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

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

doi:10.3389/fmicb.2021.789596

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

Front Microbiol. 2021 Dec 8:12:789596. doi: 10.3389/fmicb.2021.789596. eCollection 2021.

Authors

Kazusato Ohshima^{1

2

3}, Shusuke Kawakubo¹, Satoshi Muraoka¹, Fangluan Gao⁴, Kanji Ishimaru^{1

2

3}, Tomoko Kayashima^{2

5}, Shinji Fukuda^{1

2

3

6}

Affiliations

¹ Department of Biological Resource Science, Faculty of Agriculture, Saga University, Saga, Japan.
² Institute of Wild Onion Science, Saga University, Saga, Japan.
³ The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.
⁴ Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China.
⁵ Department of School Education Course, Faculty of Education, Saga University, Saga, Japan.
⁶ Saga University Center for Education and Research in Agricultural Innovation, Faculty of Agriculture, Saga University, Saga, Japan.

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.

Keywords: asymptomatic; epidemiology; evolution; potyvirus; recombination; scallion mosaic virus; turnip mosaic virus phylogenetic group; wild garlic plants.