Transcriptomic Reprogramming, Alternative Splicing and RNA Methylation in Potato (Solanum tuberosum L.) Plants in Response to Potato Virus Y Infection

Glushkevich, Anna; Spechenkova, Nadezhda; Fesenko, Igor; Knyazev, Andrey; Samarskaya, Viktoriya; Калинина, Н. В.; Taliansky, Michael; Love, Andrew J.

doi:10.3390/plants11050635

Cited by 17 publications

(14 citation statements)

References 107 publications

(154 reference statements)

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“…Identifying key candidate genes related to growth and development can provide target gene resources for molecular breeding. Previous literatures have studied the mechanisms of potato cold resistance [21], disease resistance [22], and nitrogen utilization [8] through transcriptome approach. The mechanisms involved in the growth and development of autotetraploid potato, however, are extremely complex, gene expression changes in multiple metabolic pathways occur at different developmental stages.…”

Section: Discussionmentioning

confidence: 99%

WGCNA Identifies a Comprehensive Gene Co-Expression Network Associated with Development in autotetraploid potato tissues

Li¹,

Wang²,

Wang³

2023

Preprint

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The formation and development of potato tissues and organs is a complex process regulated by a variety of genes and environmental factors. However, the regulatory mechanisms underlying the growth and development are still unclear. In this study, we used autotetraploid potato JC14 as experimental subject to analyze the transcriptome of root, stem and leaf at seedling, tuber formation and tuber expansion stages to explore the spatio-temporal expression pattern of genes and genetic development characteristics. The results identified thousands of differentially expressed genes and KEGG pathway enrichment analysis showed that these genes were mainly involved in defense response and carbohydrate metabolism pathways. A total of 12 co-expressed Gene modules were identified by Weighted Gene Co-expression Network Analysis (WGCNA), and 4 modules were screened out with the highest correlation with potato stem developmental traits. Core genes in the network were further investigated and functionally annotated by computing the connectivity of genes within the module. The results unveiled number of hub genes in stems at different developmental stages, including carbohydrate metabolism related genes, the defense response related genes, and transcription factors. These findings provide important leads for further understanding of the molecular regulation and genetic mechanisms of potato tissue development.

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Section: Discussionmentioning

confidence: 99%

WGCNA Identifies a Comprehensive Gene Co-Expression Network Associated with Development in autotetraploid potato tissues

Li¹,

Wang²,

Wang³

2023

Preprint

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“…According to these changes, PAR accumulation was significantly increased upon PVY infection compared to non-infected plants. It is thus conceivable to suggest that the PVY–plant interactions are at least partially regulated by PARylation functions [ 39 ].…”

Section: Parylation and Plant–virus Interactions: What Is Already Known?mentioning

confidence: 99%

ADP-Ribosylation and Antiviral Resistance in Plants

Spechenkova

Калинина

Завриев

et al. 2023

Viruses

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ADP-ribosylation (ADPRylation) is a versatile posttranslational modification in eukaryotic cells which is involved in the regulation of a wide range of key biological processes, including DNA repair, cell signalling, programmed cell death, growth and development and responses to biotic and abiotic stresses. Members of the poly(ADP-ribosyl) polymerase (PARP) family play a central role in the process of ADPRylation. Protein targets can be modified by adding either a single ADP-ribose moiety (mono(ADP-ribosyl)ation; MARylation), which is catalysed by mono(ADP-ribosyl) transferases (MARTs or PARP “monoenzymes”), or targets may be decorated with chains of multiple ADP-ribose moieties (PARylation), via the activities of PARP “polyenzymes”. Studies have revealed crosstalk between PARylation (and to a lesser extent, MARylation) processes in plants and plant–virus interactions, suggesting that these tight links may represent a novel factor regulating plant antiviral immunity. From this perspective, we go through the literature linking PARylation-associated processes with other plant regulation pathways controlling virus resistance. Once unraveled, these links may serve as the basis of innovative strategies to improve crop resistance to viruses under challenging environmental conditions which could mitigate yield losses.

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“…During splicing in potato ( Solanum tuberosum L .) to address Potato Virus Y infection, two WRKY transcription factors upregulate splice isoforms retained by introns during plant stress (Glushkevich et al, 2022). PMV and SPMV are both single‐stranded, positive‐sense RNA viruses.…”

Section: Plant Viruses and Effects On Host Alternative Splicingmentioning

confidence: 99%

Eukaryotic splicing machinery in the plant–virus battleground

Das

Aslam

et al. 2023

WIREs RNA

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Plant virual infections are mainly caused by plant‐virus parasitism which affects ecological communities. Some viruses are highly pathogen specific that can infect only specific plants, while some can cause widespread harm, such as tobacco mosaic virus (TMV) and cucumber mosaic virus (CMV). After a virus infects the host, undergoes a series of harmful effects, including the destruction of host cell membrane receptors, changes in cell membrane components, cell fusion, and the production of neoantigens on the cell surface. Therefore, competition between the host and the virus arises. The virus starts gaining control of critical cellular functions of the host cells and ultimately affects the fate of the targeted host plants. Among these critical cellular processes, alternative splicing (AS) is an essential posttranscriptional regulation process in RNA maturation, which amplify host protein diversity and manipulates transcript abundance in response to plant pathogens. AS is widespread in nearly all human genes and critical in regulating animal‐virus interactions. In particular, an animal virus can hijack the host splicing machinery to re‐organize its compartments for propagation. Changes in AS are known to cause human disease, and various AS events have been reported to regulate tissue specificity, development, tumour proliferation, and multi‐functionality. However, the mechanisms underlying plant–virus interactions are poorly understood. Here, we summarize the current understanding of how viruses interact with their plant hosts compared with humans, analyze currently used and putative candidate agrochemicals to treat plant‐viral infections, and finally discussed the potential research hotspots in the future.This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing

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Transcriptomic Reprogramming, Alternative Splicing and RNA Methylation in Potato (Solanum tuberosum L.) Plants in Response to Potato Virus Y Infection

Cited by 17 publications

References 107 publications

WGCNA Identifies a Comprehensive Gene Co-Expression Network Associated with Development in autotetraploid potato tissues

WGCNA Identifies a Comprehensive Gene Co-Expression Network Associated with Development in autotetraploid potato tissues

ADP-Ribosylation and Antiviral Resistance in Plants

Eukaryotic splicing machinery in the plant–virus battleground

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