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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Frontiers Media S.A.
2021-12-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2021.789596/full |
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| author | Kazusato Ohshima Kazusato Ohshima Kazusato Ohshima Shusuke Kawakubo Satoshi Muraoka Fangluan Gao Kanji Ishimaru Kanji Ishimaru Kanji Ishimaru Tomoko Kayashima Tomoko Kayashima Shinji Fukuda Shinji Fukuda Shinji Fukuda Shinji Fukuda |
| author_facet | Kazusato Ohshima Kazusato Ohshima Kazusato Ohshima Shusuke Kawakubo Satoshi Muraoka Fangluan Gao Kanji Ishimaru Kanji Ishimaru Kanji Ishimaru Tomoko Kayashima Tomoko Kayashima Shinji Fukuda Shinji Fukuda Shinji Fukuda Shinji Fukuda |
| author_sort | Kazusato Ohshima |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-14T04:29:14Z |
| format | Article |
| id | doaj.art-c6a7d6867d9c49f89ffc8d5347805580 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-14T04:29:14Z |
| publishDate | 2021-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-c6a7d6867d9c49f89ffc8d53478055802022-12-21T23:17:07ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2021-12-011210.3389/fmicb.2021.789596789596Genomic Epidemiology and Evolution of Scallion Mosaic Potyvirus From Asymptomatic Wild Japanese GarlicKazusato Ohshima0Kazusato Ohshima1Kazusato Ohshima2Shusuke Kawakubo3Satoshi Muraoka4Fangluan Gao5Kanji Ishimaru6Kanji Ishimaru7Kanji Ishimaru8Tomoko Kayashima9Tomoko Kayashima10Shinji Fukuda11Shinji Fukuda12Shinji Fukuda13Shinji Fukuda14Department of Biological Resource Science, Faculty of Agriculture, Saga University, Saga, JapanInstitute of Wild Onion Science, Saga University, Saga, JapanThe United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, JapanDepartment of Biological Resource Science, Faculty of Agriculture, Saga University, Saga, JapanDepartment of Biological Resource Science, Faculty of Agriculture, Saga University, Saga, JapanInstitute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, ChinaDepartment of Biological Resource Science, Faculty of Agriculture, Saga University, Saga, JapanInstitute of Wild Onion Science, Saga University, Saga, JapanThe United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, JapanInstitute of Wild Onion Science, Saga University, Saga, JapanDepartment of School Education Course, Faculty of Education, Saga University, Saga, JapanDepartment of Biological Resource Science, Faculty of Agriculture, Saga University, Saga, JapanInstitute of Wild Onion Science, Saga University, Saga, JapanThe United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, JapanSaga University Center for Education and Research in Agricultural Innovation, Faculty of Agriculture, Saga University, Saga, JapanScallion 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.https://www.frontiersin.org/articles/10.3389/fmicb.2021.789596/fullscallion mosaic viruspotyvirusturnip mosaic virus phylogenetic groupevolutionepidemiologyrecombination |
| spellingShingle | Kazusato Ohshima Kazusato Ohshima Kazusato Ohshima Shusuke Kawakubo Satoshi Muraoka Fangluan Gao Kanji Ishimaru Kanji Ishimaru Kanji Ishimaru Tomoko Kayashima Tomoko Kayashima Shinji Fukuda Shinji Fukuda Shinji Fukuda Shinji Fukuda Genomic Epidemiology and Evolution of Scallion Mosaic Potyvirus From Asymptomatic Wild Japanese Garlic Frontiers in Microbiology scallion mosaic virus potyvirus turnip mosaic virus phylogenetic group evolution epidemiology recombination |
| 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 | scallion mosaic virus potyvirus turnip mosaic virus phylogenetic group evolution epidemiology recombination |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2021.789596/full |
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