In silico analysis of chili encoded miRNAs targeting Chili leaf curl begomovirus and its associated satellite

Mishra, Megha; Kumar, Rajesh; Gaur, Rajarshi Kumar; Verma, Rakesh Kumar

doi:10.7324/jabb.2020.80101

Cited by 5 publications

(4 citation statements)

References 25 publications

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“…A lower (more negative) ΔG suggests a stronger and more stable interaction ( Bernhart et al, 2006 ). A complete complementary between miRNA-mRNA sequences leads to cleavage of the targeted mRNA, while partial complementary typically decreases gene expression by suppressing translation of target mRNA ( Mishra et al, 2020 ).…”

Section: Resultsmentioning

confidence: 99%

In silico identification of papaya genome-encoded microRNAs to target begomovirus genes in papaya leaf curl disease

Srivastava,

Pandey,

Singh

et al. 2024

Front. Microbiol.

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Papaya leaf curl disease (PaLCuD) is widespread and classified in the genus begomovirus (Geminiviridae), disseminated by the vector whitefly Bemisia tabaci. RNA interference (RNAi)-based antiviral innate immunity stands as a pivotal defense mechanism and biological process in limiting viral genomes to manage plant diseases. The current study aims to identify and analyze Carica Papaya locus-derived capa-microRNAs with predicted potential for targeting divergent begomovirus species-encoded mRNAs using a ‘four integrative in silico algorithms’ approach. This research aims to experimentally activate the RNAi catalytic pathway using in silico-predicted endogenous capa-miRNAs and create papaya varieties capable of assessing potential resistance against begomovirus species and monitoring antiviral capabilities. This study identified 48 predicted papaya locus-derived candidates from 23 miRNA families, which were further investigated for targeting begomovirus genes. Premised all the four algorithms combined, capa-miR5021 was the most anticipated miRNA followed by capa-miR482, capa-miR5658, capa-miR530b, capa-miR3441.2, and capa-miR414 ‘effective’ papaya locus-derived candidate capa-miRNA and respected putative binding sites for targets at the consensus nucleotide position. It was predicted to bind and target mostly to AC1 gene of the complementary strand and the AV1 gene of the virion strand of different begomovirus isolates, which were associated with replication-associated protein and encapsidation, respectively, during PaLCuD. These miRNAs were also found targeting betaC1 gene of betasatellite which were associated with retardation in leaf growth and developmental abnormalities with severe symptoms during begomovirus infection. To validate target prediction accuracy, we created an integrated Circos plot for comprehensive visualization of host–virus interaction. In silico-predicted papaya genome-wide miRNA-mediated begomovirus target gene regulatory network corroborated interactions that permit in vivo analysis, which could provide biological material and valuable evidence, leading to the development of begomovirus-resistant papaya plants. The integrative nature of our research positions it at the forefront of efforts to ensure the sustainable cultivation of papaya, particularly in the face of evolving pathogenic threats. As we move forward, the knowledge gained from this study provides a solid foundation for continued exploration and innovation in the field of papaya virology, and to the best of our knowledge, this study represents a groundbreaking endeavor, undertaken for the first time in the context of PaLCuD research.

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Section: Resultsmentioning

confidence: 99%

In silico identification of papaya genome-encoded microRNAs to target begomovirus genes in papaya leaf curl disease

Srivastava,

Pandey,

Singh

et al. 2024

Front. Microbiol.

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“…The PTGS strategy of RNAi through dsRNA results in the biogenesis of target-specific 21-24 nt small RNAs which governs begomovirus resistance in transgenic chili plants. Mishra et al ( 2020a ) identified chili miRNAs specific to essential genes of the ChiLCV through computational methods. They have predicted chili-encoded miRNAs targeting CP (V1) and Rep (C1) genes that could be used for silencing against ChiLCV infection.…”

Section: Advanced Methodsmentioning

confidence: 99%

An Overview of Chili Leaf Curl Disease: Molecular Mechanisms, Impact, Challenges, and Disease Management Strategies in Indian Subcontinent

et al. 2022

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Leaf curl disease in a chili plant is caused mainly by Chili leaf curl virus (ChiLCV) (Family: Geminiviridae, Genus: Begomovirus). ChiLCV shows a widespread occurrence in most of the chili (Capsicum spp.) growing regions. ChiLCV has a limited host range and infects tomatoes (Solanum lycopersicum), potatoes (S. tuberosum), and amaranth (Amaranthus tricolor). The virus genome is a monopartite circular single-stranded DNA molecule of 2.7 kb and associated with α and β-satellites of 1.3 and 1.4 kb, respectively. The virus genome is encapsulated in distinct twinned icosahedral particles of around 18–30 nm in size and transmitted by Bemisia tabaci (Family: Aleyrodidae, Order: Hemiptera). Recently, bipartite begomovirus has been found to be associated with leaf curl disease. The leaf curl disease has a widespread distribution in the major equatorial regions viz., Australia, Asia, Africa, Europe, and America. Besides the PCR, qPCR, and LAMP-based detection systems, recently, localized surface-plasmon-resonance (LPSR) based optical platform is used for ChiLCV detection in a 20–40 μl of sample volume using aluminum nanoparticles. Management of ChiLCV is more challenging due to the vector-borne nature of the virus, therefore integrated disease management strategies need to be followed to contain the spread and heavy crop loss. CRISPR/Cas-mediated virus resistance has gained importance in disease management of DNA and RNA viruses due to certain advantages over the conventional approaches. Therefore, CRISPR/Cas system-mediated resistance needs to be explored in chili against ChiLCV.

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“…The amiRNA approach has been deployed to develop resistance against cotton leaf curl burewala virus (CLCuD) in cotton and jatropha leaf curl gujarat virus (JLCuGV) in tobacco (Swetha et al, 2018;More et al, 2021). Recently, Mishra et al (2020b) predicted potential mir-miRNAs through in silico analysis, and found some with high sequence similarity to the V1 coat protein and C1 (Rep) genes of ChiLCV, which could be used in the future as a target in amiRNA in chilli. These studies help in understanding the viral gene expression and regulation by host miRNAs that could pave a way into design strategies for defense against ChiLCV infection.…”

Section: Gene Silencingmentioning

confidence: 99%

Current status, breeding strategies and future prospects for managing chilli leaf curl virus disease and associated begomoviruses in Chilli (Capsicum spp.)

Nalla,

Schafleitner,

Pappu

et al. 2023

Front. Plant Sci.

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Chilli leaf curl virus disease caused by begomoviruses, has emerged as a major threat to global chilli production, causing severe yield losses and economic harm. Begomoviruses are a highly successful and emerging group of plant viruses that are primarily transmitted by whiteflies belonging to the Bemisia tabaci complex. The most effective method for mitigating chilli leaf curl virus disease losses is breeding for host resistance to Begomovirus. This review highlights the current situation of chilli leaf curl virus disease and associated begomoviruses in chilli production, stressing the significant issues that breeders and growers confront. In addition, the various breeding methods used to generate begomovirus resistant chilli cultivars, and also the complicated connections between the host plant, vector and the virus are discussed. This review highlights the importance of resistance breeding, emphasising the importance of multidisciplinary approaches that combine the best of traditional breeding with cutting-edge genomic technologies. subsequently, the article highlights the challenges that must be overcome in order to effectively deploy begomovirus resistant chilli varieties across diverse agroecological zones and farming systems, as well as understanding the pathogen thus providing the opportunities for improving the sustainability and profitability of chilli production.

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In silico analysis of chili encoded miRNAs targeting Chili leaf curl begomovirus and its associated satellite

Cited by 5 publications

References 25 publications

In silico identification of papaya genome-encoded microRNAs to target begomovirus genes in papaya leaf curl disease

In silico identification of papaya genome-encoded microRNAs to target begomovirus genes in papaya leaf curl disease

An Overview of Chili Leaf Curl Disease: Molecular Mechanisms, Impact, Challenges, and Disease Management Strategies in Indian Subcontinent

Current status, breeding strategies and future prospects for managing chilli leaf curl virus disease and associated begomoviruses in Chilli (Capsicum spp.)

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