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Soybean (Glycine max) Micrornas Display Proclivity to Repress Begomovirus Genomes


Affiliations
1 ICAR-Directorate of Soybean Research, Indian Council of Agricultural Research, Indore 452 001, India
 

Small non-coding RNAs are important effector molecules in response to pathogen invasion in plants and animals. We conducted in silico analysis of the DNA genomes of two distinct species of genus Begomovirus (family Geminiviridae)-Mungbean yellow mosaic India virus (MYMIV) and Mungbean yellow mosaic virus (MYMV) -that infect soybean using a micro- RNA (miRNA) target prediction algorithm, plant small RNA target analyzing server. MYMV displays greater vulnerability to plant miRNAs with 99 miRNAs targeting its genome, whereas 70 miRNAs appear to be targeting the MYMIV genome. miRNAs derived from Glycine max, Glycine soja and Cajanus cajan display 63, 18, and 8 potential target sites on the begomovirus genomes. Among the non-host plants begomoviruses exhibit seven and six potential target sites for O. sativa, and P. trichocarpa-derived miRNAs respectively. Begomovirus ORFs encoding viral movement proteins reveal greater vulnerability for G. max-derived miRNA binding and repression. Computational analysis with ssDNA animal virus genome as negative control sequences further emphasizes that plant miRNAs preferentially target begomovirus genomes. Nine prospective soybean-derived miRNAs targeting begomovirus genes have been shown to play a role in host-microbe interactions and abiotic stress responsiveness. The study thus provides in silico evidence for the plant-derived miRNAs in antiviral immunity.

Keywords

Antiviral Resistance, Begomovirus, Micro-RNA, Soybean.
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  • Reinhart, B. J. et al., MicroRNAs in plants. Genes Dev., 2002, 16, 1616–1626.

  • Llave, C., MicroRNAs: more than a role in plant development? Mol. Plant Pathol., 2004, 5(4), 361–366.

  • Amin, I. et al., A common set of developmental miRNAs are upregulated in Nicotiana benthamiana by diverse begomoviruses. Virol. J., 2011, 8(143), 300.

  • Ramesh, S. V. et al., Plant miRNAome and antiviral resistance: a retrospective view and prospective challenges. Virus Genes, 2014, 48, 1–14.

  • Maroof, M. A. S., Tucker, D. M. and Tolin, S. A., Genomics of viral–soybean interactions. Genet. Genomics Soybean, 2008, 2, 293–319.

  • Varma, A. and Malathi, V. G., Emerging geminivirus problems – a serious threat to crop production. Ann. Appl. Biol., 2003, 142, 145–164.

  • Kozomara, A. and Griffiths-Jones, S., miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res., 2011, 39, D152–D157.

  • Dai, X. and Zhao, P. X., psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res., 2011, 39, W155–W159.

  • Lu, Y. and Xiaoyun, Y., Computational identification of novel microRNAs and their targets in Vigna unguiculata. Comp. Funct. Genomics, 2010; doi:10.1155/2010/128297.

  • Paul, S., Kundu, A. and Pal, A., Identification and expression profiling of Vigna mungo microRNAs from leaf small RNA transcriptome by deep sequencing. J. Integr. Plant Biol., 2014, 56(1), 15–23.

  • Kompelli, S. K., Kompelli, V. S. P., Enjala, C. and Suravajhala, P., Genome-wide identification of miRNAs in pigeonpea (Cajanus cajan L.). Aust. J. Crop Sci., 2015, 9(3), 215–222.

  • Naqvi, A. R., Haq, Q. M. and Mukherjee, S. K., 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., 2010, 7, 281.

  • Perez-Quintero, A., Neme, R., Zapata, A. and López, C., Plant miRNAs and their role in defense against viruses: a bioinformatics approach. BMC Plant Biol., 2010, 10, 138.

  • Kulcheski, F. R. et al., Identification of novel soybean microRNAs involved in abiotic and biotic stresses. BMC Genomics, 2011, 12(1), 307.

  • Berkhout, B. and Haasnoot, J., The interplay between virus infection and the cellular RNA interference machinery. FEBS Lett., 2006, 580, 2896–2902.

  • Mahajan, V. S., Drake, A. and Chen, J., Virus-specific host miRNAs: Antiviral defenses or promoters of persistent infection? Trends Immunol., 2009, 30, 1–7.


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  • Soybean (Glycine max) Micrornas Display Proclivity to Repress Begomovirus Genomes

Abstract Views: 357  |  PDF Views: 146

Authors

Shunmugiah V. Ramesh
ICAR-Directorate of Soybean Research, Indian Council of Agricultural Research, Indore 452 001, India
Girish K. Gupta
ICAR-Directorate of Soybean Research, Indian Council of Agricultural Research, Indore 452 001, India
Syed M. Husain
ICAR-Directorate of Soybean Research, Indian Council of Agricultural Research, Indore 452 001, India

Abstract


Small non-coding RNAs are important effector molecules in response to pathogen invasion in plants and animals. We conducted in silico analysis of the DNA genomes of two distinct species of genus Begomovirus (family Geminiviridae)-Mungbean yellow mosaic India virus (MYMIV) and Mungbean yellow mosaic virus (MYMV) -that infect soybean using a micro- RNA (miRNA) target prediction algorithm, plant small RNA target analyzing server. MYMV displays greater vulnerability to plant miRNAs with 99 miRNAs targeting its genome, whereas 70 miRNAs appear to be targeting the MYMIV genome. miRNAs derived from Glycine max, Glycine soja and Cajanus cajan display 63, 18, and 8 potential target sites on the begomovirus genomes. Among the non-host plants begomoviruses exhibit seven and six potential target sites for O. sativa, and P. trichocarpa-derived miRNAs respectively. Begomovirus ORFs encoding viral movement proteins reveal greater vulnerability for G. max-derived miRNA binding and repression. Computational analysis with ssDNA animal virus genome as negative control sequences further emphasizes that plant miRNAs preferentially target begomovirus genomes. Nine prospective soybean-derived miRNAs targeting begomovirus genes have been shown to play a role in host-microbe interactions and abiotic stress responsiveness. The study thus provides in silico evidence for the plant-derived miRNAs in antiviral immunity.

Keywords


Antiviral Resistance, Begomovirus, Micro-RNA, Soybean.

References





DOI: https://doi.org/10.18520/cs%2Fv110%2Fi3%2F424-428