Phylogeographic analysis of the full genome of Sweepovirus to trace virus dispersal and introduction to Korea

Kim, Jaedeok; Kwak, Hae-Ryun; Kim, Mi-Kyeong; Seo, Jang‐Kyun; Yang, Jung Wook; Chung, Mi-Nam; Kil, Eui-Joon; Choi, Hyun-Sug; Lee, Sukchan

doi:10.1371/journal.pone.0202174

Cited by 3 publications

(3 citation statements)

References 40 publications

(51 reference statements)

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“…In addition, SPLCV also exhibited a high frequency of mutations of up to 4.52%. Similarly, several Korean SPLCV recombinants have been identified 13 . Thus, our result suggests that mutation and recombination contribute to the genetic diversity of SPFMV and SPLCV isolates.…”

Section: Discussionmentioning

confidence: 99%

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Sweet potato viromes in eight different geographical regions in Korea and two different cultivars

Kim

Choi

et al. 2020

Sci Rep

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The sweet potato in the family Convolvulaceae is a dicotyledonous perennial plant. Here, we conducted a comprehensive sweet potato virome study using 10 different libraries from eight regions in Korea and two different sweet potato cultivars by RNA-Sequencing. Comprehensive bioinformatics analyses revealed 10 different virus species infecting sweet potato. Moreover, we identified two novel viruses infecting sweet potato referred to as Sweet potato virus E (SPVE) in the genus Potyvirus and Sweet potato virus F (SPVF) in the genus Carlavirus. Of the identified viruses, Sweet potato feathery mottle virus (SPFMV) was the dominant virus followed by Sweet potato virus C (SPVC) and SPVE in Korea. We obtained a total of 30 viral genomes for eight viruses. Our phylogenetic analyses showed many potyvirus isolates are highly correlated with geographical regions. However, two isolates of SPFMV and a single isolate of Sweet potato virus G (SPVG) were genetically distant from other known isolates. The mutation rate was the highest in SPFMV followed by SPVC and SPVG. Two different sweet potato cultivars, Beni Haruka and Hogammi, were infected by seven and five viruses, respectively. Taken together, we provide a complete list of viruses infecting sweet potato in Korea and diagnostic methods. The sweet potato [Ipomoea batatas (L.) Lam] is a dicotyledonous perennial plant and a member of the family Convolvulaceae. It is currently widely grown in tropical and temperate regions in the world 1. The sweet potato is regarded as one of the most healthful foods in the world due to its high amounts of beta-carotene, carbohydrates, and dietary fiber and diverse micronutrients 2,3. It is a very fast-growing vine plant and is usually vegetatively propagated by cutting a piece of a runner of sweet potato approximately 30 cm in length 4. According to the FAO, in 2017, China was the largest sweet potato producer (72,031,782 tons), followed by several African countries, such as Malawi (5,472,013 tons), the United Republic of Tanzania (4,244,370 tons), and Nigeria (4,013,786 tons). In Korea, the sweet potato has been cultivated since the end of the 18th century, and it is the third most important crop plant in South Korea based on production (331,514 tons) 5. In general, the tuberous roots and stems of the sweet potato are used as different food materials in Korea. Due to their vegetative propagation, most sweet potato cultivars are severely infected by various pathogens. Of the known pathogens, more than 30 different viruses infecting sweet potato have been identified so far 6. The most frequently identified viruses are DNA viruses such as Sweet potato leaf curl virus (SPLCV) in the genus Begomovirus in the family Geminiviridae, followed by RNA viruses in the family Potyviridae 7. Examples of well-known RNA viruses infecting sweet potato include Sweet potato feathery mottle virus (SPFMV), Sweet potato virus C (SPVC), Sweet potato virus G (SPVG), Sweet potato virus 2 (SPV2), Sweet potato latent virus (SPLV), and Sweet potato mild mottle virus (SP...

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Section: Discussionmentioning

confidence: 99%

“…In Korea, several studies have examined viruses infecting sweet potato [13][14][15][16] . According to the previous studies, many sweet potato germplasm collections and sweet potato cultivars grown in fields in Korea are often coinfected by different viruses 14 .…”

mentioning

confidence: 99%

Sweet potato viromes in eight different geographical regions in Korea and two different cultivars

Kim

Choi

et al. 2020

Sci Rep

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“…2014 ; Duchatel, Bronsvoort, and Lycett 2019 ), and plant ( Trovão et al. 2015 ; Kim et al. 2018 ) populations.…”

Section: Introductionmentioning

confidence: 99%

Accommodating sampling location uncertainty in continuous phylogeography

et al. 2022

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Phylogeographic inference of the dispersal history of viral lineages offers key opportunities to tackle epidemiological questions about the spread of fast-evolving pathogens across human, animal, and plant populations. In continuous space, i.e. when locations are specified by longitude and latitude, these reconstructions are however often limited by the availability or accessibility of precise sampling locations required for such spatially-explicit analyses. We here review the different approaches that can be considered when genomic sequences are associated with a geographic area of sampling instead of precise coordinates. In particular, we describe and compare the approaches to define homogeneous and heterogeneous prior ranges of sampling coordinates.

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Molecular diversity of begomoviruses and DNA satellite molecules infecting ornamental plants in India

Marwal

Gaur

2020

Applied Plant Virology

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Phylogeographic analysis of the full genome of Sweepovirus to trace virus dispersal and introduction to Korea

Cited by 3 publications

References 40 publications

Sweet potato viromes in eight different geographical regions in Korea and two different cultivars

Sweet potato viromes in eight different geographical regions in Korea and two different cultivars

Accommodating sampling location uncertainty in continuous phylogeography

Molecular diversity of begomoviruses and DNA satellite molecules infecting ornamental plants in India

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