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      KCI등재 SCIE SCOPUS

      siRNAs Derived from Cymbidium Mosaic Virus and Odontoglossum Ringspot Virus Down-modulated the Expression Levels of Endogenous Genes in Phalaenopsis equestris

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      https://www.riss.kr/link?id=A106376762

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      다국어 초록 (Multilingual Abstract)

      Interplay between Cymbidium mosaic virus (CymMV)/ Odontoglossum ringspot virus (ORSV) and its host plant Phalaenopsis equestris remain largely unknown, which led to deficiency of effective measures to control disease of P. equestris caused by infecting viruses. In this study, for the first time, we characterized viral small interfering RNAs (vsiRNAs) profiles in P. equestris co-infected with CymMV and ORSV through small RNA sequencing technology. CymMV and ORSV small interfering RNAs (siRNAs) demonstrated several general and specific/new characteristics. vsiRNAs, with A/ U bias at the first nucleotide, were predominantly 21-nt long and they were derived predominantly (90%) from viral positive-strand RNA. 21-nt siRNA duplexes with 0-nt overhangs were the most abundant 21-nt duplexes, followed by 2-nt overhangs and then 1-nt overhangs 21-nt duplexes in infected P. equestris. Continuous but heterogeneous distribution and secondary structures prediction implied that vsiRNAs originate predominantly by direct Dicer-like enzymes cleavage of imperfect duplexes in the most folded regions of the positive strand of both viruses RNA molecular. Furthermore, we totally predicted 54 target genes by vsiRNAs with psRNATarget server, including disease/stress response– related genes, RNA interference core components, cytoskeleton- related genes, photosynthesis or energy supply related genes. Gene Ontology classification showed that a majority of the predicted targets were related to cellular components and cellular processes and performed a certain function. All target genes were down-regulated with different degree by vsiRNAs as shown by realtime reverse transcription polymerase chain reaction. Taken together, CymMV and ORSV siRNAs played important roles in interplay with P. equestris by down modulating the expression levels of endogenous genes in host plant.
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      Interplay between Cymbidium mosaic virus (CymMV)/ Odontoglossum ringspot virus (ORSV) and its host plant Phalaenopsis equestris remain largely unknown, which led to deficiency of effective measures to control disease of P. equestris caused by infectin...

      Interplay between Cymbidium mosaic virus (CymMV)/ Odontoglossum ringspot virus (ORSV) and its host plant Phalaenopsis equestris remain largely unknown, which led to deficiency of effective measures to control disease of P. equestris caused by infecting viruses. In this study, for the first time, we characterized viral small interfering RNAs (vsiRNAs) profiles in P. equestris co-infected with CymMV and ORSV through small RNA sequencing technology. CymMV and ORSV small interfering RNAs (siRNAs) demonstrated several general and specific/new characteristics. vsiRNAs, with A/ U bias at the first nucleotide, were predominantly 21-nt long and they were derived predominantly (90%) from viral positive-strand RNA. 21-nt siRNA duplexes with 0-nt overhangs were the most abundant 21-nt duplexes, followed by 2-nt overhangs and then 1-nt overhangs 21-nt duplexes in infected P. equestris. Continuous but heterogeneous distribution and secondary structures prediction implied that vsiRNAs originate predominantly by direct Dicer-like enzymes cleavage of imperfect duplexes in the most folded regions of the positive strand of both viruses RNA molecular. Furthermore, we totally predicted 54 target genes by vsiRNAs with psRNATarget server, including disease/stress response– related genes, RNA interference core components, cytoskeleton- related genes, photosynthesis or energy supply related genes. Gene Ontology classification showed that a majority of the predicted targets were related to cellular components and cellular processes and performed a certain function. All target genes were down-regulated with different degree by vsiRNAs as shown by realtime reverse transcription polymerase chain reaction. Taken together, CymMV and ORSV siRNAs played important roles in interplay with P. equestris by down modulating the expression levels of endogenous genes in host plant.

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      목차 (Table of Contents)

      • Materials and Methods Results and Discussion
      • Materials and Methods Results and Discussion
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      참고문헌 (Reference)

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      6 Wu Q, "Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs" 107 : 1606-1611, 2010

      7 Niu X, "Using small RNA-seq data to detect siRNA duplexes induced by plant viruses" 8 : 163-, 2017

      8 Wang F, "Using small RNA deep sequencing data to detect human viruses" 2016 : 2596782-, 2016

      9 Lacombe S, "The rice yellow mottle virus P1 protein exhibits dual functions to suppress and activate gene silencing" 61 : 371-382, 2010

      10 Cai J, "The genome sequence of the orchid Phalaenopsis equestris" 47 : 65-72, 2015

      1 Dai X, "psRNATarget : a plant small RNA target analysis server" 39 : W155-W159, 2011

      2 Gibbs A., "Viruses of orchids in Australia : their identification, biology and control" 65 : 10-21, 2000

      3 Zettler FW, "Viruses of orchids and their control" 74 : 621-626, 1990

      4 Zheng Y, "VirusDetect : an automated pipeline for efficient virus discovery using deep sequencing of small RNAs" 500 : 130-138, 2017

      5 Koh KW, "Virus resistance in orchids" 228 : 26-38, 2014

      6 Wu Q, "Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs" 107 : 1606-1611, 2010

      7 Niu X, "Using small RNA-seq data to detect siRNA duplexes induced by plant viruses" 8 : 163-, 2017

      8 Wang F, "Using small RNA deep sequencing data to detect human viruses" 2016 : 2596782-, 2016

      9 Lacombe S, "The rice yellow mottle virus P1 protein exhibits dual functions to suppress and activate gene silencing" 61 : 371-382, 2010

      10 Cai J, "The genome sequence of the orchid Phalaenopsis equestris" 47 : 65-72, 2015

      11 Donaire L, "Structural and genetic requirements for the biogenesis of Tobacco rattle virus-derived small interfering RNAs" 82 : 5167-5177, 2008

      12 Mi S, "Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′-terminal nucleotide" 133 : 116-127, 2008

      13 Lan H, "Small interfering RNA pathway modulates persistent infection of a plant virus in its insect vector" 6 : 20699-, 2016

      14 Lan H, "Small interfering RNA pathway modulates initial viral infection in midgut epithelium of insect after ingestion of virus" 90 : 917-929, 2015

      15 Morris ER, "Receptor-like protein kinases : the keys to response" 6 : 339-342, 2003

      16 Namisha Sharma, "Recent Advances in Plant–Virus Interaction with Emphasis on Small Interfering RNAs (siRNAs)" Springer Science and Business Media LLC 55 (55): 63-77, 2013

      17 Jiang L, "RNA-dependent RNA polymerase 6 of rice(Oryza sativa)plays role in host defense against negative-strand RNA virus, Rice stripe virus" 163 : 512-519, 2012

      18 Ding S-W., "RNA-based antiviral immunity" 10 : 632-644, 2010

      19 Baulcombe D., "RNA silencing in plants" 431 : 356-363, 2006

      20 Lan H, "RNA interference-mediated knockdown and virusinduced suppression of Troponin C gene adversely affect the behavior or fitness of the green rice leafhopper, Nephotettix cincticeps" 97 : e21438-, 2018

      21 Vaucheret H., "Post-transcriptional small RNA pathways in plants : mechanisms and regulations" 20 : 759-771, 2006

      22 Molnár A, "Plant virus-derived small interfering RNAs originate predominantly from highly structured single-stranded viral RNAs" 79 : 7812-7818, 2005

      23 DeYoung BJ, "Plant NBS-LRR proteins in pathogen sensing and host defense" 7 : 1243-1249, 2006

      24 McHale L, "Plant NBS-LRR proteins : adaptable guards" 7 : 212-, 2006

      25 Hong W, "OsRDR6 plays role in host defense against double-stranded RNA virus, Rice Dwarf Phytoreovirus" 5 : 11324-, 2015

      26 Liu B, "Oryza sativa Dicer-like4 reveals a key role for small interfering RNA silencing in plant development" 19 : 2705-2718, 2007

      27 Gruenheid S, "Microbial pathogenesis and cytoskeletal function" 422 : 775-781, 2003

      28 Jones-Rhoades MW, "MicroRNAs and their regulatory roles in plants" 57 : 19-53, 2006

      29 Wong SM, "Incidence of cymbidium mosaic and odontoglossum ringspot viruses and their significance in orchid cultivation in Singapore" 13 : 235-239, 1994

      30 Lan Y, "Identification of virus-derived siRNAs and their targets in RBSDV-infected rice by deep sequencing" 58 : 227-237, 2018

      31 Sinha P, "Identification and validation of selected universal stress protein domain containing drought-responsive genes in Pigeonpea (Cajanus cajan L.)" 6 : 1065-, 2016

      32 Deleris A, "Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense" 313 : 68-71, 2006

      33 Kapoor M, "Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families and their expression analysis during reproductive development and stress in rice" 9 : 451-, 2008

      34 Mandadi KK, "Genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in Brachypodium distachyon" 27 : 71-85, 2015

      35 Blevins T, "Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing" 34 : 6233-6246, 2006

      36 Ho T, "Evidence for targeting common siRNA hotspots and GC preference by plant Dicer-like proteins" 581 : 3267-3272, 2007

      37 Wang A., "Dissecting the molecular network of virus-plant interactions : the complex roles of host factors" 53 : 45-66, 2015

      38 Mitter N, "Differential expression of Tomato spotted wilt virus-derived viral small RNAs in infected commercial and experimental host plants" 8 : e76276-, 2013

      39 Derrien B, "Degradation of the antiviral component ARGONAUTE1 by the autophagy pathway" 109 : 15942-15946, 2012

      40 Li R, "Deep sequencing of small RNAs in tomato for virus and viroid identification and strain differentiation" 7 : e37127-, 2012

      41 Niu S-C, "De novo transcriptome assembly databases for the butterfly orchid Phalaenopsis equestris" 3 : 160083-, 2016

      42 Kreuze JF, "Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs : a generic method for diagnosis, discovery and sequencing of viruses" 388 : 1-7, 2009

      43 Li R, "Complete genome sequence of a novel genotype of squash mosaic virus infecting squash in Spain" 3 : e01583-e01514, 2015

      44 R. Li, "Complete Genome Sequence of a New Tobamovirus Naturally Infecting Tomatoes in Mexico" American Society for Microbiology 1 (1): 2013

      45 Liu C, "Complemented palindrome small RNAs first discovered from SARS coronavirus" 9 : 442-, 2018

      46 Xia Z, "Characterization of small interfering RNAs derived from Sugarcane mosaic virus in infected maize plants by deep sequencing" 9 : e97013-, 2014

      47 Yan F, "Characterization of siRNAs derived from rice stripe virus in infected rice plants by deep sequencing" 155 : 935-940, 2010

      48 Li Y, "Characterization of siRNAs derived from cucumber green mottle mosaic virus in infected cucumber plants" 161 : 455-458, 2016

      49 Xu D, "Characteristics of siRNAs derived from Southern rice black-streaked dwarf virus in infected rice and their potential role in host gene regulation" 14 : 27-, 2017

      50 Kim HS, "Arabidopsis SON1 is an F-Box protein that regulates a novel induced defense response independent of both salicylic acid and systemic acquired resistance" 14 : 1469-1482, 2002

      51 Prabha K, "Applications of next generation high throughput sequencing technologies in characterization, discovery and molecular interaction of plant viruses" 24 : 157-165, 2013

      52 Yang J, "Analysis of small RNAs derived from Chinese wheat mosaic virus" 159 : 3077-3082, 2014

      53 Rubio M, "Analysis of gene expression changes in peach leaves in response to Plum pox virus infection using RNA-Seq" 16 : 164-176, 2015

      54 Earley K, "An endogenous F-box protein regulates ARGONAUTE1 in Arabidopsis thaliana" 1 : 15-, 2010

      55 Gouin E, "Actin-based motility of intracellular pathogens" 8 : 35-45, 2005

      56 Greber UF, "A superhighway to virus infection" 124 : 741-754, 2006

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