Journal of Microbiology and Biotechnology

  • 제27권4호
  • /
  • Pages.834-837
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  • 2017
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  • 1017-7825(pISSN)
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  • 1738-8872(eISSN)
한국미생물·생명공학회 (The Korean Society for Microbiology and Biotechnology)
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Genome Sequence of Spinach Cryptic Virus 1, a New Member of the Genus Alphapartitivirus (Family Partitiviridae), Identified in Spinach

  • Park, Dongbin (Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University) ;
  • Hahn, Yoonsoo (Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University)
  • 투고 : 2016.11.08
  • 심사 : 2017.01.31
  • 발행 : 2017.04.28
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초록

A distinct double-stranded RNA (dsRNA) cryptic virus, named spinach cryptic virus 1 (SpCV1), was identified from spinach transcriptome datasets. The SpCV1 genome has two dsRNA genome segments. The larger dsRNA1 has an open reading frame for a conserved RNA-dependent RNA polymerase (RdRp). The smaller dsRNA2 encodes a putative coat protein (CP). The sequence identity of SpCV1 RdRp and CP to the closest cryptic virus is 81% and 60%, respectively. Phylogenetic analysis indicates that SpCV1 is a novel member of the genus Alphapartitivirus (family Partitiviridae).

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참고문헌

  1. Nibert ML, Ghabrial SA, Maiss E, Lesker T, Vainio EJ, Jiang D, Suzuki N. 2014. Taxonomic reorganization of family Partitiviridae and other recent progress in partitivirus research. Virus Res. 188: 128-141. https://doi.org/10.1016/j.virusres.2014.04.007
  2. Willenborg J, Menzel W, Vetten HJ, Maiss E. 2009. Molecular characterization of two alphacryptovirus dsRNAs isolated from Daucus carota. Arch. Virol. 154: 541-543. https://doi.org/10.1007/s00705-009-0314-z
  3. Szego A, Enunlu N, Deshmukh SD, Veliceasa D, Hunyadi-Gulyas E, Kuhne T, et al. 2010. The genome o f Beet cryptic virus 1 shows high homology to certain cryptoviruses present in phylogenetically distant hosts. Virus Genes 40: 267-276. https://doi.org/10.1007/s11262-009-0432-4
  4. Kim DS, Jung JY, Wang Y, Oh HJ, Choi D, Jeon CO, Hahn Y. 2014. Plant RNA v irus sequences identified in kimchi by microbial metatranscriptome analysis. J. Microbiol. Biotechnol. 24: 979-986. https://doi.org/10.4014/jmb.1404.04017
  5. Xu C, Jiao C, Zheng Y, Sun H, Liu W, Cai X, et al. 2015. De novo and comparative transcriptome analysis of cultivated and wild spinach. Sci. Rep. 5: 17706.
  6. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19: 455-477. https://doi.org/10.1089/cmb.2012.0021
  7. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402. https://doi.org/10.1093/nar/25.17.3389
  8. Li H , Durbin R . 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
  9. Li H. 2011. Improving SNP discovery by base a lignment quality. Bioinformatics 27: 1157-1158. https://doi.org/10.1093/bioinformatics/btr076
  10. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797. https://doi.org/10.1093/nar/gkh340
  11. Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33: 1870-1874. https://doi.org/10.1093/molbev/msw054
  12. Lubicz JV, Rush CM, Payton M, Colberg T. 2007. Beet necrotic yellow vein virus accumulates inside resting spores and zoosporangia of its vector Polymyxa betae BNYVV infects P. betae. Virol. J. 4: 37. https://doi.org/10.1186/1743-422X-4-37
  13. McDonald SM, Nelson MI, Turner PE, Patton JT. 2016. Reassortment in segmented RNA viruses: mechanisms and outcomes. Nat. Rev. Microbiol. 14: 448-460. https://doi.org/10.1038/nrmicro.2016.46
  14. Li L, Tian Q, Du Z, Duns GJ, Chen J. 2009. A novel double-stranded RNA virus detected in Primula malacoides is a plant-isolated partitivirus closely related to partitivirus infecting fungal species. Arch. Virol. 154: 565-572. https://doi.org/10.1007/s00705-009-0342-8
  15. Lesker T, Rabenstein F, Maiss E. 2013. Molecular characterization of five betacryptoviruses infecting four clover species and dill. Arch. Virol. 158: 1943-1952. https://doi.org/10.1007/s00705-013-1691-x

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