In silico analysis of microRNA binding to the genome of Beet curly top Iran virus in tomato

References

• Ali I, Amin I, Briddon R, Mansoor S. 2013. Artificial microRNA-mediated resistance against the monopartite begomovirus cotton leaf curl burewala virus. Virol J. 10:1–8. 10.1186/1743-422X-10-231
   PubMed Web of Science ®Google Scholar
• Bartel DP. 2004. Micrornas: genomics, biogenesis, mechanism, and function. Cell. 116:281–297. 10.1016/S0092-8674(04)00045-5
   PubMed Web of Science ®Google Scholar
• Bisaro DM. 2006. Silencing suppression by geminivirus proteins. Virol J. 344:158–168. 10.1016/j.virol.2005.09.041
   Web of Science ®Google Scholar
• Bolok Yazdi H, Heydarnejad J, Massumi H. 2008. Genome characterization and genetic diversity of Beet curly top Iran Virus: a geminivirus with a novel nonanucleotide. Virus Genes. 36:539–545. 10.1007/s11262-008-0224-2
   PubMed Web of Science ®Google Scholar
• Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto YY, Sieburth L, Voinnet O. 2008. Widespread translational inhibition by plant miRNAs and siRNAs. Science. 320:1185–1190. 10.1126/science.1159151
   PubMed Web of Science ®Google Scholar
• Buchmann RC, Asad S, Wolf JN, Mohannath G, Bisaro DM. 2009. Geminivirus AL2 and L2 proteins suppress transcriptional gene silencing and cause genome-wide reductions in cytosine methylation. Virol J. 83:5005–5013. 10.1128/JVI.01771-08
   Web of Science ®Google Scholar
• Chapman EJ, Prokhnevsky AI, Gopinath K, Dolja VV, Carrington JC. 2004. Viral RNA silencing suppressors inhibit the microRNA pathway at an intermediate step. Genes Dev. 18:1179–1186. 10.1101/gad.1201204
   PubMed Web of Science ®Google Scholar
• Chellappan P, Vanitharani FC. 2004. Short-interfering rna accumulation correlates with host recovery in DNA virus infected hosts and gene silencing targets specific viral sequences. Virol J. 78:6574.
   Web of Science ®Google Scholar
• Chen X. 2004. A microRNA as a translational repressor of APETALA2 in arabidopsis flower development. Science. 303:2022–2025.10.1126/science.1088060
   PubMed Web of Science ®Google Scholar
• Duffy S, Holmes EC. 2009. Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from east african cassava mosaic viruses. J Gen Virol. 90:1539–1547. 10.1099/vir.0.009266-0
   PubMed Web of Science ®Google Scholar
• Eini O, Dogra SC, Dry IB, Randles JW. 2012. Silencing suppressor activity of a begomovirus DNA β encoded protein and its effect on heterologous helper virus replication. Virus Res. 167:97–101. 10.1016/j.virusres.2012.03.012
   PubMed Web of Science ®Google Scholar
• Gharouni Kardani S, Heydarnejad J, Zakiaghl M, Mehrvar M, Kraberger S, Varsani A. 2013. Diversity of Beet curly top Iran virus isolated from different hosts in Iran. Virus Genes. 46:571–575. 10.1007/s11262-013-0875-5
   PubMed Web of Science ®Google Scholar
• Ghildiyal M, Xu J, Seitz H, Weng Z, Zamore PD. 2010. Sorting of drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. RNA. 16:43–56.10.1261/rna.1972910
   PubMed Web of Science ®Google Scholar
• Jin W, Wu F. 2015. Characterization of miRNAs associated with Botrytis cinerea infection of tomato leaves. BMC Plant Biol. 15:1–14. 10.1186/s12870-014-0410-4
   PubMed Web of Science ®Google Scholar
• Jin D, Wang Y, Zhao Y, Chen M. 2013. MicroRNAs and their cross-talks in plant development. J Genet Genomics. 40:161–170. 10.1016/j.jgg.2013.02.003
   PubMed Web of Science ®Google Scholar
• Jones-Rhoades MW, Bartel DP. 2004. Computational identification of plant MicroRNAs and their targets, including a stress-induced miRNA. Mol Cell. 14:787–799.10.1016/j.molcel.2004.05.027
   PubMed Web of Science ®Google Scholar
• Jopling CL, Yi M, Lancaster AM, Lemon SM, Sarnow P. 2005. Modulation of hepatitis C virus RNA abundance by a liver-specific microRNA. Science. 309:1577–1581. 10.1126/science.1113329
   PubMed Web of Science ®Google Scholar
• Kim J, Jung J-H, Reyes JL, Kim Y-S, Kim S-Y, Chung K-S, Kim JA, Lee M, Lee Y, Kim VN, et al. 2005. MicroRNA-directed cleavage of ATHB15 mRNA regulates vascular development in arabidopsis inflorescence stems. Plant J. 42:84–94. 10.1111/tpj.2005.42.issue-1
   PubMed Web of Science ®Google Scholar
• Kis A, Tholt G, Ivanics M, Várallyay É, Jenes B, Havelda Z. 2015. Polycistronic artificial miRNA-mediated resistance to wheat dwarf virus in barley is highly efficient at low temperature. Mol Plant Pathol. 16:1–11.
   PubMed Web of Science ®Google Scholar
• Krüger J, Rehmsmeier M. 2006. RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res. 34:W451–W454. 10.1093/nar/gkl243
   PubMed Web of Science ®Google Scholar
• Lecellier C-H, Dunoyer P, Arar K, Lehmann-Che J, Eyquem S, Himber C, Saïb A, Voinnet O. 2005. A cellular microRNA mediates antiviral defense in human cells. Science. 308:557–560. 10.1126/science.1108784
   PubMed Web of Science ®Google Scholar
• Li L, Xu J, Yang D, Tan X, Wang H. 2010. Computational approaches for microRNA studies: a review. Mamm Genome. 21:1–12. 10.1007/s00335-009-9241-2
   PubMed Web of Science ®Google Scholar
• Llave C, Xie Z, Kasschau KD, Carrington JC. 2002. Cleavage of scarecrow-like mRNA targets directed by a class of arabidopsis miRNA. Science. 297:2053–2056. 10.1126/science.1076311
   PubMed Web of Science ®Google Scholar
• Lucioli A, Noris E, Brunetti A, Tavazza R, Ruzza V, Castillo AG, Bejarano ER, Accotto GP, Tavazza M. 2003. Tomato yellow leaf curl sardinia virus rep-derived resistance to homologous and heterologous geminiviruses occurs by different mechanisms and is vercome if virus-mediated transgene silencing is activated. Virol J. 77:6785–6798.10.1128/JVI.77.12.6785-6798.2003
   Web of Science ®Google Scholar
• Mallory AC, Bouché N. 2008. MicroRNA-directed regulation: to cleave or not to cleave. Trends Plant Sci. 13:59–367.
   Web of Science ®Google Scholar
• Mallory AC, Dugas DV, Bartel DP, Bartel B. 2004. MicroRNA regulation of nac-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs. Curr Biol. 14:1035–1046. 10.1016/j.cub.2004.06.022
   PubMed Web of Science ®Google Scholar
• Martin DP, Biagini P, Lefeuvre P, Golden M, Roumagnac P, Varsani A. 2011. Recombination in eukaryotic single stranded DNA viruses. Viruses. 3:1699–1738. 10.3390/v3091699
   PubMed Web of Science ®Google Scholar
• Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ, et al. 2008. Criteria for annotation of plant MicroRNAs. Plant Cell. 20:3186–3190. 10.1105/tpc.108.064311
   PubMed Web of Science ®Google Scholar
• Naqvi A, Haq Q, Mukherjee S. 2010. MicroRNA profiling of Tomato Leaf curl New Delhi Virus (tolcndv) infected tomato leaves indicates that deregulation of mir159/319 and mir172 might be linked with leaf curl disease. Virol J. 7:281–297. 10.1186/1743-422X-7-281
   PubMed Web of Science ®Google Scholar
• Naqvi AR, Choudhury NR, Mukherjee SK, Haq QMR. 2011. In silico analysis reveals that several tomato microRNA/microRNA∗ sequences exhibit propensity to bind to tomato leaf curl virus (ToLCV) associated genomes and most of their encoded open reading frames (ORFs). Plant Physiol Biochem. 49:13–17. 10.1016/j.plaphy.2010.09.013
   PubMed Web of Science ®Google Scholar
• Palatnik JF, Allen E, Wu X, Schommer C, Schwab R, Carrington JC, Weigel D. 2003. Control of leaf morphogenesis by microRNAs. Nature. 425:257–263. 10.1038/nature01958
   PubMed Web of Science ®Google Scholar
• Pérez-Quintero ÁL, Neme R, Zapata A, López C. 2010. Plant microRNAs and their role in defense against viruses: a bioinformatics approach. BMC Plant Biol. 10:138. 10.1186/1471-2229-10-138
   PubMed Web of Science ®Google Scholar
• Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R. 2004. Fast and effective prediction of microRNA/target duplexes. RNA. 10:1507–1517.10.1261/rna.5248604
   PubMed Web of Science ®Google Scholar
• Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP. 2002. Prediction of plant microRNA targets. Cell. 110:513–520. 10.1016/S0092-8674(02)00863-2
   PubMed Web of Science ®Google Scholar
• Rogers K, Chen X. 2013. Biogenesis, turnover, and mode of action of plant microRNAs. Plant Cell. 25:2383–2399. 10.1105/tpc.113.113159
   PubMed Web of Science ®Google Scholar
• Saunders K, Bedford ID, Stanley J. 2001. Pathogenicity of a natural recombinant associated with ageratum yellow vein disease: implications for geminivirus evolution and disease aetiology. Virol J. 282:38–47. 10.1006/viro.2000.0832
   Web of Science ®Google Scholar
• Schommer C, Bresso EG, Spinelli SV, Palatnik JF. 2012. Role of microRNA mir319 in plant development. In: Sunkar R, editor. MicroRNAs in plant development and stress responses signaling and communication in plant. Heidelberg: Springer; p. 29–47.
   Google Scholar
• Valiollahi E, Farsi M, Fevereiro P, Kakhki AM. 2014. Bioinformatic characterization and expression analysis of miRNAs in solanum lycopersicum. Plant Omics J. 7:108–116.
   Google Scholar
• Vanitharani R, Chellappan P, Pita JS, Fauquet CM. 2004. Differential roles of ac2 and ac4 of cassava geminiviruses in mediating synergism and suppression of posttranscriptional gene silencing. Virol J. 78:9487–9498. 10.1128/JVI.78.17.9487-9498.2004
   Web of Science ®Google Scholar
• Vanitharani R, Chellappan P, Fauquet C. 2005. Geminiviruses and RNA silencing. Trends in Plant Sci. 10:144–151. 10.1016/j.tplants.2005.01.005
   PubMed Web of Science ®Google Scholar
• Watanabe Y, Kishi A, Yachie N, Kanai A, Tomita M. 2007. Computational analysis of microRNA-mediated antiviral defense in humans. FEBS Lett. 581:4603–4610.10.1016/j.febslet.2007.08.049
   PubMed Web of Science ®Google Scholar
• Zhang J, Zeng R, Chen J, Liu X, Liao Q. 2008. Identification of conserved microRNAs and their targets from Solanum lycopersicum Mill. Gene. 423:1–7. 10.1016/j.gene.2008.05.023
   PubMed Web of Science ®Google Scholar