Genomic Epidemiology and Evolution of Scallion Mosaic Potyvirus From Asymptomatic Wild Japanese Garlic.

Kazusato Ohshima,Shinji Fukuda,Fangluan Gao,Satoshi Muraoka,Tomoko Kayashima,Shusuke Kawakubo,Kanji Ishimaru

doi:10.3389/fmicb.2021.789596

Kazusato Ohshima, Shinji Fukuda + Show 5 more

Open Access

https://doi.org/10.3389/fmicb.2021.789596

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Abstract

Scallion mosaic virus (ScaMV) belongs to the turnip mosaic virus phylogenetic group of potyvirus and is known to infect domestic scallion plants (Allium chinense) in China and wild Japanese garlic (Allium macrostemon Bunge) in Japan. Wild Japanese garlic plants showing asymptomatic leaves were collected from different sites in Japan during 2012–2015. We found that 73 wild Japanese garlic plants out of 277 collected plants were infected with ScaMV, identified by partial genomic nucleotide sequences of the amplified RT-PCR products using potyvirus-specific primer pairs. Sixty-three ScaMV isolates were then chosen, and those full genomic sequences were determined. We carried out evolutionary analyses of the complete polyprotein-coding sequences and four non-recombinogenic regions of partial genomic sequences. We found that 80% of ScaMV samples have recombination-like genome structure and identified 12 recombination-type patterns in the genomes of the Japanese ScaMV isolates. Furthermore, we found two non-recombinant-type patterns in the Japanese population. Because the wild plants and weeds may often serve as reservoirs of viruses, it is important to study providing the exploratory investigation before emergence in the domestic plants. This is possibly the first epidemiological and evolutionary study of a virus from asymptomatic wild plants.

Highlights

It is important to investigate the virus populations in wild host plants before they spill over and start infecting domestic plants (Ohshima et al, 2010; Nguyen et al, 2013; Gibbs et al, 2015) because the wild plants and weeds may often serve as reservoirs of viruses
We found that the garlic plants were easier to collect in southern area of Japan but harder in Hokkaido Island, probably because the southern area might be suitable for the conditions of growing wild Japanese garlic plants
Our study presents the largest and most detailed epidemiological and evolutionary analyses of a virus from asymptomatic wild plants, highlighting the importance of such studies for exploratory investigation prior to the emergence of pathogens in domestic plants because the wild plants may often serve as reservoirs of viruses

Summary

Introduction

It is important to investigate the virus populations in wild host plants before they spill over and start infecting domestic plants (Ohshima et al, 2010; Nguyen et al, 2013; Gibbs et al, 2015) because the wild plants and weeds may often serve as reservoirs of viruses. There have been many studies of the molecular epidemiology and evolution of viruses infecting domestic plants (Ohshima et al, 2002; Seo et al, 2009; Lefeuvre et al, 2010; Ohshima et al, 2016b; Fuentes et al, 2019; Gao et al, 2020), but fewer for those infecting wild plants. Virus spillover is a complex and poorly understood process, characterizing the virus populations in wild host plants is very important

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