Prediction and experimental confirmation of banana bract mosaic virus encoding miRNAs and their targets

Ramamoorthy Sankaranarayanan,Sankara Naynar Palani,Jebasingh Tennyson,Punitha Selvakumar A S,Abhishek Kumar

doi:10.1186/s41544-019-0044-7

Ramamoorthy Sankaranarayanan, Sankara Naynar Palani + Show 3 more

Open Access

https://doi.org/10.1186/s41544-019-0044-7

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Abstract

BackgroundPotyviridae is the largest plant infecting family under the monophyletic group Riboviria, infects many of the food, fodder and ornamental crops. Due to the higher mutation and recombination rate, potyvirids are evolving rapidly, adapting to the environmental chaos and expanding their hosts. Virus control measures are need to be updated as the economic importance of potyvirids is massive. microRNAs (miRNAs) are well known for their functional importance in eukaryotes and many viruses. Regardless of its biogenesis, whether canonical or noncanonical, microRNA centric antivirus approaches attract the researchers to the hopeful future of next-generation broad-spectrum antiviral measures.MethodsIn this study, we predicted and screened banana bract mosaic virus (BBrMV) encoding miRNAs by computation approaches and their targets on banana transcriptome using plant small RNA target analysis server (psRNAtarget). The target gene functions were annotated by Blast2GO. The predicted BBrMV miRNAs were experimentally screened by stem-loop RT-PCR.ResultsThe results showed that, among the predicted BBrMV miRNAs, miRNA2 is conserved throughout BBrMV isolates and has multiple virus-specific target transcripts. In addition, primary experimental validation for the predicted miRNAs revealed that miRNA2 exists in the BBrMV infected banana leaf samples.ConclusionsThe existence of BBrMV miRNA2 is confirmed by stem-loop RT-PCR followed by cloning and sequencing. The presence of miRNA of Potyviridae is rarely addressed and would definitely spread the hope to understand the virus infectious cycle. Our report would also help to better understand and manipulate potyviral infections.

Highlights

Potyviridae is the largest plant infecting family under the monophyletic group Riboviria, infects many of the food, fodder and ornamental crops
Cumulative knowledge in the field of ‘ribogenomics’, sheds lights on the existence of dozens of non-coding RNA molecules and their functionality, especially miRNA [3]. miRNA is a small non-coding RNA of ~ 24 nt in length and are highly conserved in the plant kingdom [4]. miRNA plays an important role in posttranscriptional gene regulation by binding with its target mRNA, known as ‘RNA interference’
Prediction and annotation of banana bract mosaic virus (BBrMV) encoding miRNAs There were totally seven miRNAs predicted from BBrMV genome

Summary

Introduction

Potyviridae is the largest plant infecting family under the monophyletic group Riboviria, infects many of the food, fodder and ornamental crops. MicroRNAs (miRNAs) are well known for their functional importance in eukaryotes and many viruses. More than 30% of known plant viruses belong to this family They are infecting a wide verity of economically important plants growing on diverse environmental conditions [1]. Potyviral disease management often includes vector control, cross protections (infecting the plants with less virulent viruses to render immunity against severe strains) and develop transgenic resistant varieties. These routine control measures were less efficient and viruses (2020) 2:5 are quickly evolving to evade or suppress these stratagems due to their high mutation and recombination rates [2]. A network of miRNAmRNA interactions determines most of the physiological and developmental processes of a cell [8,9,10]

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