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10.3390/plants11233256
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Article

Phylogenetic and Phylodynamic Analyses of Soybean Mosaic Virus Using 305 Coat Protein Gene Sequences

by
Hoseong Choi
1,†,
Yeonhwa Jo
2,†,
Hyunjung Chung
3,
Soo Yeon Choi
3,
Sang-Min Kim
3,
Jin-Sung Hong
4,
Bong Choon Lee
3,* and
Won Kyong Cho
2,*
1
Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea
2
College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
3
Crop Foundation Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea
4
Department of Applied Biology, Kangwon National University, Chuncheon 24341, Republic of Korea
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Plants 2022, 11(23), 3256; https://doi.org/10.3390/plants11233256
Submission received: 18 October 2022 / Revised: 23 November 2022 / Accepted: 24 November 2022 / Published: 27 November 2022
(This article belongs to the Special Issue Trends and Prospects of Genetic and Molecular Research in Plant)
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Abstract

Soybean mosaic virus (SMV) of the family Potyviridae is the most devastating virus that infects soybean plants. In this study, we obtained 83 SMV coat protein (CP) sequences from seven provinces in Korea using RT-PCR and Sanger sequencing. Phylogenetic and haplotype analyses revealed eight groups of 83 SMV isolates and a network of 50 SMV haplotypes in Korea. The phylogenetic tree using 305 SMV CP sequences available worldwide revealed 12 clades that were further divided into two groups according to the plant hosts. Recombination rarely occurred in the CP sequences, while negative selection was dominant in the SMV CP sequences. Genetic diversity analyses revealed that plant species had a greater impact on the genetic diversity of SMV CP sequences than geographical origin or location. SMV isolates identified from Pinellia species in China showed the highest genetic diversity. Phylodynamic analysis showed that the SMV isolates between the two Pinellia species diverged in the year 1248. Since the divergence of the first SMV isolate from Glycine max in 1486, major clades for SMV isolates infecting Glycine species seem to have diverged from 1791 to 1886. Taken together, we provide a comprehensive overview of the genetic diversity and divergence of SMV CP sequences.
Keywords: coat protein; haplotype; population; soybean mosaic virus coat protein; haplotype; population; soybean mosaic virus

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MDPI and ACS Style

Choi, H.; Jo, Y.; Chung, H.; Choi, S.Y.; Kim, S.-M.; Hong, J.-S.; Lee, B.C.; Cho, W.K. Phylogenetic and Phylodynamic Analyses of Soybean Mosaic Virus Using 305 Coat Protein Gene Sequences. Plants 2022, 11, 3256. https://doi.org/10.3390/plants11233256

AMA Style

Choi H, Jo Y, Chung H, Choi SY, Kim S-M, Hong J-S, Lee BC, Cho WK. Phylogenetic and Phylodynamic Analyses of Soybean Mosaic Virus Using 305 Coat Protein Gene Sequences. Plants. 2022; 11(23):3256. https://doi.org/10.3390/plants11233256

Chicago/Turabian Style

Choi, Hoseong, Yeonhwa Jo, Hyunjung Chung, Soo Yeon Choi, Sang-Min Kim, Jin-Sung Hong, Bong Choon Lee, and Won Kyong Cho. 2022. "Phylogenetic and Phylodynamic Analyses of Soybean Mosaic Virus Using 305 Coat Protein Gene Sequences" Plants 11, no. 23: 3256. https://doi.org/10.3390/plants11233256

APA Style

Choi, H., Jo, Y., Chung, H., Choi, S. Y., Kim, S.-M., Hong, J.-S., Lee, B. C., & Cho, W. K. (2022). Phylogenetic and Phylodynamic Analyses of Soybean Mosaic Virus Using 305 Coat Protein Gene Sequences. Plants, 11(23), 3256. https://doi.org/10.3390/plants11233256

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