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

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 colle...

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Autores principales: Ohshima, Kazusato, Kawakubo, Shusuke, Muraoka, Satoshi, Gao, Fangluan, Ishimaru, Kanji, Kayashima, Tomoko, Fukuda, Shinji
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8692251/
https://www.ncbi.nlm.nih.gov/pubmed/34956155
http://dx.doi.org/10.3389/fmicb.2021.789596
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author Ohshima, Kazusato
Kawakubo, Shusuke
Muraoka, Satoshi
Gao, Fangluan
Ishimaru, Kanji
Kayashima, Tomoko
Fukuda, Shinji
author_facet Ohshima, Kazusato
Kawakubo, Shusuke
Muraoka, Satoshi
Gao, Fangluan
Ishimaru, Kanji
Kayashima, Tomoko
Fukuda, Shinji
author_sort Ohshima, Kazusato
collection PubMed
description 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.
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spelling pubmed-86922512021-12-23 Genomic Epidemiology and Evolution of Scallion Mosaic Potyvirus From Asymptomatic Wild Japanese Garlic Ohshima, Kazusato Kawakubo, Shusuke Muraoka, Satoshi Gao, Fangluan Ishimaru, Kanji Kayashima, Tomoko Fukuda, Shinji Front Microbiol Microbiology 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. Frontiers Media S.A. 2021-12-08 /pmc/articles/PMC8692251/ /pubmed/34956155 http://dx.doi.org/10.3389/fmicb.2021.789596 Text en Copyright © 2021 Ohshima, Kawakubo, Muraoka, Gao, Ishimaru, Kayashima and Fukuda. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Ohshima, Kazusato
Kawakubo, Shusuke
Muraoka, Satoshi
Gao, Fangluan
Ishimaru, Kanji
Kayashima, Tomoko
Fukuda, Shinji
Genomic Epidemiology and Evolution of Scallion Mosaic Potyvirus From Asymptomatic Wild Japanese Garlic
title Genomic Epidemiology and Evolution of Scallion Mosaic Potyvirus From Asymptomatic Wild Japanese Garlic
title_full Genomic Epidemiology and Evolution of Scallion Mosaic Potyvirus From Asymptomatic Wild Japanese Garlic
title_fullStr Genomic Epidemiology and Evolution of Scallion Mosaic Potyvirus From Asymptomatic Wild Japanese Garlic
title_full_unstemmed Genomic Epidemiology and Evolution of Scallion Mosaic Potyvirus From Asymptomatic Wild Japanese Garlic
title_short Genomic Epidemiology and Evolution of Scallion Mosaic Potyvirus From Asymptomatic Wild Japanese Garlic
title_sort genomic epidemiology and evolution of scallion mosaic potyvirus from asymptomatic wild japanese garlic
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8692251/
https://www.ncbi.nlm.nih.gov/pubmed/34956155
http://dx.doi.org/10.3389/fmicb.2021.789596
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