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Kim J, Kwak HR, Kim M, Seo JK, Yang JW, Chung MN, Kil EJ, Choi HS, Lee S. Phylogeographic analysis of the full genome of Sweepovirus to trace virus dispersal and introduction to Korea. PLoS One 2018; 13:e0202174. [PMID: 30102735 PMCID: PMC6089449 DOI: 10.1371/journal.pone.0202174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 07/26/2018] [Indexed: 01/04/2023] Open
Abstract
Sweet potato is a vegetatively propagated crop that is produced for both growth in Korean fields and for export out of the country. The viruses that are present in introduced sweet potatoes can spread both domestically and to foreign countries. Determining the time and path of virus movement could help curtail its spread and prevent future dispersal of related viruses. Determining the consequences of past virus and sweet potato dispersal could provide insight into the ecological and economic risks associated with other sweet potato-infecting viral invasions. We therefore applied Bayesian phylogeographic inferences and recombination analyses of the available Sweepovirus sequences (including 25 Korean Sweepovirus genomes) and reconstructed a plausible history of Sweepovirus diversification and movement across the globe. The Mediterranean basin and Central America were found to be the launchpad of global Sweepovirus dispersal. Currently, China and Brazil are acting as convergence regions for Sweepoviruses. Recently reported Korean Sweepovirus isolates were introduced from China in a recent phase and the regions around China and Brazil continue to act as centers of Sweepovirus diversity and sites of ongoing Sweepovirus evolution. The evidence indicates that the region is an epidemiological hotspot, which suggests that novel Sweepovirus variants might be found.
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Affiliation(s)
- Jaedeok Kim
- Crop Protection Division, National Institute of Agricultural Science, Wanju, Korea
- Department of Genetic Engineering, Sungkyunkwan University, Suwon, Korea
| | - Hae-Ryun Kwak
- Crop Protection Division, National Institute of Agricultural Science, Wanju, Korea
| | - Mikyeong Kim
- Crop Protection Division, National Institute of Agricultural Science, Wanju, Korea
| | - Jang-Kyun Seo
- Graduate school of International Agricultural Technology, Seoul National University, Pyeongchang, Korea
| | - Jung Wook Yang
- Bioenergy Crop Research Institute, National Institute of Crop Science, Muan, Korea
| | - Mi-Nam Chung
- Research Policy Bureau, Rural Development Administration, Jeonju, Korea
| | - Eui-Joon Kil
- Department of Genetic Engineering, Sungkyunkwan University, Suwon, Korea
| | - Hong-Soo Choi
- Crop Protection Division, National Institute of Agricultural Science, Wanju, Korea
| | - Sukchan Lee
- Department of Genetic Engineering, Sungkyunkwan University, Suwon, Korea
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Kim J, Yang JW, Kwak HR, Kim MK, Seo JK, Chung MN, Lee HU, Lee KB, Nam SS, Kim CS, Lee GS, Kim JS, Lee S, Choi HS. Virus Incidence of Sweet Potato in Korea from 2011 to 2014. THE PLANT PATHOLOGY JOURNAL 2017; 33:467-477. [PMID: 29018310 PMCID: PMC5624489 DOI: 10.5423/ppj.oa.08.2016.0167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 06/03/2017] [Accepted: 06/06/2017] [Indexed: 06/07/2023]
Abstract
A nationwide survey was performed to investigate the current incidence of viral diseases in Korean sweet potatoes for germplasm and growing fields from 2011 to 2014. A total of 83.8% of the germplasm in Korea was infected with viruses in 2011. Commercial cultivars that were used to supply growing fields were infected at a rate of 62.1% in 2012. Among surveyed viruses, the incidence of five Potyvirus species that infect sweet potato decreased between 2012 and 2013, and then increased again in 2014. Representatively, the incidence of Sweet potato feathery mottle virus (SPFMV) was 87.0% in 2012, 20.7% in 2013 and then increased to 35.3% in 2014. Unlike RNA viruses, DNA viruses were shown to decrease continuously. The incidence of Sweet potato leaf curl virus (SPLCV) was 5.5% in 2003, 59.5% in 2011, and 47.4% in 2012. It then decreased continuously year by year to 33.2% in 2013, and then 25.6% in 2014. While the infection rate of each virus species showed a tendency to decline, the virus infection status was more variable in 2013 and 2014. Nevertheless, the high rate of single infections and mixed infection combinations were more variable than the survey results from 2012. As shown in the results from 2013, the most prevalent virus infection was a single infection at 27.6%, with the highest rate of infection belonging to sweet potato symptomless virus-1 (SPSMV-1) (12.9%). Compared to 2013, infection combinations were more varied in 2014, with a total of 122 kinds of mixed infection.
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Affiliation(s)
- Jaedeok Kim
- Crop Protection Division, National Academy of Agricultural Science, Wanju 55365,
Korea
- Department of Genetic Engineering, Sungkyunkwan University, Suwon 16419,
Korea
| | - Jung wook Yang
- Bioenergy Crop Research Institute, National Institute of Crop Science, Muan 58541,
Korea
| | - Hae-Ryun Kwak
- Crop Protection Division, National Academy of Agricultural Science, Wanju 55365,
Korea
| | - Mi-Kyeong Kim
- Crop Protection Division, National Academy of Agricultural Science, Wanju 55365,
Korea
| | - Jang-Kyun Seo
- Crop Protection Division, National Academy of Agricultural Science, Wanju 55365,
Korea
| | - Mi-Nam Chung
- Bioenergy Crop Research Institute, National Institute of Crop Science, Muan 58541,
Korea
| | - Hyeong-un Lee
- Bioenergy Crop Research Institute, National Institute of Crop Science, Muan 58541,
Korea
| | - Kyeong-Bo Lee
- Bioenergy Crop Research Institute, National Institute of Crop Science, Muan 58541,
Korea
| | - Sang Sik Nam
- Bioenergy Crop Research Institute, National Institute of Crop Science, Muan 58541,
Korea
| | - Chang-Seok Kim
- Crop Protection Division, National Academy of Agricultural Science, Wanju 55365,
Korea
| | - Gwan-Seok Lee
- Crop Protection Division, National Academy of Agricultural Science, Wanju 55365,
Korea
| | - Jeong-Soo Kim
- Plant Medicine Major, Department of Bioresource Sciences, Andong National University, Andong 36729,
Korea
| | - Sukchan Lee
- Department of Genetic Engineering, Sungkyunkwan University, Suwon 16419,
Korea
| | - Hong-Soo Choi
- Crop Protection Division, National Academy of Agricultural Science, Wanju 55365,
Korea
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Borah BK, Dasgupta I. PCR-RFLP analysis indicates that recombination might be a common occurrence among the cassava infecting begomoviruses in India. Virus Genes 2012; 45:327-32. [PMID: 22696049 DOI: 10.1007/s11262-012-0770-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 05/29/2012] [Indexed: 10/28/2022]
Abstract
Cassava mosaic disease (CMD) is caused in India by two bipartite begomoviruses, Indian cassava mosaic virus (ICMV), and Sri Lankan cassava mosaic virus (SLCMV). Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used as a rapid means of investigating the molecular diversity of ICMV and SLCMV in 38 samples of CMD-affected cassava plants under field conditions in new areas of cassava cultivation, along with traditional areas in southern India. A very large proportion of the samples showed SLCMV, based on a discriminatory PCR between SLCMV and ICMV, reported earlier. PCR-RFLP analysis of three regions of viral DNA indicated that in most samples, although the AC1 and the AV1 resembled SLCMV, as expected, the intergenic regions (binding site for host replication machinery) resembled ICMV more closely, indicating recombination events between ICMV and SLCMV. Results also indicate that the AC1 is more conserved within SLCMV compared to the AV1 gene.
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Affiliation(s)
- Basanta Kumar Borah
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Delhi 110021, India
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