Novel targets for engineering Physostegia chlorotic mottle and tomato brown rugose fruit virus-resistant tomatoes: in silico prediction of tomato microRNA targets

Gaafar, Yahya Z. A.; Ziebell, Heiko

doi:10.7717/peerj.10096

Cited by 20 publications

(14 citation statements)

References 103 publications

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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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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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“…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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“…Several studies have suggested the gene silencing of target viruses using host-delivered miRNAs using computational algorithms. Genome-wide identification and comprehensive analysis of highly potential candidate miRNA targets against plant viruses have therefore been discovered [32][33][34]. The current study was designed by an equal novel computational approach for predicting novel targets against SCYLV in order to combat Polereovirus infection in sugarcane cultivars.…”

Section: Discussionmentioning

confidence: 99%

Potential Targets for Evaluation of Sugarcane Yellow Leaf Virus Resistance in Sugarcane Cultivars: In silico Sugarcane miRNA and Target Network Prediction

Ashraf¹,

Feng²,

Shen³

et al. 2021

Preprint

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The Sugarcane yellow leaf virus (SCYLV) is associated with sugarcane yellow leaf disease (SCYLD) and is considered to be the most economically deleterious emerging pathogen that represents a potential threat and danger to sugarcane cultivation in China. Over the last two decades, high genetic diversity in the SCYLV genotypes was observed worldwide, with a greater chance of YLD incidence for sugarcane injury. SCYLV infection has significantly damaged its economic traits and is responsible for substantial losses in biomass production in sugarcane cultivars. This study aims to identify and comprehensively analyze sugarcane microRNAs (miRNAs) as therapeutic targets against SCYLV using plant miRNA prediction tools. Mature sugarcane miRNAs are retrieved and are used for hybridization of the SCYLV. A total of seven common sugarcane miRNAs were selected based on consensus genomic positions. The biologically significant, top ranked ssp-miR528 was consensually predicted to have a potentially unique hybridization site at nucleotide position 4162 for targeting the ORF5 of the SCYLV genome; this was predicted by all the algorithms used in this study. Then, the miRNA–mRNA regulatory network was generated using the Circos algorithm, which was used to predict novel targets. There are no acceptable commercial SCYLV-resistant sugarcane varieties available at present. Therefore, the predicted biological data offer valuable evidence for the generation of SCYLV-resistant sugarcane plants.

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Novel targets for engineering Physostegia chlorotic mottle and tomato brown rugose fruit virus-resistant tomatoes: in silico prediction of tomato microRNA targets

Cited by 20 publications

References 103 publications

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

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

Potential Targets for Evaluation of Sugarcane Yellow Leaf Virus Resistance in Sugarcane Cultivars: In silico Sugarcane miRNA and Target Network Prediction

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