Version 1
: Received: 19 May 2023 / Approved: 22 May 2023 / Online: 22 May 2023 (11:48:26 CEST)
Version 2
: Received: 8 June 2023 / Approved: 8 June 2023 / Online: 8 June 2023 (10:58:12 CEST)
How to cite:
Ashraf, M.A.; Feng, X.; Ghaffar, H.; Brown, J.K.; Shahid, I.; Yu, N.; Zhang, S. The In Silico Sugarcane Genome-Encoded MicroRNA and Target Network Prediction for Targeting the SCMV. Preprints2023, 2023051521. https://doi.org/10.20944/preprints202305.1521.v1
Ashraf, M.A.; Feng, X.; Ghaffar, H.; Brown, J.K.; Shahid, I.; Yu, N.; Zhang, S. The In Silico Sugarcane Genome-Encoded MicroRNA and Target Network Prediction for Targeting the SCMV. Preprints 2023, 2023051521. https://doi.org/10.20944/preprints202305.1521.v1
Ashraf, M.A.; Feng, X.; Ghaffar, H.; Brown, J.K.; Shahid, I.; Yu, N.; Zhang, S. The In Silico Sugarcane Genome-Encoded MicroRNA and Target Network Prediction for Targeting the SCMV. Preprints2023, 2023051521. https://doi.org/10.20944/preprints202305.1521.v1
APA Style
Ashraf, M.A., Feng, X., Ghaffar, H., Brown, J.K., Shahid, I., Yu, N., & Zhang, S. (2023). The In Silico Sugarcane Genome-Encoded MicroRNA and Target Network Prediction for Targeting the SCMV. Preprints. https://doi.org/10.20944/preprints202305.1521.v1
Chicago/Turabian Style
Ashraf, M.A., Naitong Yu and Shuzhen Zhang. 2023 "The In Silico Sugarcane Genome-Encoded MicroRNA and Target Network Prediction for Targeting the SCMV" Preprints. https://doi.org/10.20944/preprints202305.1521.v1
Abstract
Sugarcane mosaic virus (SCMV) is a deleterious pathogen which causes widespread Sugarcane mosaic disease (SCMD) and is classified in the genus Potyvirus (Potyviridae), disseminated by the aphid vector. RNA interference (RNAi)-mediated antiviral innate immunity is a key biological process and antiviral defence system to interfere with viral genomes for controlling plant pathogens. The current study aims to analyze sugarcane (Saccharum officinarum L. and Saccharum spp.) locus-derived microRNAs (sof-miRNAs/ssp-miRNAs) with predicted potential for targeting the SCMV +ssRNA-encoded mRNAs, using ‘five algorithms’ approach. The ultimate goal in this research is to mobilize the in silico endogenous predicted sof-miRNAs/ssp-miRNAs to trigger RNAi catalytic pathway experimentally and generate sugarcane cultivars for evaluating potential antiviral resistance monitoring capability and capacity for SCMV. Experimentally validated mature sugarcane (S. officinarum, 2n = 8X = 80) and (S. spp., 2n = 100-120) sof-miRNAs/ssp-miRNAs (n = 28) were acquired for alignment with the SCMV genome. Of the 28 targeting mature locus-derived sof-miRNAs/ssp-miRNAs investigated, one sugarcane miRNA homolog, sof-miR159c, was concluded to localize potential binding site at genomic nucleotide site 3847 targeting CL ORF of SCMV. In order to validate target prediction accuracy, whether the sugarcane sof-miRNA/ssp-miRNA might bind predicted SCMV mRNA target(s), we created an integrated Circos plot. Genome-wide in-silico-predicted miRNA-mediated target gene regulatory network validated interactions that warrant in vivo analysis. The current work provides valuable evidence and biological material for generating SCMV-resistant sugarcane varieties.
Keywords
potyvirus; in silico tools; sugarcane mosaic virus; miRNA; RNA interference
Subject
Biology and Life Sciences, Biology and Biotechnology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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