Identification of Viruses Infecting Oats in Korea by Metatranscriptomics

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.

Analysis of Wheat Virome in Korea Using Illumina and Oxford Nanopore Sequencing Platforms

“…BYDV is transmitted by the bird cherry-oat aphid ( Rhopalosiphum padi ) and is the most devastating cereal crop virus causing ~11 to 33% of yield loss in wheat fields worldwide [ 48 ]. BYDV infections have been reported in barley, oats, and wheat in Korea [ 43 , 49 ]. Our study identified infections with the BYDV strains PAS and PAV, while other strains, such as CYDV, were not detected.…”

Metatranscriptomic Analysis of Plant Viruses in Imported Pear and Kiwifruit Pollen

“…Thus, it has been introduced into more plant virome studies and diagnostic purposes ( Villamor et al, 2019 ). Virome studies on fruit trees using RNA-seq have been extensively employed in the past few years ( Jo et al, 2018a , 2020 ; Kim et al, 2022 ). However, few studies have been performed on the virome in fruit pollen samples ( Jonghe et al, 2018 ).…”

Pathogen Eradication in Garlic in the Phytobiome Context: Should We Aim for Complete Cleaning?

“…In this report, we employed a metatranscriptomic approach to identify endophyte taxa in garlic bulb tissues. This method has already enabled the identification of a high number of endophytes in the living plant tissues of other plants, e.g., grapes [ 28 ] and oats [ 29 ]. Using RNA sequencing (RNASeq) to record expressed transcripts provides a closer look at active members of a plant’s microbiome [ 30 ].…”