Computational Biology and Machine Learning Approaches Identify Rubber Tree (Hevea brasiliensis Muell. Arg.) Genome Encoded MicroRNAs Targeting Rubber Tree Virus 1

Ashraf, Muhammad Aleem; Tariq, Hafiza Kashaf; Hu, Xiaowen; Khan, Jallat; Zou, Zhi

doi:10.3390/app122412908

Cited by 8 publications

(9 citation statements)

References 47 publications

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“…In our previous studies, we have investigated experimentally validated mature locus-derived microRNAs in the sugarcane genome, which were predicted to be targets of SCBGAV, SCYLV, and SCBV based on in silico criteria [37][38][39]. Several studies have identified complex host-virus interactions and have investigated miRNAs targeting plant viruses using an in silico approach [86][87][88][89][90][91][92]. miRNAs have emerged as novel endogenous targets for multiple levels of miRNA gene-level regulation [53,93,94].…”

Section: Discussionmentioning

confidence: 99%

In Silico Identification of Sugarcane Genome-Encoded MicroRNAs Targeting Sugarcane Mosaic Virus

Wenzhi,

Ashraf,

Ghaffar

et al. 2024

Microbiology Research

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Sugarcane mosaic virus (SCMV) (genus, Potyvirus; family, Potyviridae) is widespread, deleterious, and the most damaging pathogen of sugarcane (Saccharum officinarum L. and Saccharum spp.) that causes a substantial barrier to producing high sugarcane earnings. Sugarcane mosaic disease (SCMD) is caused by a single or compound infection of SCMV disseminated by several aphid vectors in a non-persistent manner. SCMV has flexuous filamentous particle of 700–750 nm long, which encapsidated in a positive-sense, single-stranded RNA molecule of 9575 nucleotides. RNA interference (RNAi)-mediated antiviral innate immunity is an evolutionarily conserved key biological process in eukaryotes and has evolved as an antiviral defense system to interfere with viral genomes for controlling infections in plants. 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 a predictive approach that involves five algorithms. The ultimate goal of this research is to mobilize the in silico- predicted endogenous sof-miRNAs/ssp-miRNAs to experimentally trigger the catalytic RNAi pathway and generate sugarcane cultivars to evaluate the potential antiviral resistance surveillance ability and capacity for SCMV. Experimentally validated mature sugarcane (S. officinarum, 2n = 8X = 80) and (S. spp., 2n = 100–120) sof-miRNA/ssp-miRNA sequences (n = 28) were downloaded from the miRBase database and aligned with the SCMV genome (KY548506). Among the 28 targeted mature locus-derived sof-miRNAs/ssp-miRNAs evaluated, one sugarcane miRNA homolog, sof-miR159c, was identified to have a predicted miRNA binding site, at nucleotide position 3847 of the SCMV genome targeting CI ORF. To verify the accuracy of the target prediction accuracy and to determine whether the sugarcane sof-miRNA/ssp-miRNA could bind the predicted SCMV mRNA target(s), we constructed an integrated Circos plot. A genome-wide in silico-predicted miRNA-mediated target gene regulatory network was implicated to validate interactions necessary to warrant in vivo analysis. The current work provides valuable computational evidence for the generation of SCMV-resistant sugarcane cultivars.

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Section: Discussionmentioning

confidence: 99%

In Silico Identification of Sugarcane Genome-Encoded MicroRNAs Targeting Sugarcane Mosaic Virus

Wenzhi,

Ashraf,

Ghaffar

et al. 2024

Microbiology Research

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“…The ICMV-Ker is a bipartite begomovirus that spread to India and nearby locales in Southeast Asia during the past two decades. Several studies have investigated potential endogenous host-plant mature microRNAs that may target plant viruses based on in silico criteria [ 69 , 70 , 71 , 72 , 73 , 74 , 75 , 76 , 77 ]. The miRNAs have evolved as key endogenous biomolecules for regulating gene expression.…”

Section: Discussionmentioning

confidence: 99%

In Silico Identification of Cassava Genome-Encoded MicroRNAs with Predicted Potential for Targeting the ICMV-Kerala Begomoviral Pathogen of Cassava

Ashraf

Ali

Brown

et al. 2023

Viruses

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Cassava mosaic disease (CMD) is caused by several divergent species belonging to the genus Begomovirus (Geminiviridae) transmitted by the whitefly Bemisia tabaci cryptic species group. In India and other parts of Asia, the Indian cassava mosaic virus-Kerala (ICMV-Ker) is an emergent begomovirus of cassava causing damage that results in reduced yield loss and tuber quality. Double-stranded RNA-mediated interference (RNAi) is an evolutionary conserved mechanism in eukaryotes and highly effective, innate defense system to inhibit plant viral replication and/or translation. The objective of this study was to identify and characterize cassava genome-encoded microRNAs (mes-miRNA) that are predicted to target ICMV-Ker ssDNA-encoded mRNAs, based on four in silico algorithms: miRanda, RNA22, Tapirhybrid, and psRNA. The goal is to deploy the predicted miRNAs to trigger RNAi and develop cassava plants with resistance to ICMV-Ker. Experimentally validated mature cassava miRNA sequences (n = 175) were downloaded from the miRBase biological database and aligned with the ICMV-Ker genome. The miRNAs were evaluated for base-pairing with the cassava miRNA seed regions and to complementary binding sites within target viral mRNAs. Among the 175 locus-derived mes-miRNAs evaluated, one cassava miRNA homolog, mes-miR1446a, was identified to have a predicted miRNA target binding site, at position 2053 of the ICMV-Ker genome. To predict whether the cassava miRNA might bind predicted ICMV-Ker mRNA target(s) that could disrupt viral infection of cassava plants, a cassava locus-derived miRNA–mRNA regulatory network was constructed using Circos software. The in silico-predicted cassava locus-derived mes-miRNA-mRNA network corroborated interactions between cassava mature miRNAs and the ICMV-Ker genome that warrant in vivo analysis, which could lead to the development of ICMV-Ker resistant cassava plants.

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“…In our previous studies, we have investigated experimentally validated sugarcane genome-encoded mature microRNAs that were predicted to target SCBGAV, SCYLV and SCBV based on in silico criteria [37][38][39]. Several studies have identified complex host-virus interactions and have investigated host-plant miRNAs targeting plant viruses using an in silico approach [97][98][99][100][101][102][103]. The miRNAs have evolved as novel endogenous targets for multiple layers of miRNA-gene level regulation [52,104,105].…”

Section: Discussionmentioning

confidence: 99%

The In Silico Sugarcane Genome-Encoded MicroRNA and Target Network Prediction for Targeting the SCMV

Ashraf¹,

Feng²,

Ghaffar³

et al. 2023

Preprint

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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.

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Computational Biology and Machine Learning Approaches Identify Rubber Tree (Hevea brasiliensis Muell. Arg.) Genome Encoded MicroRNAs Targeting Rubber Tree Virus 1

Cited by 8 publications

References 47 publications

In Silico Identification of Sugarcane Genome-Encoded MicroRNAs Targeting Sugarcane Mosaic Virus

In Silico Identification of Sugarcane Genome-Encoded MicroRNAs Targeting Sugarcane Mosaic Virus

In Silico Identification of Cassava Genome-Encoded MicroRNAs with Predicted Potential for Targeting the ICMV-Kerala Begomoviral Pathogen of Cassava

The In Silico Sugarcane Genome-Encoded MicroRNA and Target Network Prediction for Targeting the SCMV

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