MicroRNAs regulate tolerance mechanisms in sugarcane (Saccharum spp.) under aluminum stress

Silva, Jóice de Oliveira Leite; Silva, Renan Gonçalves da; Nogueira, Lucas de Faria; Zingaretti, Sônia Marli

doi:10.1590/1984-70332021v21n1a5

Cited by 3 publications

(2 citation statements)

References 36 publications

(39 reference statements)

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“…RNAibased amiRNA constructs have been used in research to induce antiviral resistance in plants against plant viruses such as tomato [25,26], cucumber [27], rice [28], and cotton [29]. Mature miRNAs in the sugarcane genome have been predicted, identified, isolated, analyzed, and validated to evaluate host-virus interactions and gene regulation, and they have been associated with abiotic and biotic stresses [30][31][32][33][34][35][36][37][38][39][40]. Recently, experimental validations of 35 conserved mature locus-derived high-confidence sof-miRNAs/ssp-miRNAs in the sugarcane genome and further depositions in the miRBase database were reported.…”

Section: Introductionmentioning

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: Introductionmentioning

confidence: 99%

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

Wenzhi,

Ashraf,

Ghaffar

et al. 2024

Microbiology Research

View full text Add to dashboard Cite

show abstract

“…RNAi-based amiRNA construct has been deployed in research to create antiviral resistance in plants against plant viral species such as tomato [25,26], cucumber [27], rice [28] and cotton [29]. Mature miRNAs in sugarcane genome have been predicted, identified, isolated, analyzed, and validated for evaluation of host-virus interactions, gene regulation and was associated with abiotic and biotic stresses [30][31][32][33][34][35][36][37][38][39][40]. Recently, experimental validation of 35 conserved mature sugarcane genome-encoded, high-confidence sof-miRNAs/ssp-miRNAs and further deposition in the miRBase database were reported.…”

Section: Introductionmentioning

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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Comparative genome-wide characterization of salt responsive micro RNA and their targets through integrated small RNA and de novo transcriptome profiling in sugarcane and its wild relative Erianthus arundinaceus

Vignesh,

Mahadevaiah,

Selvamuthu

et al. 2023

3 Biotech

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MicroRNAs regulate tolerance mechanisms in sugarcane (Saccharum spp.) under aluminum stress

Cited by 3 publications

References 36 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

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

Comparative genome-wide characterization of salt responsive micro RNA and their targets through integrated small RNA and de novo transcriptome profiling in sugarcane and its wild relative Erianthus arundinaceus

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