Identification of Viruses Infecting Oats in Korea by Metatranscriptomics.

Na-Kyeong Kim,Hyo-Jeong Lee,Rae-Dong Jeong,Sang-Min Kim

doi:10.3390/plants11030256

Abstract

Controlling infectious plant viruses presents a constant challenge in agriculture. As a source of valuable nutrients for human health, the cultivation of oats (Avena sativa L.) has recently been increased in Korea. To date, however, few studies have been undertaken to identify the viruses infecting oats in this country. In this study, we carried out RNA-sequencing followed by bioinformatics analyses to understand the virosphere in six different geographical locations in Korea where oats are cultivated. We identified three different virus species, namely, barley yellow dwarf virus (BYDV) (BYDV-PAV and BYDV-PAS), cereal yellow dwarf virus (CYDV) (CYDV-RPS and CYDV-RPV), and rice black-streaked dwarf virus (RBSDV). Based on the number of virus-associated reads and contigs, BYDV-PAV was a dominant virus infecting winter oats in Korea. Interestingly, RBSDV was identified in only a single region, and this is the first report of this virus infecting oats in Korea. Single nucleotide polymorphisms analyses indicated that most BYDV, CYDV, and RBSDV isolates show considerable genetic variations. Phylogenetic analyses indicated that BYDVs and CYDVs were largely grouped in isolates from Asia and USA, whereas RBSDV was genetically similar to isolates from China. Overall, the findings of this study provide a preliminary characterization of the types of plant viruses infecting oats in six geographical regions of Korea.

Highlights

Plant viruses cause significant yield reduction and economic losses in many crops worldwide
Various detection assays such as polymerase chain reaction (PCR), quantitative real time polymerase chain reaction, enzyme-linked immunosorbent assay, and loop-mediated isothermal amplification can be conducted for specific viral diseases, given prior knowledge of the sequence or antibody
To examine viruses infecting oat plants, we collected 323 oat samples from plantations located in six different regions of Korea from March to June 2020 (Table 1 and Figure 1a)

Summary

Introduction

Plant viruses cause significant yield reduction and economic losses in many crops worldwide. CYDV (CYDV-RPV and CYDV-RPS) encode a P0 viral suppressor of RNA silencing that is not seen in BYDV [20], and these viruses, which can have severe effect on wheat growth, are the most commonly reported species [21] Various detection assays such as polymerase chain reaction (PCR), quantitative real time polymerase chain reaction, enzyme-linked immunosorbent assay, and loop-mediated isothermal amplification can be conducted for specific viral diseases, given prior knowledge of the sequence or antibody. Studies have identified unknown or novel viruses using RNA-sequencing for barley [30], apple [31], peach [32], sweet potato [27], garlic [33], and plum [34] Each of these studies described analyses in agricultural crops and showed the advantages of HTS technology for identifying coinfection of pathogens. We revealed viral communities in six different geographical regions of oat fields in Korea

Results

Viral Genome Assembly and Analyses of SNPs of Identified Viruses

Phylogenetic Analyses of Identifified Viruses

Sample Preparation

Transcriptome Assembly and Virus Identification

Viral Sequence Mapping and Genome Assembly