Journal of Microbiology and Biotechnology

  • 제27권7호
  • /
  • Pages.1324-1330
  • /
  • 2017
  • /
  • 1017-7825(pISSN)
  • /
  • 1738-8872(eISSN)
한국미생물·생명공학회 (The Korean Society for Microbiology and Biotechnology)
권호 표지
DOI QR코드

DOI QR Code

Genome Sequences of Spinach Deltapartitivirus 1, Spinach Amalgavirus 1, and Spinach Latent Virus Identified in Spinach Transcriptome

  • 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 : 2017.03.21
  • 심사 : 2017.05.11
  • 발행 : 2017.07.28
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

Complete genome sequences of three new plant RNA viruses, Spinach deltapartitivirus 1 (SpDPV1), Spinach amalgavirus 1 (SpAV1), and Spinach latent virus (SpLV), were identified from a spinach (Spinacia oleracea) transcriptome dataset. The RNA-dependent RNA polymerases (RdRps) of SpDPV1, SpAV1, and SpLV showed 72%, 53%, and 93% amino acid sequence identities with the homologous RdRp of the most closely related virus, respectively, suggesting that SpDPV1 and SpAV1 were novel viruses. Sequence similarity and phylogenetic analyses revealed that SpDPV1 belonged to the genus Deltapartitivirus of the family Partitiviridae, SpAV1 to the genus Amalgavirus of the family Amalgaviridae, and SpLV to the genus Ilarvirus of the family Bromoviridae. Based on the demarcation criteria, SpDPV1 and SpAV1 are considered as novel species of the genera Deltapartitivirus and Amalgavirus, respectively. This is the first report of these two viruses from spinach.

키워드

참고문헌

  1. Irish BM, Correll JC, Feng C, Bentley T, de Los Reyes BG. 2008. Characterization of a resistance locus (Pfs-1) to the spinach downy mildew pathogen (Peronospora farinosa f. sp. spinaciae) and development of a molecular marker linked to Pfs-1. Phytopathology 98: 894-900. https://doi.org/10.1094/PHYTO-98-8-0894
  2. Shi A, Mou B. 2016. Genetic diversity and association analysis of leafminer (Liriomyza langei) resistance in spinach (Spinacia oleracea). Genome 59: 581-588. https://doi.org/10.1139/gen-2016-0075
  3. Takahata S, Yago T, Iwabuchi K, Hirakawa H, Suzuki Y, Onodera Y. 2016. Comparison of spinach sex chromosomes with sugar beet autosomes reveals extensive synteny and low recombination at the male-determining locus. J. Hered. 107: 679-685. https://doi.org/10.1093/jhered/esw055
  4. 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.
  5. Yan J, Yu L, Xuan J, Lu Y, Lu S, Zhu W. 2016. De novo transcriptome sequencing and gene expression profiling of spinach (Spinacia oleracea L.) leaves under heat stress. Sci. Rep. 6: 19473. https://doi.org/10.1038/srep19473
  6. Scholthof KB, Adkins S, Czosnek H, Palukaitis P, Jacquot E, Hohn T, et al. 2011. Top 10 plant viruses in molecular plant pathology. Mol. Plant Pathol. 12: 938-954. https://doi.org/10.1111/j.1364-3703.2011.00752.x
  7. Roossinck MJ. 2010. Lifestyles of plant viruses. Philos. Trans. R. Soc. Lond. B Biol. Sci. 365: 1899-1905. https://doi.org/10.1098/rstb.2010.0057
  8. Mihara T, Nishimura Y, Shimizu Y, Nishiyama H, Yoshikawa G, Uehara H, et al. 2016. Linking virus genomes with host taxonomy. Viruses 8: 66. https://doi.org/10.3390/v8030066
  9. Elbeaino T, Kubaa RA, Tuzlali HT, Digiaro M. 2016. Pittosporum cryptic virus 1: genome sequence completion using next-generation sequencing. Arch. Virol. 161: 2039-2042. https://doi.org/10.1007/s00705-016-2860-5
  10. Kim DS, Jung JY, Wang Y, Oh HJ, Choi D, Jeon CO, et al. 2014. Plant RNA virus sequences identified in kimchi by microbial metatranscriptome analysis. J. Microbiol. Biotechnol. 24: 979-986. https://doi.org/10.4014/jmb.1404.04017
  11. Liu H, Fu Y, Xie J, Cheng J, Ghabrial SA, Li G, et al. 2012. Discovery of novel dsRNA viral sequences by in silico cloning and implications for viral diversity, host range and evolution. PLoS One 7: e42147. https://doi.org/10.1371/journal.pone.0042147
  12. Nibert ML, Pyle JD, Firth AE. 2016. A +1 ribosomal frameshifting motif prevalent among plant amalgaviruses. Virology 498: 201-208. https://doi.org/10.1016/j.virol.2016.07.002
  13. Park D, Hahn Y. 2017. Genome sequence of spinach cryptic virus 1, a new member of the genus Alphapartitivirus (family Partitiviridae), was identified in spinach. J. Microbiol. Biotechnol. [In Press].
  14. 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
  15. 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
  16. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760. https://doi.org/10.1093/bioinformatics/btp324
  17. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078-2079. https://doi.org/10.1093/bioinformatics/btp352
  18. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. 2011. Integrative genomics viewer. Nat. Biotechnol. 29: 24-26. https://doi.org/10.1038/nbt.1754
  19. 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
  20. 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
  21. McGuffin LJ, Bryson K, Jones DT. 2000. The PSIPRED protein structure prediction server. Bioinformatics 16: 404-405. https://doi.org/10.1093/bioinformatics/16.4.404
  22. Crooks GE, Hon G, Chandonia JM, Brenner SE. 2004. WebLogo: a sequence logo generator. Genome Res. 14: 1188-1190. https://doi.org/10.1101/gr.849004
  23. Schneider TD, Stephens RM. 1990. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 18: 6097-6100. https://doi.org/10.1093/nar/18.20.6097
  24. Elbeaino T, Kubaa RA, Digiaro M, Minafra A, Martelli GP. 2011. The complete nucleotide sequence and genome organization of Fig cryptic virus, a novel bipartite dsRNA virus infecting fig, widely distributed in the Mediterranean basin. Virus Genes 42: 415-421. https://doi.org/10.1007/s11262-011-0581-0
  25. Bruenn J. 1993. A closely related group of RNA-dependent RNA polymerases from double-stranded RNA viruses. Nucleic Acids Res. 21: 5667-5669. https://doi.org/10.1093/nar/21.24.5667
  26. 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
  27. Crawford LJ, Osman TA, Booy FP, Coutts RH, Brasier CM, Buck KW. 2006. Molecular characterization of a partitivirus from Ophiostoma himal-ulmi. Virus Genes 33: 33-39. https://doi.org/10.1007/s11262-005-0028-6
  28. Magallon S, Castillo A. 2009. Angiosperm diversification through time. Am. J. Bot. 96: 349-365. https://doi.org/10.3732/ajb.0800060
  29. Blawid R, Stephan D, Maiss E. 2007. Molecular characterization and detection of Vicia cryptic virus in different Vicia faba cultivars. Arch. Virol. 152: 1477-1488. https://doi.org/10.1007/s00705-007-0966-5
  30. Sabanadzovic S, Abou Ghanem-Sabanadzovic N, Valverde RA. 2010. A novel monopartite dsRNA virus from rhododendron. Arch. Virol. 155: 1859-1863. https://doi.org/10.1007/s00705-010-0770-5
  31. Firth AE, Jagger BW, Wise HM, Nelson CC, Parsawar K, Wills NM, et al. 2012. Ribosomal frameshifting used in influenza A virus expression occurs within the sequence UCC_UUU_CGU and is in the +1 direction. Open Biol. 2: 120109.
  32. Depierreux D, Vong M, Nibert ML. 2016. Nucleotide sequence of Zygosaccharomyces bailii virus Z: evidence for +1 programmed ribosomal frameshifting and for assignment to family Amalgaviridae. Virus Res. 217: 115-124. https://doi.org/10.1016/j.virusres.2016.02.008
  33. Ge X, Scott SW, Zimmerman MT. 1997. The complete sequence of the genomic RNAs of spinach latent virus. Arch. Virol. 142: 1213-1226. https://doi.org/10.1007/s007050050153
  34. Scott SW, Zimmerman MT, Ge X. 2003. Viruses in subgroup 2 of the genus Ilarvirus share both serological relationships and characteristics at the molecular level. Arch. Virol. 148: 2063-2075. https://doi.org/10.1007/s00705-003-0148-z
  35. Li W, Adkins S, Hilf ME. 2008. Characterization of complete sequences of RNA 1 and RNA 2 of Citrus variegation virus. Arch. Virol. 153: 385-388. https://doi.org/10.1007/s00705-007-1090-2

피인용 문헌

  1. Identification of Two Novel Amalgaviruses in the Common Eelgrass (Zostera marina) and in Silico Analysis of the Amalgavirus +1 Programmed Ribosomal Frameshifting Sites vol.34, pp.2, 2017, https://doi.org/10.5423/ppj.nt.11.2017.0243
  2. Identification of a novel plant RNA virus species of the genus Amalgavirus in the family Amalgaviridae from chia (Salvia hispanica) vol.41, pp.5, 2017, https://doi.org/10.1007/s13258-019-00782-1