Identifying and Predicting the Function of Long non-coding RNAs in the Expression Profile of PVY Infected Potato

Document Type : Research Paper

Authors

1 Ph.D. Student, Department of Plant Pathology, Faculty of Plant Production, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran

2 *Corresponding author. Associate Professor, Department of Plant Pathology, Faculty of Plant Production, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran.

3 Assistant Professor, Department of Plant Pathology, Faculty of Plant Production, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran

4 Associate Professor, Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran. E-mail address: ahmadvandra@gmail.com

5 Professor, Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.

6 Associate Professor, Department of Horticultural Sciences, Faculty of Plant Production, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran

Abstract

Objective
Potato Virus Y is one of the most important damaging and limiting factors of potato cultivation. Plants cope with harmful conditions by regulating the expressions of genes at different levels including transcription, post-transcription and translation, using stress tolerance or resistance mechanisms. Therefore, regulatory factors play a very important role in gene expression regulation under stress conditions. Long non-coding RNAs are one of the most important regulatory elements of genes. The present study was conducted with the aim of identifying lncRNAs and investigation of their expression changes in PVY infected potato plants.
Materials and methods
In this research CLC Genimic Workbench software was used for data analysis. After identifying lncRNAs, the genes affected by them were also analyzed. Then, Gene Ontology enrichment and KEGG pathway analysis were performed using STRING analysis and finally, the interactions between the identified lncRNAs and potato miRNAs were investigated.
Results
According to the obtained results, a total of 3742 sequences were identified as novel lncRNAs in PVY infected potato transcriptome, of which 769 were differentially expressed. So that 310 lncRNAs were down-regulated and 459 were up-regulated in potato in response to PVY infection. Gene Ontology analysis of co-expressed genes with identified lncRNAs show the vital role of these genes in various biological processes, biosynthesis of cellular components, protein complex formation and signal transduction. Also, genes involved in biological processes related to creating defense response against stress, hypersensitive reaction, trehalose metabolism, antiviral responses related to RNA silencing and signaling pathways to induce systemic resistance, were co-expressed with identified lncRNAs in this study. The results of co-expression network between lncRNAs and miRNAs showed interactions between 56 lncRNAs and 5 miRNAs. The most interaction was observed between lncRNAs with stumiR6024-3p.
Conclusions
Considering the interactions between examined lncRNAs and the genes involved in defense responses against stress, it is concluded that the expression changes of these lncRNAs are an important part of the response mechanism to viral disease. The obtained results can be a step towards a better understanding of lncRNAs and their function in the development of PVY tolerance and resistance cultivars.

Keywords

References

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Agricultural Biotechnology Journal
Volume 16, Issue 2
June 2024
Pages 109-130

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