Phylogenetic analysis of two Ukrainian isolates of Wheat streak mosaic virus

Mishchenko, L. T.; Dunich, A. A.; Skrypkina, I. Ya.; Kozub, N. O.

doi:10.7124/bc.000997

Biopolym. Cell. 2019; 35(1):64-77.

http://dx.doi.org/10.7124/bc.000997

Viruses and Cell

Phylogenetic analysis of two Ukrainian isolates of Wheat streak mosaic virus

1Mishchenko L. T., 1Dunich A. A., 2Skrypkina I. Ya., 3Kozub N. O.

Educational and Scientific Center "Institute of Biology and Medicine",
Taras Shevchenko National University of Kyiv
64/13, Volodymyrska Str., Kyiv, Ukraine, 01601
Institute of Molecular Biology and Genetics, NAS of Ukraine
150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03143
Institute of Food Biotechnology and Genomics, NAS of Ukraine
2A, Osipovskogo Str., Kyiv, Ukraine, 04123

Abstract

The study of molecular characteristics and, in particular, the nucleotide (nt) and amino acid (aa) sequences of the viral genomes, is necessary to know the changes in their geographical range, phylogenetic relationships, viruses’ evolution, and their emergence as new epidemics. Aim. Phylogenetic analysis of the coat protein (CP) gene sequences of two new Ukrainian isolates of Wheat streak mosaic virus: Ukraine-Mal-18 and Ukraine-Ep-18. Results. The nucleotide sequences of 676 nt region of the CP gene of two Ukrainian WSMV isolates were compared with the sequences of 72 WSMV isolates/strains from GenBank. The phylogenetic analysis showed that the Ukrainian WSMV isolates cluster with the clade B or WSMV-ΔE isolates (originating from Europe and Asia) and have a typical for this clade triplet deletion at the position 8412-8414 nt in the CP gene. The isolate Ukraine-Mal-18 has the highest level of the sequence identity (93.5%-95.9% nt and 93.6-95.0% aa) with the clade B isolates. The Ukraine-Ep-18 isolate shares 89.2%-91.4% (nt) and 88.6-87.1% (aa) identity with the clade B isolates. Additionally, both Ukrainian WSMV isolates have a number of unique aa substitutions in the central CP gene domain. Conclusions. Ukrainian WSMV isolates belong to the clade B. But Ukraine-Mal-18 and Ukraine-Ep-18 have some differences from other members of the clade: i) a higher divergence compared to other B isolates (the Ukraine-Mal-18 has 12 aa substitutions, the Ukraine-Ep-18 has 25 aa substitutions, whereas the other clade B isolates have no more than 2 aa substitutions); ii) have aa substitution identical with the B1 non-crop isolates of this virus, many aa substitutions are in the same motifs as the substitutions of B1 grass WSMV isolates.

Keywords: Wheat streak mosaic virus, Triticum aestivum, phylogenetic analysis, sequencing, coat protein

Full text: (PDF, in English)

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