, and the transcriptional regulatory factors that may bind to the high-transcriptional activity region of the upstream non-coding region of the swnK gene were screened by this system. The results showed that the high transcriptional activity region was located at -656 bp and -392 bp of the upstream regulatory region of the swnK gene. A total of nine candidate transcriptional regulator molecules, including a C2H2 type transcription factor, seven annotated proteins, and an unannotated protein, were screened out through the Y1H system, which were bound to the upstream high transcriptional activity region of the swnK gene. This study provides new insight into the transcriptional regulation of the swnK gene and lays the foundation for further exploration of the regulatory mechanisms of SW biosynthesis in fungal endophytic locoweeds.
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Affiliation(s)
- Jiaqi Xue
- School of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Haodong Zhang
- School of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Qingmei Zhao
- College of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China
| | - Shengwei Cui
- School of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Kun Yu
- School of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Ruohan Sun
- School of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Yongtao Yu
- School of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
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Feng Q, Wang H, Yang X, Hu Z, Zhou X, Xiang L, Xiong X, He X, Zhu Y, Li G, Zhao J, Ji Y, Hu X, Pu M, Zhou S, Zhao Z, Zhang J, Huang Y, Fan J, Wang W, Li Y. Osa-miR160a confers broad-spectrum resistance to fungal and bacterial pathogens in rice. THE NEW PHYTOLOGIST 2022; 236:2216-2232. [PMID: 36101507 PMCID: PMC9828417 DOI: 10.1111/nph.18491] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/27/2022] [Indexed: 06/15/2023]
Abstract
Rice production is threatened by multiple pathogens. Breeding cultivars with broad-spectrum disease resistance is necessary to maintain and improve crop production. Previously we found that overexpression of miR160a enhanced rice blast disease resistance. However, it is unclear whether miR160a also regulates resistance against other pathogens, and what the downstream signaling pathways are. Here, we demonstrate that miR160a positively regulates broad-spectrum resistance against the causative agents of blast, leaf blight and sheath blight in rice. Mutations of miR160a-targeted Auxin Response Factors result in different alteration of resistance conferred by miR160a. miR160a enhances disease resistance partially by suppressing ARF8, as mutation of ARF8 in MIM160 background partially restores the compromised resistance resulting from MIM160. ARF8 protein binds directly to the promoter and suppresses the expression of WRKY45, which acts as a positive regulator of rice immunity. Mutation of WRKY45 compromises the enhanced blast resistance and bacterial leaf blight resistance conferred by arf8 mutant. Overall, our results reveal that a microRNA coordinates rice broad-spectrum disease resistance by suppressing multiple target genes that play different roles in disease resistance, and uncover a new regulatory pathway mediated by the miR160a-ARF8 module. These findings provide new resources to potentially improve disease resistance for breeding in rice.
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Affiliation(s)
- Qin Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - He Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Xue‐Mei Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Zhang‐Wei Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Xin‐Hui Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Ling Xiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Xiao‐Yu Xiong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Xiao‐Rong He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Yong Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Guo‐Bang Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Jing‐Hao Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Yun‐Peng Ji
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Xiao‐Hong Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Mei Pu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Shi‐Xin Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Zhi‐Xue Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Ji‐Wei Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Yan‐Yan Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Jing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Wen‐Ming Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
| | - Yan Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengdu611130China
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5
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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; 11:6773084. [PMID: 36283679 PMCID: PMC9596168 DOI: 10.1093/gigascience/giac093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [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)
| | - 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
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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: 0] [Impact Index Per Article: 0] [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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7
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Yang X, Gu X, Ding J, Yao L, Gao X, Zhang M, Meng Q, Wei S, Fu J. Gene expression analysis of resistant and susceptible rice cultivars to sheath blight after inoculation with Rhizoctonia solani. BMC Genomics 2022; 23:278. [PMID: 35392815 PMCID: PMC8991730 DOI: 10.1186/s12864-022-08524-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 03/23/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rice sheath blight, caused by Rhizoctonia solani Kühn (teleomorph: Thanatephorus cucumeris), is one of the most severe diseases in rice (Oryza sativa L.) worldwide. Studies on resistance genes and resistance mechanisms of rice sheath blight have mainly focused on indica rice. Rice sheath blight is a growing threat to rice production with the increasing planting area of japonica rice in Northeast China, and it is therefore essential to explore the mechanism of sheath blight resistance in this rice subspecies. RESULTS In this study, RNA-seq technology was used to analyse the gene expression changes of leaf sheath at 12, 24, 36, 48, and 72 h after inoculation of the resistant cultivar 'Shennong 9819' and susceptible cultivar 'Koshihikari' with R. solani. In the early stage of R. solani infection of rice leaf sheaths, the number of differentially expressed genes (DEGs) in the inoculated leaf sheaths of resistant and susceptible cultivars showed different regularity. After inoculation, the number of DEGs in the resistant cultivar fluctuated, while the number of DEGs in the susceptible cultivar increased first and then decreased. In addition, the number of DEGs in the susceptible cultivar was always higher than that in the resistant cultivar. After inoculation with R. solani, the overall transcriptome changes corresponding to multiple biological processes, molecular functions, and cell components were observed in both resistant and susceptible cultivars. These included metabolic process, stimulus response, biological regulation, catalytic activity, binding and membrane, and they were differentially regulated. The phenylalanine metabolic pathway; tropane, piperidine, and pyridine alkaloid biosynthesis pathways; and plant hormone signal transduction were significantly enriched in the early stage of inoculation of the resistant cultivar Shennong 9819, but not in the susceptible cultivar Koshihikari. This indicates that the response of the resistant cultivar Shennong 9819 to pathogen stress was faster than that of the susceptible cultivar. The expression of plant defense response marker PR1b gene, transcription factor OsWRKY30 and OsPAL1 and OsPAL6 genes that induce plant resistance were upregulated in the resistant cultivar. These data suggest that in the early stage of rice infection by R. solani, there is a pathogen-induced defence system in resistant rice cultivars, involving the expression of PR genes, key transcription factors, PAL genes, and the enrichment of defence-related pathways. CONCLUSION The transcriptome data revealed the molecular and biochemical differences between resistant and susceptible cultivars of rice after inoculation with R. solani, indicating that resistant cultivars have an immune response mechanism in the early stage of pathogen infection. Disease resistance is related to the overexpression of PR genes, key transcriptome factors, and PAL genes, which are potential targets for crop improvement.
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Affiliation(s)
- Xiaohe Yang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110161, Liaoning, China.,Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007, Heilongjiang, China
| | - Xin Gu
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007, Heilongjiang, China
| | - Junjie Ding
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007, Heilongjiang, China
| | - Liangliang Yao
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007, Heilongjiang, China
| | - Xuedong Gao
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007, Heilongjiang, China
| | - Maoming Zhang
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007, Heilongjiang, China
| | - Qingying Meng
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007, Heilongjiang, China
| | - Songhong Wei
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110161, Liaoning, China.
| | - Junfan Fu
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110161, Liaoning, China.
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Xu M, Li G, Guo Y, Gao Y, Zhu L, Liu Z, Tian R, Gao C, Han P, Wang N, Guo F, Bao J, Jia C, Feng H, Huang L. A fungal microRNA-like RNA subverts host immunity and facilitates pathogen infection by silencing two host receptor-like kinase genes. THE NEW PHYTOLOGIST 2022; 233:2503-2519. [PMID: 34981514 DOI: 10.1111/nph.17945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Small RNAs (sRNAs) play important roles in various biological processes by silencing their corresponding target genes in most eukaryotes. However, cross-kingdom regulation mediated by fungal microRNA-like RNAs (milRNAs) in plant-pathogen interactions is still largely unknown. Using molecular, genetic, histological, and biochemical approaches, we found that the apple tree Valsa canker pathogen Valsa mali milRNA Vm-milR1 could suppress the host immunity by silencing two host receptor-like kinase genes, MdRLKT1 and MdRLKT2. Vm-milR1 was highly induced during V. mali infection. Deletion of Vm-milR1 precursor abolished the generation of Vm-milR1 and reduced the virulence of V. mali. Inoculation of Vm-milR1 deletion mutants induced the host defence responses, including reactive oxygen species (ROS) accumulation, callose deposition, and high expression of defence-related genes. Furthermore, Vm-milR1 was confirmed to be able to suppress the expression of MdRLKT1 and MdRLKT2 in a sequence-specific manner. Moreover, overexpression of either MdRLKT1 or MdRLKT2 enhanced apple resistance to V. mali by activating the host defence responses. Furthermore, knockdown of MdRLKT1 or MdRLKT2 compromised the host resistance to V. mali. Our study revealed that V. mali was equipped with Vm-milR1 as an sRNA effector to silence host receptor-like kinase genes, suppress the host defence responses, and facilitate pathogen infection.
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Affiliation(s)
- Ming Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Guangyao Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yan Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yuqi Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lihua Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhaoyang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Runze Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chen Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Pengliang Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ning Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Feiran Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jiyuan Bao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Conghui Jia
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hao Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Piombo E, Vetukuri RR, Broberg A, Kalyandurg PB, Kushwaha S, Funck Jensen D, Karlsson M, Dubey M. Role of Dicer-Dependent RNA Interference in Regulating Mycoparasitic Interactions. Microbiol Spectr 2021; 9:e0109921. [PMID: 34549988 PMCID: PMC8557909 DOI: 10.1128/spectrum.01099-21] [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: 07/29/2021] [Accepted: 08/11/2021] [Indexed: 12/17/2022] Open
Abstract
Dicer-like proteins (DCLs) play a vital role in RNA interference (RNAi), by cleaving RNA filament into small RNAs. Although DCL-mediated RNAi can regulate interspecific communication between pathogenic/mutualistic organisms and their hosts, its role in mycoparasitic interactions is yet to be investigated. In this study, we deleted dcl genes in the mycoparasitic fungus Clonostachys rosea and characterize the functions of DCL-dependent RNAi in mycoparasitism. Deletion of dcl2 resulted in a mutant with reduced secondary metabolite production, antagonism toward the plant-pathogenic fungus Botrytis cinerea, and reduced ability to control Fusarium foot rot disease on wheat, caused by Fusarium graminearum. Transcriptome sequencing of the in vitro interaction between the C. rosea Δdcl2 strain and B. cinerea or F. graminearum identified the downregulation of genes coding for transcription factors, membrane transporters, hydrolytic enzymes, and secondary metabolites biosynthesis enzymes putatively involved in antagonistic interactions, in comparison with the C. rosea wild-type interaction. A total of 61 putative novel microRNA-like RNAs (milRNAs) were identified in C. rosea, and 11 were downregulated in the Δdcl2 mutant. In addition to putative endogenous gene targets, these milRNAs were predicted to target B. cinerea and F. graminearum virulence factor genes, which showed an increased expression during interaction with the Δdcl2 mutant incapable of producing the targeting milRNAs. In summary, this study constitutes the first step in elucidating the role of RNAi in mycoparasitic interactions, with important implications for biological control of plant diseases, and poses the base for future studies focusing on the role of cross-species RNAi regulating mycoparasitic interactions. IMPORTANCE Small RNAs mediated RNA interference (RNAi) known to regulate several biological processes. Dicer-like endoribonucleases (DCLs) play a vital role in the RNAi pathway by generating sRNAs. In this study, we investigated a role of DCL-mediated RNAi in interference interactions between mycoparasitic fungus Clonostachys rosea and the two fungal pathogens Botrytis cinerea and Fusarium graminearum (here called mycohosts). We found that the dcl mutants were not able to produce 11 sRNAs predicted to finetune the regulatory network of genes known to be involved in production of hydrolytic enzymes, antifungal compounds, and membrane transporters needed for antagonistic action of C. rosea. We also found C. rosea sRNAs putatively targeting known virulence factors in the mycohosts, indicating RNAi-mediated cross-species communication. Our study expanded the understanding of underlying mechanisms of cross-species communication during interference interactions and poses a base for future works studying the role of DCL-based cross-species RNAi in fungal interactions.
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Affiliation(s)
- Edoardo Piombo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ramesh R. Vetukuri
- Department of Plant Breeding, Horticum, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Anders Broberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Pruthvi B. Kalyandurg
- Department of Plant Breeding, Horticum, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Sandeep Kushwaha
- Department of Plant Breeding, Horticum, Swedish University of Agricultural Sciences, Lomma, Sweden
- National Institute of Animal Biotechnology, Hyderabad, Telangana, India
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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10
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Prathi NB, Durga Rani CV, Balachandran SM, Prakasam V, Chandra Mohan Y, Nagalakshmi S, Srivastava SK, Sundaram RM, Mangrauthia SK. Genome-Wide Expression Profiling of Small RNAs in Indian Strain of Rhizoctonia solani AG1-1A Reveals Differential Regulation of milRNAs during Pathogenesis and Crosstalk of Gene Regulation. J Fungi (Basel) 2021; 7:jof7070561. [PMID: 34356939 PMCID: PMC8304579 DOI: 10.3390/jof7070561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/26/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022] Open
Abstract
Rhizoctonia solani AG1-1A is a necrotrophic fungus that causes sheath blight disease in rice. The reliable resistant source against this phytopathogenic fungus is not available in the gene pool of rice. Better understanding of pathogen genomics and gene regulatory networks are critical to devise alternate strategies for developing resistance against this noxious pathogen. In this study, miRNA-like RNAs (milRNAs) of an Indian strain of R. solani were identified by deep sequencing of small RNAs. We identified 128 known and 22 novel milRNAs from 20,963,123 sequence reads. These milRNAs showed 1725 target genes in the fungal genome which include genes associated with growth, development, pathogenesis and virulence of R. solani. Notably, these fungal milRNAs showed their target genes in host (rice) genome also which were later verified by qRT-PCR. The host target genes are associated with auxin metabolism, hypersensitive response, defense genes, and genes related to growth and development of rice. Osa-vacuolar-sorting receptor precursor: Rhi-milR-13, Osa-KANADI1:Rhi-milR-124, Osa-isoflavone reductase: Rhi-milR-135, Osa-nuclear transcription factor Y:Rhi-milR-131, Osa-NB-ARC domain containing protein: Rhi-milR-18, and Osa-OsFBX438: Rhi-milR-142 are notable potential regulons of host target genes: fungal milRNAs that need to be investigated for better understanding of the crosstalk of RNAi pathways between R. solani and rice. The detailed expression analysis of 17 milRNAs by qRT-PCR was analysed during infection at different time points of inoculation, at different growth stages of the host, in four different genotypes of the host, and also in four different strains of fungi which revealed differential regulation of milRNAs associated with pathogenesis and virulence. This study highlights several important findings on fungal milRNAs which need to be further studied and characterized to decipher the gene expression and regulation of this economically important phytopathogen.
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Affiliation(s)
- Naresh Babu Prathi
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad 500030, India; (N.B.P.); (C.V.D.R.); (Y.C.M.)
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research, Hyderabad 500030, India; (S.M.B.); (V.P.); (S.N.); (R.M.S.)
| | - Chagamreddy Venkata Durga Rani
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad 500030, India; (N.B.P.); (C.V.D.R.); (Y.C.M.)
| | - Sena Munuswamy Balachandran
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research, Hyderabad 500030, India; (S.M.B.); (V.P.); (S.N.); (R.M.S.)
| | - Vellaisamy Prakasam
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research, Hyderabad 500030, India; (S.M.B.); (V.P.); (S.N.); (R.M.S.)
| | - Yeshala Chandra Mohan
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad 500030, India; (N.B.P.); (C.V.D.R.); (Y.C.M.)
| | - Sanivarapu Nagalakshmi
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research, Hyderabad 500030, India; (S.M.B.); (V.P.); (S.N.); (R.M.S.)
| | - Sunil K. Srivastava
- Department of Microbiology, Swami Shraddhanand College, University of Delhi, Alipur, Delhi 110036, India;
| | - Raman Meenakshi Sundaram
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research, Hyderabad 500030, India; (S.M.B.); (V.P.); (S.N.); (R.M.S.)
| | - Satendra K. Mangrauthia
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research, Hyderabad 500030, India; (S.M.B.); (V.P.); (S.N.); (R.M.S.)
- Correspondence: or ; Tel.: +91-40-24591342
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11
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Su Z, Wang X, Xuan X, Sheng Z, Jia H, Emal N, Liu Z, Zheng T, Wang C, Fang J. Characterization and Action Mechanism Analysis of VvmiR156b/c/d-VvSPL9 Module Responding to Multiple-Hormone Signals in the Modulation of Grape Berry Color Formation. Foods 2021; 10:foods10040896. [PMID: 33921800 PMCID: PMC8073990 DOI: 10.3390/foods10040896] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/06/2021] [Accepted: 04/14/2021] [Indexed: 12/11/2022] Open
Abstract
In recent years, more and more reports have shown that the miR156-SPL module can participate in the regulation of anthocyanin synthesis in plants. However, little is known about how this module responds to hormonal signals manipulating this process in grapes. In this study, exogenous GA, ABA, MeJA, and NAA were used to treat the 'Wink' grape berries before color conversion, anthocyanin and other related quality physiological indexes (such as sugar, aroma) were determined, and spatio-temporal expression patterns of related genes were analyzed. The results showed that the expression levels of VvmiR156b/c/d showed a gradually rising trend with the ripening and color formation of grape berries, and the highest expression levels were detected at day 28 after treatment, while the expression level of VvSPL9 exhibited an opposite trend as a whole, which further verifies that VvmiR156b/c/d can negatively regulate VvSPL9. Besides, VvmiR156b/c/d was positively correlated with anthocyanin content and related genes levels, while the expression pattern of VvSPL9 showed a negative correlation. Analysis of promoter cis-elements and GUS staining showed that VvmiR156b/c/d contained a large number of hormone response cis-elements (ABA, GA, SA, MeJA, and NAA) and were involved in hormone regulation. Exogenous ABA and MeJA treatments significantly upregulated the expression levels of VvmiR156b/c/d and anthocyanin structural genes in the early stage of color conversion and made grape berries quickly colored. Interestingly, GA treatment downregulated the expression levels of VvmiR156b/c/d and anthocyanin structural genes in the early color-change period, but significantly upregulated in the middle color-change and ripening stages, therefore GA mainly modulated grape berry coloring in the middle- and late-ripening stages. Furthermore, NAA treatment downregulated the expression levels of VvmiR156b/c/d and anthocyanin structural genes and delayed the peak expression of genes. Meanwhile, to further recognize the potential functions of VvmiR156b/c/d, the mature tomato transient trangenetic system was utilized in this work. Results showed that transient overexpression of VvmiR156b/c/d in tomato promoted fruit coloring and overexpression of VvSPL9 inhibited fruit coloration. Finally, a regulatory network of the VvmiR156b/c/d-VvSPL9 module responsive to hormones modulating anthocyanin synthesis was developed. In conclusion, VvmiR156b/c/d-mediated VvSPL9 participated in the formation of grape color in response to multi-hormone signals.
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Affiliation(s)
- Ziwen Su
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.S.); (X.X.); (Z.S.); (H.J.); (N.E.); (Z.L.); (T.Z.); (J.F.)
- Institute of Pomology, Jiangsu Academy of Agricultural Science, Nanjing 210014, China;
| | - Xicheng Wang
- Institute of Pomology, Jiangsu Academy of Agricultural Science, Nanjing 210014, China;
| | - Xuxian Xuan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.S.); (X.X.); (Z.S.); (H.J.); (N.E.); (Z.L.); (T.Z.); (J.F.)
| | - Zilu Sheng
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.S.); (X.X.); (Z.S.); (H.J.); (N.E.); (Z.L.); (T.Z.); (J.F.)
| | - Haoran Jia
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.S.); (X.X.); (Z.S.); (H.J.); (N.E.); (Z.L.); (T.Z.); (J.F.)
| | - Naseri Emal
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.S.); (X.X.); (Z.S.); (H.J.); (N.E.); (Z.L.); (T.Z.); (J.F.)
| | - Zhongjie Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.S.); (X.X.); (Z.S.); (H.J.); (N.E.); (Z.L.); (T.Z.); (J.F.)
| | - Ting Zheng
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.S.); (X.X.); (Z.S.); (H.J.); (N.E.); (Z.L.); (T.Z.); (J.F.)
| | - Chen Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.S.); (X.X.); (Z.S.); (H.J.); (N.E.); (Z.L.); (T.Z.); (J.F.)
- Correspondence:
| | - Jinggui Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.S.); (X.X.); (Z.S.); (H.J.); (N.E.); (Z.L.); (T.Z.); (J.F.)
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12
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Meng H, Wang S, Yang W, Ding X, Li N, Chu Z, Li X. Identification of virulence associated milRNAs and their bidirectional targets in Rhizoctonia solani and maize during infection. BMC PLANT BIOLOGY 2021; 21:155. [PMID: 33771101 PMCID: PMC8004440 DOI: 10.1186/s12870-021-02930-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/10/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND Anastomosis group 1 IA (AG1-IA) of Rhizoctonia solani is the major agent of banded leaf and sheath blight (BLSB) disease that causes severe yield loss in many worldwide crops. MicroRNAs (miRNAs) are ~ 22 nt non-coding RNAs that negatively regulate gene expression levels by mRNA degradation or translation inhibition. A better understanding of miRNA function during AG1-IA infection can expedite to elucidate the molecular mechanisms of fungi-host interactions. RESULTS In this study, we sequenced three small RNA libraries obtained from the mycelium of AG1-IA isolate, non-infected maize sheath and mixed maize sheath 3 days after inoculation. In total, 137 conserved and 34 novel microRNA-like small RNAs (milRNAs) were identified from the pathogen. Among these, one novel and 17 conserved milRNAs were identified as potential virulence-associated (VA) milRNAs. Subsequently, the prediction of target genes for these milRNAs was performed in both AG1-IA and maize, while functional annotation of these targets suggested a link to pathogenesis-related biological processes. Further, expression patterns of these virulence-associated milRNAs demonstrated that theyparticipate in the virulence of AG1-IA. Finally, regulation of one maize targeting gene, GRMZM2G412674 for Rhi-milRNA-9829-5p, was validated by dual-luciferase assay and identified to play a positive role in BLSB resistance in two maize mutants. These results suggest the global differentially expressed milRNAs of R. solani AG1-IA that participate in the regulation of target genes in both AG1-IA and maize to reinforce its pathogenicity. CONCLUSIONS Our data have provided a comprehensive overview of the VA-milRNAs of R. solani and identified that they are probably the virulence factors by directly interfered in host targeting genes. These results offer new insights on the molecular mechanisms of R.solani-maize interactions during the process of infection.
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Affiliation(s)
- Hongxu Meng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Shaoli Wang
- Yantai Academy of Agricultural Sciences, Yan'tai, 265500, Shandong, People's Republic of China
| | - Wei Yang
- Key Laboratory of Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Xinhua Ding
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Ning Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Zhaohui Chu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China.
| | - Xiaoming Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China.
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13
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Di R, Liu QY, Song SH, Tian DM, He JN, Ge Y, Wang XY, Hu WP, Mwacharo JM, Pan ZY, Wang JD, Ma Q, Cao GL, Jin HH, Liang XJ, Chu MX. Expression characteristics of pineal miRNAs at ovine different reproductive stages and the identification of miRNAs targeting the AANAT gene. BMC Genomics 2021; 22:217. [PMID: 33765915 PMCID: PMC7992348 DOI: 10.1186/s12864-021-07536-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 03/15/2021] [Indexed: 11/30/2022] Open
Abstract
Background Many recent studies have shown that miRNAs play important roles in the regulation of animal reproduction, including seasonal reproduction. The pineal gland is a crucial hub in the regulation of seasonal reproduction. However, little is known about the expression characteristics of pineal miRNAs in different reproductive seasons (anestrus and breeding season). Therefore, the expression profiles and regulatory roles of ovine pineal miRNAs were investigated during different reproductive stages using Solexa sequencing technology and dual luciferase reporter assays. Results A total of 427 miRNAs were identified in the sheep pineal gland. Significant differences in miRNA expression were demonstrated between anestrus and the breeding season in terms of the frequency distributions of miRNA lengths, number of expressed miRNAs, and specifically and highly expressed miRNAs in each reproductive stage. KEGG analysis of the differentially expressed (DE) miRNAs between anestrus and the breeding season indicated that they are significantly enriched in pathways related to protein synthesis, secretion and uptake. Furthermore, transcriptome analysis revealed that many target genes of DE miRNAs in the ribosome pathway showed relatively low expression in the breeding season. On the other hand, analyses combining miRNA-gene expression data with target relationship validation in vitro implied that miR-89 may participate in the negative regulation of aralkylamine N-acetyltransferase (AANAT) mRNA expression by targeting its 3’UTR at a unique binding site. Conclusions Our results provide new insights into the expression characteristics of sheep pineal miRNAs at different reproductive stages and into the negative regulatory effects of pineal miRNAs on AANAT mRNA expression. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07536-y.
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Affiliation(s)
- Ran Di
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Qiu-Yue Liu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Shu-Hui Song
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China
| | - Dong-Mei Tian
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China
| | - Jian-Ning He
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Ying Ge
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Xiang-Yu Wang
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Wen-Ping Hu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Joram-Mwashigadi Mwacharo
- Small Ruminant Genomics, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Zhang-Yuan Pan
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Jian-Dong Wang
- Research Center of Grass and Livestock, NingXia Academy of Agricultural and Forestry Sciences, No. 590, East Yellow River Road, Yinchuan, 750002, China
| | - Qing Ma
- Research Center of Grass and Livestock, NingXia Academy of Agricultural and Forestry Sciences, No. 590, East Yellow River Road, Yinchuan, 750002, China
| | - Gui-Ling Cao
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Hui-Hui Jin
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Xiao-Jun Liang
- Research Center of Grass and Livestock, NingXia Academy of Agricultural and Forestry Sciences, No. 590, East Yellow River Road, Yinchuan, 750002, China.
| | - Ming-Xing Chu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China.
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Feng Q, Li Y, Zhao ZX, Wang WM. Contribution of Small RNA Pathway to Interactions of Rice with Pathogens and Insect Pests. RICE (NEW YORK, N.Y.) 2021; 14:15. [PMID: 33547972 PMCID: PMC7867673 DOI: 10.1186/s12284-021-00458-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 01/28/2021] [Indexed: 05/20/2023]
Abstract
Small RNAs (sRNAs) are mainly classified into microRNAs (miRNAs) and small interfering RNAs (siRNAs) according to their origin. miRNAs originate from single-stranded RNA precursors, whereas siRNAs originate from double-stranded RNA precursors that are synthesized by RNA-dependent RNA polymerases. Both of single-stranded and double-stranded RNA precursors are processed into sRNAs by Dicer-like proteins. Then, the sRNAs are loaded into ARGONAUTE proteins, forming RNA-induced silencing complexes (RISCs). The RISCs repress the expression of target genes with sequences complementary to the sRNAs through the cleavage of transcripts, the inhibition of translation or DNA methylation. Here, we summarize the recent progress of sRNA pathway in the interactions of rice with various parasitic organisms, including fungi, viruses, bacteria, as well as insects. Besides, we also discuss the hormone signal in sRNA pathway, and the emerging roles of circular RNAs and long non-coding RNAs in rice immunity. Obviously, small RNA pathway may act as a part of rice innate immunity to coordinate with growth and development.
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Affiliation(s)
- Qin Feng
- Rice Research Institute and Research Center for Crop Disease and Insect Pests, Sichuan Agricultural University at Wenjiang, 211 Huimin Road, Wenjiang District, Chengdu, 611130 China
| | - Yan Li
- Rice Research Institute and Research Center for Crop Disease and Insect Pests, Sichuan Agricultural University at Wenjiang, 211 Huimin Road, Wenjiang District, Chengdu, 611130 China
| | - Zhi-Xue Zhao
- Rice Research Institute and Research Center for Crop Disease and Insect Pests, Sichuan Agricultural University at Wenjiang, 211 Huimin Road, Wenjiang District, Chengdu, 611130 China
| | - Wen-Ming Wang
- Rice Research Institute and Research Center for Crop Disease and Insect Pests, Sichuan Agricultural University at Wenjiang, 211 Huimin Road, Wenjiang District, Chengdu, 611130 China
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Feng H, Xu M, Gao Y, Liang J, Guo F, Guo Y, Huang L. Vm-milR37 contributes to pathogenicity by regulating glutathione peroxidase gene VmGP in Valsa mali. MOLECULAR PLANT PATHOLOGY 2021; 22:243-254. [PMID: 33278058 PMCID: PMC7814965 DOI: 10.1111/mpp.13023] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/18/2020] [Accepted: 11/05/2020] [Indexed: 05/22/2023]
Abstract
MicroRNAs play important roles in various biological processes by regulating their corresponding target genes. However, the function and regulatory mechanism of fungal microRNA-like RNAs (milRNAs) are still largely unknown. In this study, a milRNA (Vm-milR37) was isolated and identified from Valsa mali, which causes the most serious disease on the trunk of apple trees in China. Based on the results of deep sequencing and quantitative reverse transcription PCR, Vm-milR37 was found to be expressed in the mycelium, while it was not expressed during the V. mali infection process. Overexpression of Vm-milR37 did not affect vegetative growth, but significantly decreased pathogenicity. Based on degradome sequencing, the target of Vm-milR37 was identified as VmGP, a glutathione peroxidase. The expression of Vm-milR37 and VmGP showed a divergent trend in V. mali-apple interaction samples and Vm-milR37 overexpression transformants. The expression of VmGP could be suppressed significantly by Vm-milR37 when coexpressed in tobacco leaves. Deletion of VmGP showed significantly reduced pathogenicity compared with the wild type. VmGP deletion mutants showed more sensitivity to hydrogen peroxide. Apple leaves inoculated with Vm-milR37 overexpression transformants and VmGP deletion mutant displayed increased accumulation of reactive oxygen species compared with the wild type. Thus, Vm-milR37 plays a critical role in pathogenicity by regulating VmGP, which contributes to the oxidative stress response during V. mali infection. These results provide important evidence to define the roles of milRNAs and their corresponding target genes in pathogenicity.
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Affiliation(s)
- Hao Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Ming Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life SciencesNorthwest A&F UniversityYanglingChina
| | - Yuqi Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Jiahao Liang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Feiran Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Yan Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
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16
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A Comprehensive Analysis of MicroRNAs Expressed in Susceptible and Resistant Rice Cultivars during Rhizoctonia solani AG1-IA Infection Causing Sheath Blight Disease. Int J Mol Sci 2020; 21:ijms21217974. [PMID: 33120987 PMCID: PMC7662745 DOI: 10.3390/ijms21217974] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/08/2020] [Accepted: 10/08/2020] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs regulate plant responses to fungal infections and immunity. In this study, miRNAs were identified in six rice cultivars during a Rhizoctonia solani Kühn AG1-IA infection using a deep sequencing approach. Known and novel miRNAs were analyzed in these rice cultivars, and a set of fungal infection/immunity-associated miRNAs and target genes were quantified by reverse transcription (RT)-qPCR in six rice cultivars. Additionally, the relative expression of these miRNAs was analyzed in different time points of the infection, wild species of rice, and in response to different strains of R. solani. Osa-miR1320-5p showed preferential expression during the fungal infection in all the six rice genotypes, while Osa-miR156d, Osa-miR159b, Osa-miR820c, and Osa-miR1876 were differentially regulated in susceptible and resistant genotypes. A greater degree of downregulation of miRNAs was observed during the initial time points of infection (24-72 h), suggesting a maximum molecular activity of rice-R. solani interaction and resistance response of the host during the early phase of infection. After R. solani infection, the expression of Osa-miR820c and Osa-miR156d was downregulated in Oryza rufipogon, O. alta, O. latifolia, and O. minuta, while Osa-miR397b was downregulated in all the wild rice species except O. officinalis. This study provided comprehensive information on the repertoire of miRNAs expressed in six sheath blight disease-susceptible and resistant indica and aus rice cultivars.
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17
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Xu M, Guo Y, Tian R, Gao C, Guo F, Voegele RT, Bao J, Li C, Jia C, Feng H, Huang L. Adaptive regulation of virulence genes by microRNA-like RNAs in Valsa mali. THE NEW PHYTOLOGIST 2020; 227:899-913. [PMID: 32222083 DOI: 10.1111/nph.16561] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/16/2020] [Indexed: 06/10/2023]
Abstract
MicroRNAs play important roles in the regulation of gene expression in plants and animals. However, little information is known about the action mechanism and function of fungal microRNA-like RNAs (milRNAs). In this study, combining deep sequencing, molecular and histological assays, milRNAs and their targets in the phytopathogenic fungus Valsa mali were isolated and identified. A critical milRNA, Vm-milR16, was identified to adaptively regulate the expression of virulence genes. Fourteen isolated milRNAs showed high expression abundance. Based on the assessment of a pathogenicity function of these milRNAs, Vm-milR16 was found to be a critical milRNA in V. mali by regulating sucrose non-fermenting 1 (VmSNF1), 4,5-DOPA dioxygenase extradiol (VmDODA), and a hypothetical protein (VmHy1). During V. mali infection, Vm-milR16 is downregulated, while its targets are upregulated. Overexpression of Vm-milR16, but not mutated Vm-milR16, significantly reduces the expression of targets and virulence of V. mali. Furthermore, deletion of VmSNF1, VmDODA and VmHy1 significantly reduce virulence of V. mali. All three targets seem to be essential for oxidative stress response and VmSNF1 is required for expression of pectinase genes during V. mali-host interaction. Our results demonstrate Vm-milRNAs contributing to the infection of V. mali on apple trees by adaptively regulating virulence genes.
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Affiliation(s)
- Ming Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yan Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Runze Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chen Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Feiran Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ralf T Voegele
- Department of Phytopathology, Institute of Phytomedicine, Faculty of Agricultural Sciences, University of Hohenheim, 70599, Stuttgart, Germany
| | - Jiyuan Bao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chenjing Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Conghui Jia
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hao Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
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18
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Molla KA, Karmakar S, Molla J, Bajaj P, Varshney RK, Datta SK, Datta K. Understanding sheath blight resistance in rice: the road behind and the road ahead. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:895-915. [PMID: 31811745 PMCID: PMC7061877 DOI: 10.1111/pbi.13312] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 11/15/2019] [Accepted: 11/22/2019] [Indexed: 05/03/2023]
Abstract
Rice sheath blight disease, caused by the basidiomycetous necrotroph Rhizoctonia solani, became one of the major threats to the rice cultivation worldwide, especially after the adoption of high-yielding varieties. The pathogen is challenging to manage because of its extensively broad host range and high genetic variability and also due to the inability to find any satisfactory level of natural resistance from the available rice germplasm. It is high time to find remedies to combat the pathogen for reducing rice yield losses and subsequently to minimize the threat to global food security. The development of genetic resistance is one of the alternative means to avoid the use of hazardous chemical fungicides. This review mainly focuses on the effort of better understanding the host-pathogen relationship, finding the gene loci/markers imparting resistance response and modifying the host genome through transgenic development. The latest development and trend in the R. solani-rice pathosystem research with gap analysis are provided.
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Affiliation(s)
- Kutubuddin A. Molla
- ICAR‐National Rice Research InstituteCuttackIndia
- Laboratory of Translational Research on Transgenic CropsDepartment of BotanyUniversity of CalcuttaKolkataIndia
- The Huck Institute of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPAUSA
- Department of Plant Pathology and Environmental MicrobiologyThe Pennsylvania State UniversityUniversity ParkPAUSA
| | - Subhasis Karmakar
- Laboratory of Translational Research on Transgenic CropsDepartment of BotanyUniversity of CalcuttaKolkataIndia
| | - Johiruddin Molla
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Prasad Bajaj
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Swapan K. Datta
- Laboratory of Translational Research on Transgenic CropsDepartment of BotanyUniversity of CalcuttaKolkataIndia
| | - Karabi Datta
- Laboratory of Translational Research on Transgenic CropsDepartment of BotanyUniversity of CalcuttaKolkataIndia
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19
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Xu X, Zhong C, Tan M, Song Y, Qi X, Xu Q, Chen X. Identification of MicroRNAs and Their Targets That Respond to Powdery Mildew Infection in Cucumber by Small RNA and Degradome Sequencing. Front Genet 2020; 11:246. [PMID: 32273882 PMCID: PMC7113371 DOI: 10.3389/fgene.2020.00246] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/02/2020] [Indexed: 01/04/2023] Open
Abstract
Powdery mildew (PM) is a prevalent disease known to limit cucumber production worldwide. MicroRNAs (miRNAs) are single-stranded molecules that regulate host defense responses through posttranscriptional gene regulation. However, which specific miRNAs are involved and how they regulate cucumber PM resistance remain elusive. A PM-resistant single-segment substitution line, SSSL508-28, was developed previously using marker-assisted backcrossing of the PM-susceptible cucumber inbred D8 line. In this study, we applied small RNA and degradome sequencing to identify PM-responsive miRNAs and their target genes in the D8 and SSSL508-28 lines. The deep sequencing resulted in the identification of 156 known and 147 novel miRNAs. Among them, 32 and six differentially expressed miRNAs (DEMs) were detected in D8 and SSSL508-28, respectively. The positive correlation between DEMs measured by small RNA sequencing and stem-loop quantitative real-time reverse transcription-polymerase chain reaction confirmed the accuracy of the observed miRNA abundances. The 32 DEMs identified in the PM-susceptible D8 were all upregulated, whereas four of the six DEMs identified in the PM-resistant SSSL508-28 were downregulated. Using in silico and degradome sequencing approaches, 517 and 20 target genes were predicted for the D8 and SSSL508-28 DEMs, respectively. Comparison of the DEM expression profiles with the corresponding mRNA expression profiles obtained in a previous study with the same experimental design identified 60 and three target genes in D8 and SSSL508-28, respectively, which exhibited inverse expression patterns with their respective miRNAs. In particular, five DEMs were located in the substituted segment that contained two upregulated DEMs, Csa-miR172c-3p and Csa-miR395a-3p, in D8 and two downregulated DEMs, Csa-miR395d-3p and Csa-miR398b-3p, in SSSL508-28. One gene encoding L-aspartate oxidase, which was targeted by Csa-miR162a, was also located on the same segment and was specifically downregulated in PM-inoculated D8 leaves. Our results will facilitate the future use of miRNAs in breeding cucumber varieties with enhanced resistance to PM.
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Affiliation(s)
- Xuewen Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Cailian Zhong
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Min Tan
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Ya Song
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Xiaohua Qi
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Qiang Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Xuehao Chen
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, China
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin, China
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20
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Shao J, Wang L, Liu Y, Qi Q, Wang B, Lu S, Liu C. Identification of milRNAs and their target genes in Ganoderma lucidum by high-throughput sequencing and degradome analysis. Fungal Genet Biol 2020; 136:103313. [DOI: 10.1016/j.fgb.2019.103313] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 08/09/2019] [Accepted: 11/15/2019] [Indexed: 12/15/2022]
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21
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Characteristic Dissection of Xanthomonas oryzae pv. o ryzae Responsive MicroRNAs in Rice. Int J Mol Sci 2020; 21:ijms21030785. [PMID: 31991765 PMCID: PMC7037501 DOI: 10.3390/ijms21030785] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 01/19/2020] [Accepted: 01/23/2020] [Indexed: 12/03/2022] Open
Abstract
MicroRNAs (miRNAs) are crucial player in plant-pathogen interaction. While the evidence has demonstrated that rice miRNAs mediate immune response to pathogens invasion, the roles of miRNAs on Xanthomonas oryzae pv. oryzae (Xoo) attack remain be in place. Herein, we monitored the responsive changes of rice miRNAs at 0, 8, 24 h across Xoo strain PXO86 infection in its compatible rice variety IR24 and incompatible variety IRBB5 by small RNA sequencing, and the genes targeted by miRNAs were also detected via degradome technology. The faithfulness of sequencing data was validated through quantitative real-time stem-loop reverse transcription-polymerase chain reaction assay. Bioinformatic analysis showed that the differentially expressed miRNAs could be divided into three immunity-related clusters, and 80 regulatory units were emerged in infection process, which comprises 29 differentially expressed known miRNAs and 38 cleaved targets. Furthermore, the miRNA presumptive function of separate immunity cluster in rice-Xoo interplay was confirmed through overexpressing osa-miR164a, osa-miR167d and osa-miR159b, and the disruption of regulatory units, osa-miR164a/OsNAC60, osa-miR167d-5p/OsWD40-174 and osa-miR159b/OsMYBGA, OsLRR-RLK2, OsMPK20-4, may reset rice defense response to Xoo infestation in a controllable manner. These findings provide new insights into the complex roles of characteristic miRNAs and their targets in rice-Xoo interactions.
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22
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Gabriel AF, Costa MC, Enguita FJ, Leitão AL. Si vis pacem para bellum: A prospective in silico analysis of miRNA-based plant defenses against fungal infections. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 288:110241. [PMID: 31521215 DOI: 10.1016/j.plantsci.2019.110241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/31/2019] [Accepted: 08/25/2019] [Indexed: 06/10/2023]
Abstract
Fungal pathogens are an important threat for plant crops, being responsible for important reductions of production yields and a consequent economic impact. Among the molecular mediators of fungal infections of plant crops, non-coding RNAs (ncRNAs) have been described as relevant players either in the plant immune responses and mechanism of defense or in the colonization of plant tissues by fungi. Acting as a mechanism of defense, some plant small ncRNAs such as miRNAs and tasiRNAs can be secreted by cells and directed to target the transcriptome of pathogenic fungi, triggering an RNAi-like interference mechanism able to silence the expression of specific fungal genes. The detailed knowledge of this mechanism of defense against fungal pathogens could open new possibilities for the protection of human important crops. To infer putative functional relationships mediated by ncRNA communication, we performed a prospective analysis to determine potential plant miRNAs able to target the genome of fungal pathogens, which resulted in the description of enriched specific plant miRNA families and their putative fungal targets that could be further studied in the context of plant-fungi interactions. The expression profile of specific members of the enriched miRNAs families showed an infection-dependent behavior in laboratory models of infection. Plant miRNAs showed sequence complementarity with coding genes of their cognate fungal pathogens. Plant miRNAs could potentially target fungal genes belonging to functional families related to stress response, membrane architecture, vacuolar transport, membrane traffic, and anabolic processes. Families of specific infection-responsive miRNAs are included in the putative plant defense mechanism.
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Affiliation(s)
- André F Gabriel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal
| | - Marina C Costa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal.
| | - Ana Lúcia Leitão
- Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal; MEtRICs, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, Caparica, 2829-516, Portugal.
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23
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Fang H, Jiang W, Jing Z, Mu X, Xiong Z. miR-937 regulates the proliferation and apoptosis via targeting APAF1 in breast cancer. Onco Targets Ther 2019; 12:5687-5699. [PMID: 31410016 PMCID: PMC6645689 DOI: 10.2147/ott.s207091] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/31/2019] [Indexed: 01/13/2023] Open
Abstract
Background: Previous research had shown that an imbalance in cell proliferation and apoptosis is a vital mechanism for tumorigenesis and cancer progression that may directly influence biological behaviors of cancer. microRNAs are associated with the occurrence and development of tumors. This study aimed to explore the influence of miR-937 on breast cancer regulation of APAF1 expression. Methods: Cancer Genome Altas microarray analysis (fold change > 2, p<0.05) was used to verify differentially expressed microRNAs and RT-qPCR was used to detect miR-937 mRNA level in breast cancer. Cell viability and proliferation were measured using CCK8 and colony formation assays, respectively, after the miR-937 mimics/inhibitors and their negative control were transfected into MCF7 cells. The variations in cell cycle and apoptosis were examined using flow cytometry. DAVID database was used to perform GO enrichment analysis. We use dual luciferase report system to detect the effect of miR-937 on the transcriptional activity of APAF1. APAF1 protein level was determined by Western blot assay. Results: miR-937 was up-regulated in breast cancer cell lines and high miR-937 expression is associated with a poorer survival rate in cancer patients. miR-937 overexpression promoted the viability, down-regulated the G1 phase ratios and increased the ability of colony formation in breast cancer cells. miR-937 inhibition inhibited the viability and the ability of colony formation, promoted the apoptosis and up-regulated the G1 phase ratios. Our results showed that miR-937 targeted bind to the APAF1-3'UTR. APAF1 overexpression inhibited the viability and the ability of colony formation, promoted the apoptosis and up-regulated the G1 phase ratios. After cells were co-transfection miR-937 mimics and APAF1, cell apoptosis level was increased. Conclusion: APAF1 up-regulation or APAF1 down-regulation in breast cancer may regulate cell proliferation and apoptosis.
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Affiliation(s)
- Huiying Fang
- Department of Breast Disease, Chongqing University Cancer Hospital, Chongqing City, 400000, People's Republic of China
| | - Wei Jiang
- Department of Breast Disease, Chongqing University Cancer Hospital, Chongqing City, 400000, People's Republic of China
| | - Zhouhong Jing
- Department of Breast Disease, Chongqing University Cancer Hospital, Chongqing City, 400000, People's Republic of China
| | - Xiaosong Mu
- Department of Breast Disease, Chongqing University Cancer Hospital, Chongqing City, 400000, People's Republic of China
| | - Zhongxun Xiong
- Department of Breast Disease, Chongqing University Cancer Hospital, Chongqing City, 400000, People's Republic of China
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24
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Hu W, Luo H, Yang Y, Wang Q, Hong N, Wang G, Wang A, Wang L. Comprehensive analysis of full genome sequence and Bd-milRNA/target mRNAs to discover the mechanism of hypovirulence in Botryosphaeria dothidea strains on pear infection with BdCV1 and BdPV1. IMA Fungus 2019; 10:3. [PMID: 32647612 PMCID: PMC7325678 DOI: 10.1186/s43008-019-0008-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 05/06/2019] [Indexed: 11/23/2022] Open
Abstract
Pear ring rot disease, mainly caused by Botryosphaeria dothidea, is widespread in most pear and apple-growing regions. Mycoviruses are used for biocontrol, especially in fruit tree disease. BdCV1 (Botryosphaeria dothidea chrysovirus 1) and BdPV1 (Botryosphaeria dothidea partitivirus 1) influence the biological characteristics of B. dothidea strains. BdCV1 is a potential candidate for the control of fungal disease. Therefore, it is vital to explore interactions between B. dothidea and mycovirus to clarify the pathogenic mechanisms of B. dothidea and hypovirulence of B. dothidea in pear. A high-quality full-length genome sequence of the B. dothidea LW-Hubei isolate was obtained using Single Molecule Real-Time sequencing. It has high repeat sequence with 9.3% and DNA methylation existence in the genome. The 46.34 Mb genomes contained 14,091 predicted genes, which of 13,135 were annotated. B. dothidea was predicted to express 3833 secreted proteins. In bioinformatics analysis, 351 CAZy members, 552 transporters, 128 kinases, and 1096 proteins associated with plant-host interaction (PHI) were identified. RNA-silencing components including two endoribonuclease Dicer, four argonaute (Ago) and three RNA-dependent RNA polymerase (RdRp) molecules were identified and expressed in response to mycovirus infection. Horizontal transfer of the LW-C and LW-P strains indicated that BdCV1 induced host gene silencing in LW-C to suppress BdPV1 transmission. To investigate the role of RNA-silencing in B. dothidea defense, we constructed four small RNA libraries and sequenced B. dothidea micro-like RNAs (Bd-milRNAs) produced in response to BdCV1 and BdPV1 infection. Among these, 167 conserved and 68 candidate novel Bd-milRNAs were identified, of which 161 conserved and 20 novel Bd-milRNA were differentially expressed. WEGO analysis revealed involvement of the differentially expressed Bd-milRNA-targeted genes in metabolic process, catalytic activity, cell process and response to stress or stimulus. BdCV1 had a greater effect on the phenotype, virulence, conidiomata, vertical and horizontal transmission ability, and mycelia cellular structure biological characteristics of B. dothidea strains than BdPV1 and virus-free strains. The results obtained in this study indicate that mycovirus regulates biological processes in B. dothidea through the combined interaction of antiviral defense mediated by RNA-silencing and milRNA-mediated regulation of target gene mRNA expression.
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Affiliation(s)
- Wangcheng Hu
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People's Republic of China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People's Republic of China.,Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People's Republic of China
| | - Hui Luo
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People's Republic of China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People's Republic of China.,Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People's Republic of China
| | - Yuekun Yang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People's Republic of China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People's Republic of China.,Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People's Republic of China
| | - Qiong Wang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People's Republic of China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People's Republic of China.,Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People's Republic of China
| | - Ni Hong
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People's Republic of China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People's Republic of China.,Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People's Republic of China
| | - Guoping Wang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People's Republic of China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People's Republic of China.,Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People's Republic of China
| | - Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3 Canada
| | - Liping Wang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People's Republic of China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People's Republic of China.,Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People's Republic of China
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25
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Li W, Jia Y, Liu F, Wang F, Fan F, Wang J, Zhu J, Xu Y, Zhong W, Yang J. Integration Analysis of Small RNA and Degradome Sequencing Reveals MicroRNAs Responsive to Dickeya zeae in Resistant Rice. Int J Mol Sci 2019; 20:E222. [PMID: 30626113 PMCID: PMC6337123 DOI: 10.3390/ijms20010222] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/26/2018] [Accepted: 12/31/2018] [Indexed: 12/20/2022] Open
Abstract
Rice foot rot disease caused by the pathogen Dickeya zeae (formerly known as Erwinia chrysanthemi pv. zeae), is a newly emerging damaging bacterial disease in China and the southeast of Asia, resulting in the loss of yield and grain quality. However, the genetic resistance mechanisms mediated by miRNAs to D. zeae are unclear in rice. In the present study, 652 miRNAs including osa-miR396f predicted to be involved in multiple defense responses to D. zeae were identified with RNA sequencing. A total of 79 differentially expressed miRNAs were detected under the criterion of normalized reads ≥10, including 51 known and 28 novel miRNAs. Degradome sequencing identified 799 targets predicted to be cleaved by 168 identified miRNAs. Among them, 29 differentially expressed miRNA and target pairs including miRNA396f-OsGRFs were identified by co-expression analysis. Overexpression of the osa-miR396f precursor in a susceptible rice variety showed enhanced resistance to D. zeae, coupled with significant accumulation of transcripts of osa-miR396f and reduction of its target the Growth-Regulating Factors (OsGRFs). Taken together, these findings suggest that miRNA and targets including miR396f-OsGRFs have a role in resisting the infections by bacteria D. zeae.
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Affiliation(s)
- Wenqi Li
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Yulin Jia
- United States Department of Agriculture-Agriculture Research Service, Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, USA.
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
| | - Fangquan Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Fangjun Fan
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Jun Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Jinyan Zhu
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Yang Xu
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Weigong Zhong
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Jie Yang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
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Lee Marzano SY, Neupane A, Domier L. Transcriptional and Small RNA Responses of the White Mold Fungus Sclerotinia sclerotiorum to Infection by a Virulence-Attenuating Hypovirus. Viruses 2018; 10:E713. [PMID: 30558121 PMCID: PMC6315951 DOI: 10.3390/v10120713] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/06/2018] [Accepted: 12/10/2018] [Indexed: 12/19/2022] Open
Abstract
Mycoviruses belonging to the family Hypoviridae cause persistent infection of many different host fungi. We previously determined that the white mold fungus, Sclerotiniasclerotiorum, infected with Sclerotinia sclerotiorum hypovirus 2-L (SsHV2-L) exhibits reduced virulence, delayed/reduced sclerotial formation, and enhanced production of aerial mycelia. To gain better insight into the cellular basis for these changes, we characterized changes in mRNA and small RNA (sRNA) accumulation in S.sclerotiorum to infection by SsHV2-L. A total of 958 mRNAs and 835 sRNA-producing loci were altered after infection by SsHV2-L, among which >100 mRNAs were predicted to encode proteins involved in the metabolism and trafficking of carbohydrates and lipids. Both S. sclerotiorum endogenous and virus-derived sRNAs were predominantly 22 nt in length suggesting one dicer-like enzyme cleaves both. Novel classes of endogenous small RNAs were predicted, including phasiRNAs and tRNA-derived small RNAs. Moreover, S. sclerotiorum phasiRNAs, which were derived from noncoding RNAs and have the potential to regulate mRNA abundance in trans, showed differential accumulation due to virus infection. tRNA fragments did not accumulate differentially after hypovirus infection. Hence, in-depth analysis showed that infection of S. sclerotiorum by a hypovirulence-inducing hypovirus produced selective, large-scale reprogramming of mRNA and sRNA production.
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Affiliation(s)
- Shin-Yi Lee Marzano
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA.
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD 57006, USA.
| | - Achal Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA.
| | - Leslie Domier
- United States Department of Agriculture, Agricultural Research Service, Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA.
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Wang C, Jogaiah S, Zhang W, Abdelrahman M, Fang JG. Spatio-temporal expression of miRNA159 family members and their GAMYB target gene during the modulation of gibberellin-induced grapevine parthenocarpy. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3639-3650. [PMID: 29905866 DOI: 10.1093/jxb/ery172] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 05/22/2018] [Indexed: 05/18/2023]
Abstract
Grapevine, Vitis vinifera, is an important economic fruit crop that is highly sensitive to gibberellin (GA), and the exogenous application of GA can efficiently induce grapevine parthenocarpy. However, the molecular mechanisms underlying this process remain elusive. In this study, morphological changes during flower development in response to GA treatments were examined in the 'Zuijinxiang' cultivar. To obtain insights into the roles of miRNA159s in GA-induced grapevine parthenocarpy, VvmiR159a, VvmiR159b, VvmiR159c, and their target gene VvGAMYB were isolated, sequenced and characterized. Spatial-temporal expression analyses showed that VvmiR159c exhibited the highest expression levels at 4 d before flowering, followed by a gradual decrease, while VvGAMYB displayed an opposite pattern of expression with the lowest expression at the corresponding stage in response to GA treatment. A cleavage interaction between VvmiR159s and VvGAMYB and variations of their cleavage roles were confirmed in grapevine floral development. In addition, the potential roles of VvmiR159s in GA signaling were investigated through DELLA-protein repressors, indicating that GA-DELLA (SLR1)-VvmiR159c-VvGAMYB is the key signaling regulatory module in grapevine. Our findings provide novel insights into the GA-responsive roles of VvmiR159s in modulating grapevine floral development, which have important implications for the molecular breeding of high-quality seedless grapevine berry.
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Affiliation(s)
- Chen Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Sudisha Jogaiah
- Plant Healthcare and Diagnostic Center, Department of Studies in Biotechnology and Microbiology, Karnatak University, Dharwad, India
| | - WenYing Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Mostafa Abdelrahman
- Department of Botany, Faculty of Sciences, Aswan University, Aswan, Egypt
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Japan
| | - Jing Gui Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
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28
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Niu D, Zhang X, Song X, Wang Z, Li Y, Qiao L, Wang Z, Liu J, Deng Y, He Z, Yang D, Liu R, Wang Y, Zhao H. Deep Sequencing Uncovers Rice Long siRNAs and Its Involvement in Immunity Against Rhizoctonia solani. PHYTOPATHOLOGY 2018; 108:60-69. [PMID: 28876208 DOI: 10.1094/phyto-03-17-0119-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Small RNA (sRNA) is a class of noncoding RNA that can silence the expression of target genes. In rice, the majority of characterized sRNAs are within the range of 21 to 24 nucleotides (nt) long, whose biogenesis and function are associated with a specific sets of components, such as Dicer-like (OsDCLs) and Argonaute proteins (OsAGOs). Rice sRNAs longer than 24 nt are occasionally reported, with biogenesis and functional mechanism uninvestigated, especially in a context of defense responses against pathogen infection. By using deep sequencing, we identified a group of rice long small interfering RNAs (lsiRNAs) that are within the range of 25 to 40 nt in length. Our results show that some rice lsiRNAs are differentially expressed upon infection of Rhizoctonia solani, the causal agent of the rice sheath blight disease. Bioinformatic analysis and experimental validation indicate that some rice lsiRNAs can target defense-related genes. We further demonstrate that rice lsiRNAs are neither derived from RNA degradation nor originated as secondary small interfering RNAs (siRNAs). Moreover, lsiRNAs require OsDCL4 for biogenesis and OsAGO18 for function. Therefore, our study indicates that rice lsiRNAs are a unique class of endogenous sRNAs produced in rice, which may participate in response against pathogens.
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Affiliation(s)
- Dongdong Niu
- First, second, third, fourth, sixth, seventh, and fourteenth authors: College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; first, second, third, fourth, sixth, and fourteenth authors: Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education; second author: Institute of Industrial Crops, Shanxi Academy of Agricultural Sciences, Taiyuan 030000, Shanxi, China; fifth and twelfth authors: Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, China; eighth, ninth, and tenth authors: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; eleventh author: College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; and thirteenth author: State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xin Zhang
- First, second, third, fourth, sixth, seventh, and fourteenth authors: College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; first, second, third, fourth, sixth, and fourteenth authors: Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education; second author: Institute of Industrial Crops, Shanxi Academy of Agricultural Sciences, Taiyuan 030000, Shanxi, China; fifth and twelfth authors: Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, China; eighth, ninth, and tenth authors: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; eleventh author: College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; and thirteenth author: State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiaoou Song
- First, second, third, fourth, sixth, seventh, and fourteenth authors: College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; first, second, third, fourth, sixth, and fourteenth authors: Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education; second author: Institute of Industrial Crops, Shanxi Academy of Agricultural Sciences, Taiyuan 030000, Shanxi, China; fifth and twelfth authors: Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, China; eighth, ninth, and tenth authors: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; eleventh author: College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; and thirteenth author: State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Zhihui Wang
- First, second, third, fourth, sixth, seventh, and fourteenth authors: College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; first, second, third, fourth, sixth, and fourteenth authors: Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education; second author: Institute of Industrial Crops, Shanxi Academy of Agricultural Sciences, Taiyuan 030000, Shanxi, China; fifth and twelfth authors: Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, China; eighth, ninth, and tenth authors: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; eleventh author: College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; and thirteenth author: State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Yanqiang Li
- First, second, third, fourth, sixth, seventh, and fourteenth authors: College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; first, second, third, fourth, sixth, and fourteenth authors: Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education; second author: Institute of Industrial Crops, Shanxi Academy of Agricultural Sciences, Taiyuan 030000, Shanxi, China; fifth and twelfth authors: Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, China; eighth, ninth, and tenth authors: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; eleventh author: College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; and thirteenth author: State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Lulu Qiao
- First, second, third, fourth, sixth, seventh, and fourteenth authors: College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; first, second, third, fourth, sixth, and fourteenth authors: Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education; second author: Institute of Industrial Crops, Shanxi Academy of Agricultural Sciences, Taiyuan 030000, Shanxi, China; fifth and twelfth authors: Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, China; eighth, ninth, and tenth authors: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; eleventh author: College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; and thirteenth author: State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Zhaoyun Wang
- First, second, third, fourth, sixth, seventh, and fourteenth authors: College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; first, second, third, fourth, sixth, and fourteenth authors: Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education; second author: Institute of Industrial Crops, Shanxi Academy of Agricultural Sciences, Taiyuan 030000, Shanxi, China; fifth and twelfth authors: Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, China; eighth, ninth, and tenth authors: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; eleventh author: College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; and thirteenth author: State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Junzhong Liu
- First, second, third, fourth, sixth, seventh, and fourteenth authors: College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; first, second, third, fourth, sixth, and fourteenth authors: Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education; second author: Institute of Industrial Crops, Shanxi Academy of Agricultural Sciences, Taiyuan 030000, Shanxi, China; fifth and twelfth authors: Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, China; eighth, ninth, and tenth authors: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; eleventh author: College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; and thirteenth author: State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Yiwen Deng
- First, second, third, fourth, sixth, seventh, and fourteenth authors: College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; first, second, third, fourth, sixth, and fourteenth authors: Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education; second author: Institute of Industrial Crops, Shanxi Academy of Agricultural Sciences, Taiyuan 030000, Shanxi, China; fifth and twelfth authors: Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, China; eighth, ninth, and tenth authors: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; eleventh author: College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; and thirteenth author: State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Zuhua He
- First, second, third, fourth, sixth, seventh, and fourteenth authors: College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; first, second, third, fourth, sixth, and fourteenth authors: Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education; second author: Institute of Industrial Crops, Shanxi Academy of Agricultural Sciences, Taiyuan 030000, Shanxi, China; fifth and twelfth authors: Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, China; eighth, ninth, and tenth authors: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; eleventh author: College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; and thirteenth author: State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Donglei Yang
- First, second, third, fourth, sixth, seventh, and fourteenth authors: College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; first, second, third, fourth, sixth, and fourteenth authors: Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education; second author: Institute of Industrial Crops, Shanxi Academy of Agricultural Sciences, Taiyuan 030000, Shanxi, China; fifth and twelfth authors: Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, China; eighth, ninth, and tenth authors: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; eleventh author: College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; and thirteenth author: State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Renyi Liu
- First, second, third, fourth, sixth, seventh, and fourteenth authors: College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; first, second, third, fourth, sixth, and fourteenth authors: Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education; second author: Institute of Industrial Crops, Shanxi Academy of Agricultural Sciences, Taiyuan 030000, Shanxi, China; fifth and twelfth authors: Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, China; eighth, ninth, and tenth authors: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; eleventh author: College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; and thirteenth author: State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Yanli Wang
- First, second, third, fourth, sixth, seventh, and fourteenth authors: College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; first, second, third, fourth, sixth, and fourteenth authors: Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education; second author: Institute of Industrial Crops, Shanxi Academy of Agricultural Sciences, Taiyuan 030000, Shanxi, China; fifth and twelfth authors: Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, China; eighth, ninth, and tenth authors: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; eleventh author: College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; and thirteenth author: State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Hongwei Zhao
- First, second, third, fourth, sixth, seventh, and fourteenth authors: College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; first, second, third, fourth, sixth, and fourteenth authors: Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education; second author: Institute of Industrial Crops, Shanxi Academy of Agricultural Sciences, Taiyuan 030000, Shanxi, China; fifth and twelfth authors: Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, China; eighth, ninth, and tenth authors: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; eleventh author: College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; and thirteenth author: State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
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Torres-Martínez S, Ruiz-Vázquez RM. The RNAi Universe in Fungi: A Varied Landscape of Small RNAs and Biological Functions. Annu Rev Microbiol 2017; 71:371-391. [PMID: 28657888 DOI: 10.1146/annurev-micro-090816-093352] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA interference (RNAi) is a conserved eukaryotic mechanism that uses small RNA molecules to suppress gene expression through sequence-specific messenger RNA degradation, translational repression, or transcriptional inhibition. In filamentous fungi, the protective function of RNAi in the maintenance of genome integrity is well known. However, knowledge of the regulatory role of RNAi in fungi has had to wait until the recent identification of different endogenous small RNA classes, which are generated by distinct RNAi pathways. In addition, RNAi research on new fungal models has uncovered the role of small RNAs and RNAi pathways in the regulation of diverse biological functions. In this review, we give an up-to-date overview of the different classes of small RNAs and RNAi pathways in fungi and their roles in the defense of genome integrity and regulation of fungal physiology and development, as well as in the interaction of fungi with biotic and abiotic environments.
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