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Kapytina A, Kolchenko M, Kerimbek N, Pozharskiy AS, Nizamdinova G, Taskuzhina A, Adilbayeva K, Khusnitdinova M, Amidullayeva M, Moisseyev R, Kachiyeva Z, Gritsenko D. Distribution of Wheat-Infecting Viruses and Genetic Variability of Wheat Streak Mosaic Virus and Barley Stripe Mosaic Virus in Kazakhstan. Viruses 2024; 16:96. [PMID: 38257796 PMCID: PMC10819362 DOI: 10.3390/v16010096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Wheat is an essential cereal crop for the economy and food safety of Kazakhstan. In the present work, a screening of wheat and barley from different regions of Kazakhstan was conducted using newly developed specific primers for reverse transcription PCR and loop-mediated isothermal amplification (LAMP) assays. In total, 82 and 19 of 256 samples of wheat and barley tested positive for wheat streak mosaic virus (WSMV) and barley stripe mosaic virus (BSMV), respectively. A phylogenetic analysis using two independent methods revealed that most of the analyzed isolates had a European origin. Molecular data on the distribution and diversity of cereal viruses in Kazakhstan were obtained for the first time and will help lay a foundation for the implementation of genetics and genomics in wheat phyto-epidemiology in the country.
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Affiliation(s)
- Anastasiya Kapytina
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
| | - Mariya Kolchenko
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
| | - Nazym Kerimbek
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
- Department of Molecular Biology and Genetics, Al Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Alexandr S. Pozharskiy
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
| | - Gulnaz Nizamdinova
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
| | - Aisha Taskuzhina
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
- Department of Molecular Biology and Genetics, Al Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Kamila Adilbayeva
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
| | - Marina Khusnitdinova
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
| | - Malika Amidullayeva
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
| | - Ruslan Moisseyev
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
- Department of Molecular Biology and Genetics, Al Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Zulfiya Kachiyeva
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
- Research Institute of Applied and Fundamental Medicine, Kazakh National Medical University, Almaty 050000, Kazakhstan
| | - Dilyara Gritsenko
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
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Nourinejhad Zarghani S, Al Kubrusli R, Iancev S, Jalkanen R, Büttner C, von Bargen S. Molecular Population Genetics of Aspen Mosaic-Associated Virus in Finland and Sweden. Viruses 2023; 15:1678. [PMID: 37632020 PMCID: PMC10460043 DOI: 10.3390/v15081678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
Aspen mosaic-associated virus (AsMaV) is a newly identified Emaravirus, in the family Fimoviridae, Bunyavirales, associated with mosaic symptoms in aspen trees (Populus tremula). Aspen trees are widely distributed in Europe and understanding the population structure of AsMaV may aid in the development of better management strategies. The virus genome consists of five negative-sense single-stranded RNA (-ssRNA) molecules. To investigate the genetic diversity and population parameters of AsMaV, different regions of the genome were amplified and analyzed and full-length sequence of the divergent isolates were cloned and sequenced. The results show that RNA3 or nucleoprotein is a good representative for studying genetic diversity in AsMaV. Developed RT-PCR-RFLP was able to identify areas with a higher number of haplotypes and could be applied for screening the large number of samples. In general, AsMaV has a conserved genome and based on the phylogenetic studies, geographical structuring was observed in AsMaV isolates from Sweden and Finland, which could be attributed to founder effects. The genome of AsMaV is under purifying selection but not distributed uniformly on genomic RNAs. Distant AsMaV isolates displayed amino acid sequence variations compared to other isolates, and bioinformatic analysis predicted potential post-translational modification sites in some viral proteins.
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Affiliation(s)
- Shaheen Nourinejhad Zarghani
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany; (S.N.Z.); (R.A.K.); (C.B.)
| | - Rim Al Kubrusli
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany; (S.N.Z.); (R.A.K.); (C.B.)
| | - Serghei Iancev
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany; (S.N.Z.); (R.A.K.); (C.B.)
| | | | - Carmen Büttner
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany; (S.N.Z.); (R.A.K.); (C.B.)
| | - Susanne von Bargen
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany; (S.N.Z.); (R.A.K.); (C.B.)
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Verchot J, Herath V, Jordan R, Hammond J. Genetic Diversity among Rose Rosette Virus Isolates: A Roadmap towards Studies of Gene Function and Pathogenicity. Pathogens 2023; 12:pathogens12050707. [PMID: 37242377 DOI: 10.3390/pathogens12050707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/11/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
The phylogenetic relationships of ninety-five rose rosette virus (RRV) isolates with full-length genomic sequences were analyzed. These isolates were recovered mostly from commercial roses that are vegetatively propagated rather than grown from seed. First, the genome segments were concatenated, and the maximum likelihood (ML) tree shows that the branches arrange independent of their geographic origination. There were six major groups of isolates, with 54 isolates in group 6 and distributed in two subgroups. An analysis of nucleotide diversity across the concatenated isolates showed lower genetic differences among RNAs encoding the core proteins required for encapsidation than the latter genome segments. Recombination breakpoints were identified near the junctions of several genome segments, suggesting that the genetic exchange of segments contributes to differences among isolates. The ML analysis of individual RNA segments revealed different relationship patterns among isolates, which supports the notion of genome reassortment. We tracked the branch positions of two newly sequenced isolates to highlight how genome segments relate to segments of other isolates. RNA6 has an interesting pattern of single-nucleotide mutations that appear to influence amino acid changes in the protein products derived from ORF6a and ORF6b. The P6a proteins were typically 61 residues, although three isolates encoded P6a proteins truncated to 29 residues, and four proteins extended 76-94 residues. Homologous P5 and P7 proteins appear to be evolving independently. These results suggest greater diversity among RRV isolates than previously recognized.
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Affiliation(s)
- Jeanmarie Verchot
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX 77845, USA
| | - Venura Herath
- Department of Agriculture Biology, Faculty of Agriculture, University of Peradeniya, Peradeniya 20400, Sri Lanka
| | - Ramon Jordan
- Floral and Nursery Plants Research Unit, US National Arboretum, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - John Hammond
- Floral and Nursery Plants Research Unit, US National Arboretum, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
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