1 |
Hong, W., Qian, D., Sun, R., Jiang, L., Wang, Y., Wei, C., Zhang, Z. and Li, Y. 2015. OsRDR6 plays role in host defense against double-stranded RNA virus, Rice Dwarf Phytoreovirus. Sci Rep. 5:11324.
DOI
|
2 |
Jiang, L., Qian, D., Zheng, H., Meng, L.-Y, Chen, J., Le, W.-J., Zhou, T., Zhou, Y.-J., Wei, C.-H. and Li, Y. 2012. RNAdependent RNA polymerase 6 of rice (Oryza sativa) plays role in host defense against negative-strand RNA virus, Rice stripe virus. Virus Res. 163:512-519.
DOI
|
3 |
Jones-Rhoades, M. W., Bartel, D. P. and Bartel, B. 2006. MicroRNAs and their regulatory roles in plants. Annu. Rev. Plant Biol. 57:19-53.
DOI
|
4 |
Kapoor, M., Arora, R., Lama, T., Nijhawan, A., Khurana, J. P., Tyagi, A. K. and Kapoor, S. 2008. 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. BMC Genomics 9:451.
DOI
|
5 |
Kim, H. S. and Delaney, T. P. 2002. Arabidopsis SON1 is an FBox protein that regulates a novel induced defense response independent of both salicylic acid and systemic acquired resistance. Plant Cell 14:1469-1482.
DOI
|
6 |
Koh, K. W., Lu, H.-C. and Chan, M.-T. 2014. Virus resistance in orchids. Plant Sci. 228:26-38.
DOI
|
7 |
Kreuze, J. F., Perez, A., Untiveros, M., Quispe, D., Fuentes, S., Barker, I. and Simon, R. 2009. 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. Virology 388:1-7.
DOI
|
8 |
Lacombe, S., Bangratz, M., Vignols, F. and Brugidou, C. 2010. The rice yellow mottle virus P1 protein exhibits dual functions to suppress and activate gene silencing. Plant J. 61:371-382.
DOI
|
9 |
Lan, H., Hong, X., Huang, R., Lin, X., Li, Q., Li, K. and Zhou, T. 2018a. RNA interference-mediated knockdown and virusinduced suppression of Troponin C gene adversely affect the behavior or fitness of the green rice leafhopper, Nephotettix cincticeps. Arch. Insect Biochem. Physiol. 97:e21438.
DOI
|
10 |
Lan, H., Chen, H., Liu, Y., Jiang, C., Mao, Q., Jia, D., Chen, Q. and Wei, T. 2015. Small interfering RNA pathway modulates initial viral infection in midgut epithelium of insect after ingestion of virus. J. Virol. 90:917-929.
DOI
|
11 |
McHale, L., Tan, X., Koehl, P. and Michelmore, R. W. 2006. Plant NBS-LRR proteins: adaptable guards. Genome Biol. 7:212.
|
12 |
Liu, B., Chen, Z., Song, X., Liu, C., Cui, X., Zhao, X., Fang, J., Xu, W., Zhang, H., Wang, X., Chu, C., Deng, X., Xue, Y. and Cao, X. 2007. Oryza sativa Dicer-like4 reveals a key role for small interfering RNA silencing in plant development. Plant Cell 19:2705-2718.
DOI
|
13 |
Liu, C., Chen, Z., Hu, Y., Ji, H., Yu, D., Shen, W., Li, S., Ruan, J., Bu, W. and Gao, S. 2018. Complemented palindrome small RNAs first discovered from SARS coronavirus. Genes 9:442.
DOI
|
14 |
Mandadi, K. K. and Scholthof, K.-B. G. 2015. Genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in Brachypodium distachyon. Plant Cell 27:71-85.
DOI
|
15 |
Mi, S., Cai, T., Hu, Y., Chen, Y., Hodges, E., Ni, F., Wu, L., Li, S., Zhou, H., Long, C., Chen, S., Hannon, G. J. and Qi, Y. 2008. Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5'-terminal nucleotide. Cell 133:116-127.
DOI
|
16 |
Mitter, N., Koundal, V., Williams, S. and Pappu, H. 2013. Differential expression of Tomato spotted wilt virus-derived viral small RNAs in infected commercial and experimental host plants. PLoS ONE 8:e76276.
DOI
|
17 |
Molnar, A., Csorba, T., Lakatos, L., Varallyay, E., Lacomme, C. and Burgyan, J. 2005. Plant virus-derived small interfering RNAs originate predominantly from highly structured singlestranded viral RNAs. J. Virol. 79:7812-7818.
DOI
|
18 |
Li, R., Gao, S., Berendsen, S., Fei, Z. and Ling, K.-S. 2015. Complete genome sequence of a novel genotype of squash mosaic virus infecting squash in Spain. Genome Announc. 3:e01583-14.
|
19 |
Lan, H., Wang, H., Chen, Q., Chen, H., Jia, D., Mao, Q. and Wei, T. 2016. Small interfering RNA pathway modulates persistent infection of a plant virus in its insect vector. Sci. Rep. 6:20699.
DOI
|
20 |
Lan, Y., Li, Y., E. Z., Sun, F., Du, L., Xu, Q., Zhou, T., Zhou, Y. and Fan, Y. 2018b. Identification of virus-derived siRNAs and their targets in RBSDV-infected rice by deep sequencing. J. Basic Microbiol. 58:227-237.
DOI
|
21 |
Li, R., Gao, S., Fei, Z. and Ling, K.-S. 2013. Complete genome sequence of a new tobamovirus naturally infecting tomatoes in Mexico. Genome Announc. 1:e00794-13.
|
22 |
Li, R., Gao, S., Hernandez, A. G., Wechter, W. P., Fei, Z. and Ling, K.-S. 2012. Deep sequencing of small RNAs in tomato for virus and viroid identification and strain differentiation. PLoS ONE 7:e37127.
DOI
|
23 |
Li, Y., Deng, C., Shang, Q., Zhao, X., Liu, X. and Zhou, Q. 2016. Characterization of siRNAs derived from cucumber green mottle mosaic virus in infected cucumber plants. Arch. Virol. 161:455-458.
DOI
|
24 |
Sharma, N., Sahu, P. P., Puranik, S. and Prasad, M. 2013. Recent advances in plant-virus interaction with emphasis on small interfering RNAs (siRNAs). Mol. Biotechnol. 55:63-77.
DOI
|
25 |
Morris, E. R. and Walker, J. C. 2003. Receptor-like protein kinases: the keys to response. Curr. Opin. Plant Biol. 6:339-342.
DOI
|
26 |
Niu, S.-C., Xu, Q., Zhang, G.-Q., Zhang, Y.-Q., Tsai, W.-C., Hsu, J.-L., Liang, C.-K., Luo, Y.-B. and Liu, Z.-J. 2016. De novo transcriptome assembly databases for the butterfly orchid Phalaenopsis equestris. Sci. Data 3:160083.
DOI
|
27 |
Niu, X., Sun, Y., Chen, Z., Li, R., Padmanabhan, C., Ruan, J., Kreuze, J. F., Ling, K., Fei, Z. and Gao, S. 2017. Using small RNA-seq data to detect siRNA duplexes induced by plant viruses. Genes 8:163.
DOI
|
28 |
Prabha, K., Baranwal, V. K. and Jain, R. K. 2013. Applications of next generation high throughput sequencing technologies in characterization, discovery and molecular interaction of plant viruses. Indian J. Virol. 24:157-165.
DOI
|
29 |
Rubio, M., Rodriguez-Moreno, L., Ballester, A. R., de Moura, M. C., Bonghi, C., Candresse, T. and Martinez-Gomez, P. 2015. Analysis of gene expression changes in peach leaves in response to Plum pox virus infection using RNA-Seq. Mol. Plant Pathol. 16:164-176.
DOI
|
30 |
Sinha, P., Pazhamala, L. T., Singh, V. K., Saxena, R. K., Krishnamurthy, L., Azam, S., Khan, A. W. and Varshney, R. K. 2016. Identification and validation of selected universal stress protein domain containing drought-responsive genes in Pigeonpea (Cajanus cajan L.). Front. Plant Sci. 6:1065.
DOI
|
31 |
Vaucheret, H. 2006. Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev. 20:759-771.
DOI
|
32 |
Wang, A. 2015. Dissecting the molecular network of virus-plant interactions: the complex roles of host factors. Annu. Rev. Phytopathol. 53:45-66.
DOI
|
33 |
Wang, F., Sun, Y., Ruan, J., Chen, R., Chen, X., Chen, C., Kreuze, J. F., Fei, Z., Zhu, X. and Gao, S. 2016. Using small RNA deep sequencing data to detect human viruses. BioMed Res. Int. 2016:2596782.
|
34 |
Xu, D. and Zhou, G. 2017. Characteristics of siRNAs derived from Southern rice black-streaked dwarf virus in infected rice and their potential role in host gene regulation. Virol. J. 14:27.
DOI
|
35 |
Wong, S. M., Chng, C. G., Lee, Y. H., Tan, K. and Zettler, F. W. 1994. Incidence of cymbidium mosaic and odontoglossum ringspot viruses and their significance in orchid cultivation in Singapore. Crop Prot. 13:235-239.
DOI
|
36 |
Wu, Q., Luo, Y., Lu, R., Lau, N., Lai, E. C., Li, W.-X. and Ding, S.-W. 2010. Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proc. Natl. Acad. Sci. U. S. A. 107:1606-1611.
DOI
|
37 |
Xia, Z., Peng, J., Li, Y., Chen, L., Li, S., Zhou, T. and Fan, Z. 2014. Characterization of small interfering RNAs derived from Sugarcane mosaic virus in infected maize plants by deep sequencing. PLoS ONE 9:e97013.
DOI
|
38 |
Zettler, F. W., Ko, N. J., Wisler, G. C., Elliott, M. S. and Wong, S. M. 1990. Viruses of orchids and their control. Plant Dis. 74:621-626.
DOI
|
39 |
Yan, F., Zhang, H., Adams, M. J., Yang, J., Peng, J., Antoniw, J. F., Zhou, Y. and Chen, J. 2010. Characterization of siRNAs derived from rice stripe virus in infected rice plants by deep sequencing. Arch. Virol. 155:935-940.
DOI
|
40 |
Yang, J., Zheng, S.-L., Zhang, H.-M., Liu, X.-Y., Li, J., Li, J.-M. and Chen, J.-P. 2014. Analysis of small RNAs derived from Chinese wheat mosaic virus. Arch. Virol. 159:3077-3082.
DOI
|
41 |
Zheng, Y., Gao, S., Padmanabhan, C., Li, R., Galvez, M., Gutierrez, D., Fuentes, S., Ling, K.-S., Kreuze, J. and Fei, Z. 2017. VirusDetect: an automated pipeline for efficient virus discovery using deep sequencing of small RNAs. Virology 500:130-138.
DOI
|
42 |
Greber, U. F. and Way, M. 2006. A superhighway to virus infection. Cell 124:741-754.
DOI
|
43 |
Ding, S.-W. 2010. RNA-based antiviral immunity. Nat. Rev. Immunol. 10:632-644.
DOI
|
44 |
Baulcombe, D. 2006. RNA silencing in plants. Nature 431:356-363.
DOI
|
45 |
Blevins, T., Rajeswaran, R., Shivaprasad, P. V., Beknazariants, D., Si-Ammour, A., Park, H.-S., Vazquez, F., Robertson, D., Meins, F. Jr., Hohn, T. and Pooggin, M. M. 2006. Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing. Nucleic Acids Res. 34:6233-6246.
DOI
|
46 |
Cai, J., Liu, X., Vanneste, K., Proost, S., Tsai, W.-C., Liu, K.-W., Chen, L.-J., He, Y., Xu, Q., Bian, C., Zheng, Z., Sun, F., Liu, W., Hsiao, Y.-Y., Pan, Z.-J., Hsu, C.-C., Yang, Y.-P., Hsu, Y.-C., Chuang, Y.-C., Dievart, A., Dufayard, J.-F., Xu, X., Wang, J.-Y., Wang, J., Xiao, X.-J., Zhao, X.-M., Du, R., Zhang, G.-Q., Wang, M., Su, Y.-Y., Xie, G.-C., Liu, G.-H., Li, L.-Q., Huang, L.-Q., Luo, Y.-B., Chen, H.-H., Van de Peer, Y. and Liu, Z.-J. 2015. The genome sequence of the orchid Phalaenopsis equestris. Nat. Genet. 47:65-72.
DOI
|
47 |
Dai, X. and Zhao, P. X. 2011. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res. 39:W155-W159.
DOI
|
48 |
Deleris, A., Gallego-Bartolome, J., Bao, J., Kasschau, K. D., Carrington, J. C. and Voinnet, O. 2006. Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense. Science 313:68-71.
DOI
|
49 |
Derrien, B., Baumberger, N., Schepetilnikov, M., Viotti, C., De Cillia, J., Ziegler-Graff, V., Isono, E., Schumacher, K. and Genschik, P. 2012. Degradation of the antiviral component ARGONAUTE1 by the autophagy pathway. Proc. Natl. Acad. Sci. U. S. A. 109:15942-15946.
DOI
|
50 |
DeYoung, B. J. and Innes, R. W. 2006. Plant NBS-LRR proteins in pathogen sensing and host defense. Nat. Immunol. 7:1243-1249.
DOI
|
51 |
Gouin, E., Welch, M. D. and Cossart, P. 2005. Actin-based motility of intracellular pathogens. Curr. Opin. Microbiol. 8:35-45.
DOI
|
52 |
Donaire, L., Barajas, D., Martinez-García, B., Martinez-Priego, L., Pagan, I. and Llave, C. 2008. Structural and genetic requirements for the biogenesis of Tobacco rattle virus-derived small interfering RNAs. J. Virol. 82:5167-5177.
DOI
|
53 |
Earley, K., Smith, M. R., Weber, R., Gregory, B. D. and Poethig, R. S. 2010. An endogenous F-box protein regulates ARGONAUTE1 in Arabidopsis thaliana. Silence 1:15.
DOI
|
54 |
Gibbs, A. 2000. Viruses of orchids in Australia: their identification, biology and control. Aust. Orchid Rev. 65:10-21.
|
55 |
Gruenheid, S. and Finlay, B. B. 2003. Microbial pathogenesis and cytoskeletal function. Nature 422:775-781.
DOI
|
56 |
Ho, T., Wang, H., Pallett, D. and Dalmay, T. 2007. Evidence for targeting common siRNA hotspots and GC preference by plant Dicer-like proteins. FEBS Lett. 581:3267-3272.
DOI
|