Biopolym. Cell. 2018; 34(3):229-238.
Genomics, Transcriptomics and Proteomics
Phylogenetic analysis of Ukrainian seed-transmitted isolate of Soybean mosaic virus
1Mishchenko L. T., 1Dunich A. A., 2Shcherbatenko I. S.
  1. Educational and Scientific Center "Institute of Biology and Medicine",
    Taras Shevchenko National University of Kyiv
    64/13, Volodymyrska Str., Kyiv, Ukraine, 01601
  2. D. K. Zabolotny Institute of Microbiology and Virology, NAS of Ukraine
    154, Academika Zabolotnogo Str., Kyiv, Ukraine, 03143

Abstract

Soybean mosaic virus (SMV) is seed transmitted and can cause significant reductions in the yield and seed quality in soybean (Glycine max). The seed transmission rate of different SMV isolates is 0–43 %. The question regarding SMV genes involved in the seed transmission of its isolates remains open. The phylogenetic studies of Ukrainian seed-transmitted SMV isolates have not been conducted. Aim. Phylogenetic analysis of the CP gene region of the SMV isolate, which has the ability to seed transmission. Methods. RNA extraction from plant material, RT-PCR, sequencing, phylogenetic analysis. Results. For the first time, the phylogenetic analysis of 430 nt CP gene sequence of seed-transmitted SMV isolate SKS-18 was performed. The highest level of the nucleotide sequences identity (98.8 %) and amino acid sequences (98.6 %), the isolate SKS-18 has with the Iranian isolates Ar33, Lo3, American isolate VA2, and Ukrainian isolate UA1Gr. Two unique amino acid substitutions (Ser→Cys at position 1 and Lys→Ala at position 2) in the studied CP gene region of SKS-18 are revealed. Conclusions. The isolate SKS-18 is localized in the same cluster with the isolates of the highest nucleotide identity, that may be due to their similar variability. Unique amino acid substitutions in the studied CP gene region of SKS-18 can be involved to its seed transmission and other important functions of the infectious cycle, the identification of which is necessary for the development of effective plant protection measures against viral diseases.
Keywords: Soybean mosaic virus, Glycine max, seed transmission, sequencing, phylogenetic analysis

References

[1] Hull R. Matthews’ Plant Virology, 4th edn. London: Academic Press, 2002; 1029 p.
[2] Domier LL, Steinlage TA, Hobbs HA, Wang Y, Herrera-Rodriguez G, Haudenshield JS, McCoppin NK, Hartman GL. Similarities in seed and aphid transmission among Soybean mosaic virus isolates. Plant Dis. 2007; 91(5):546-50.
[3] Jossey S, Hobbs HA, Domier LL. Role of soybean mosaic virus-encoded proteins in seed and aphid transmission in soybean. Phytopathology. 2013;103(9):941-8.
[4] Song Y, Li C, Zhao L, Karthikeyan A, Li N, Li K, Zhi H. Disease spread of a popular Soybean mosaic virus strain (SC7) in Southern China and effects on two susceptible soybean cultivars. Philippine Agricultural Scientist. 2016; 99(4):355-64.
[5] Bashar T. Characterization of seed transmission of Soybean mosaic virus in soybean. Electronic Thesis and Dissertation Repository. 2015; 105 p.
[6] Ahangaran A, Habibi MK, Mohammadi GH, Winter S, García-Arenal F. Analysis of Soybean mosaic virus genetic diversity in Iran allows the characterization of a new mutation resulting in overcoming Rsv4-resistance. J Gen Virol. 2013;94(Pt 11):2557-68.
[7] Eggenberger AL, Hajimorad MR, Hill JH. Gain of virulence on Rsv1-genotype soybean by an avirulent Soybean mosaic virus requires concurrent mutations in both P3 and HC-Pro. Mol Plant Microbe Interact. 2008;21(7):931-6.
[8] Zhou GC, Shao ZQ, Ma FF, Wu P, Wu XY, Xie ZY, Yu DY, Cheng H, Liu ZH, Jiang ZF, Chen QS, Wang B, Chen JQ. The evolution of soybean mosaic virus: An updated analysis by obtaining 18 new genomic sequences of Chinese strains/isolates. Virus Res. 2015;208:189-98.
[9] Seo JK, Ohshima K, Lee HG, Son M, Choi HS, Lee SH, Sohn SH, Kim KH. Molecular variability and genetic structure of the population of soybean mosaic virus based on the analysis of complete genome sequences. Virology. 2009;393(1):91-103.
[10] Domier LL, Latorre IJ, Steinlage TA, McCoppin N, Hartman GL. Variability and transmission by Aphis glycines of North American and Asian Soybean mosaic virus isolates. Arch Virol. 2003;148(10):1925-41.
[11] Jo Y, Choi H, Bae M, Kim SM, Kim SL, Lee BC, Cho WK, Kim KH. De novo Genome Assembly and Single Nucleotide Variations for Soybean Mosaic Virus Using Soybean Seed Transcriptome Data. Plant Pathol J. 2017;33(5):478-487.
[12] Sherepitko DV, Budzanivska IG, Polischuk VP, Boyko AL. Sequencing and phylogenetic analysis of Soybean mosaic virus isolated in Ukraine. Biopolym. Cell. 2011; 27(6):472–79.
[13] Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol. 2016;33(7):1870-4.
[14] Huelsenbeck JP, Rannala B. Maximum likelihood estimation of phylogeny using stratigraphic data. Paleobiology. 1997; 23(2):174-80.
[15] Korber B. HIV signature and sequence variation analysis. In: Computational analysis of HIV molecular sequences, Eds. Rodrigo AG, Learn GH. Dordrecht, Netherlands: Kluwer Academic Publishers, 2002. 55-72.
[16] Mishchenko LT, Polischuk VP, Molchanetc OV, Dunich AA Seed transmission of Soybean mosaic virus and its phylogenetic analysis. ScienceRise: Biological Science. 2016; 3(3):18-25.
[17] Jezewska M, Trzmiel K, Zarzyn´ska-Nowak A, Lewandowska M. Identification of Soybean mosaic virus in Poland. J Plant Pathol. 2015; 97(2):357-62.
[18] Kim W-S, Lim Y-H, Kim K-H. Complete genome sequences of the genomic RNA of Soybean mosaic virus strains G7H and G5. Plant Pathol J. 2003; 19(3):171–6.
[19] Seo JK, Lee HG, Choi HS, Lee SH, Kim KH. Infectious in vivo transcripts from a full-length clone of Soybean mosaic virus strain G5H. Plant Pathol J. 2009; 25(1):54-61.
[20] Hajimorad MR, Eggenberger AL, Hill JH. Evolution of Soybean mosaic virus-G7 molecularly cloned genome in Rsv1-genotype soybean results in emergence of a mutant capable of evading Rsv1-mediated recognition. Virol. 2003; 314(2):497–509.
[21] Seo JK, Lee HG, Kim KH. Systemic gene delivery into soybean by simple rub-inoculation with plasmid DNA of a Soybean mosaic virus-based vector. Arch Virol. 2009;154(1):87-99.
[22] Gagarinova AG, Babu M, Poysa V, Hill JH, Wang A. Identification and molecular characterization of two naturally occurring Soybean mosaic virus isolates that are closely related but differ in their ability to overcome Rsv4 resistance. Virus Res. 2008;138(1-2):50-6.
[23] Chowda-Reddy RV, Sun H, Chen H, Poysa V, Lin H, Gijzen M, Wang A. Mutations in the P3 protein of Soybean mosaic virus G2 isolates determine virulence on Rsv4-genotype soybean. Mol Plant Microbe Interaction. 2011; 24(1):37-43.
[24] Kanematsu S, Hidaka S, Naito S. Nucleotide sequences of the coat protein genes of soybean mosaic virus 5 strains. Ann Phytopathol Soc Jpn. 1995; 61:284–85.
[25] Shigemori I. Studies on the breeding on soybeans for the resistance to soybean mosaic virus (SMV). Bull Nagano Chushin Agr Ex Station. 1991; 10:1–61.
[26] Kanematsu S, Nakano M. Comparison between Japanese and US strain of soybean mosaic virus using differential soybean cultivars. Bull Tohoku Agric Res Cent. 2015; 117: 59–62.
[27] Mishchenko LT, Dunich AA, Shevchenko TP, Budzanivska IG, Polischuk VP, Andriychuk OM, Molchanets OV, Antipov IO. Detection of Soybean mosaic virus in some left-bank forest-steppe regions of Ukraine. Mikrobiol Zh. 2017; 79(3):125-36.