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. 2011 Feb 18;26(1):47–53. doi: 10.1007/s12250-011-3170-9

Molecular characterization of segments S7 to S10 of a southern rice black-streaked dwarf virus isolate from maize in northern China

Xiao Yin 1, Fei-fei Xu 1, Fang-qiang Zheng 1, Xiang-dong Li 1,✉, Bao-shen Liu 2, Chun-qing Zhang 2
PMCID: PMC8222491  PMID: 21331890

Abstract

Southern rice black-streaked dwarf virus (SRBSDV) is a novel Fijivirus prevalent in rice in southern and central China, and northern Vietnam. Its genome has 10 segments of double-stranded RNA named S1 to S10 according to their size. An isolate of SRBSDV, JNi4, was obtained from naturally infected maize plants from Ji’ning, Shandong province, in the 2008 maize season. Segments S7 to S10 of JNi4 share nucleotide identities of 72.6%–73.1%, 72.3%–73%, 73.9%–74.5% and 77.3%–79%, respectively, with corresponding segments of Rice black-streaked dwarf virus isolates, and identities of 99.7%, 99.1%–99.7%, 98.9%–99.5%, and 98.6%–99.2% with those of SRBSDV isolates HN and GD. JNi4 forms a separate branch with GD and HN in the phylogenetic trees constructed with genomic sequences of S7 to S10. These results confirm the proposed taxonomic status of SRBSDV as a distinct species of the genus Fijivirus and indicate that JNi4 is an isolate of SRBSDV. Shandong is so far the northernmost region where SRBSDV is found in China.

Key words: Southern rice black-streaked dwarf virus (SRBSDV), Maize rough dwarf disease (MRD), Identity, Phylogenetic analysis

Footnotes

Foundation items: National Natural Science Foundation of China (30971895, 31011130031); Special Research Funds for the Doctoral Program of Higher Education (20080434006); Grants from Ministry of Science and Technology (2009ZX08003-014B) and Shandong province (2009GG10009021); Modern maize industrial system of Shandong province.

These authors contributed equally.

References

  • 1.Anzola J. V., Xu Z. K., Asamizu T., et al. Segment-specific inverted repeats found adjacent to conserved terminal sequences in wound tumor virus genome and defective interfering RNAs. Proc Nat Acad Sci USA. 1987;84:8301–8305. doi: 10.1073/pnas.84.23.8301. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 2.Bao Y. X., Xu X. Y., Wang J. Q., et al. Analysis of the atmospheric dynamical backgrounds for the great immigration events of white back planthoppper (Sogatella furcifera) Acta Ecol Sin. 2007;27:4527–4535. [Google Scholar]
  • 3.Chen J., Zhu Q. Q., Yuan C. Y., et al. Molecular characterization of Rice black-streaked dwarf virus isolates causing maize rough dwarf disease in Shandong. Acta Phytopathol Sin. 2008;38:540–543. [Google Scholar]
  • 4.Distéfano A. J., Conci L. R., Muñoz Hidalgo M., et al. Sequence analysis of genome segments S4 and S8 of Mal de Río Cuarto virus (MRCV): evidence that the virus should be a separate Fijivirus species. Arch Virol. 2002;147:1699–1709. doi: 10.1007/s00705-002-0840-4. [DOI] [PubMed] [Google Scholar]
  • 5.Distefano A. J., Hopp H. E., del Vas M. Sequence analysis of genome segments S5 and S10 of Mal de Rio Cuarto virus (Fijivirus, Reoviridae) Arch Virol. 2005;150:1241–1248. doi: 10.1007/s00705-004-0477-6. [DOI] [PubMed] [Google Scholar]
  • 6.Fang S., Yu J., Feng J., et al. Identification of rice black-streaked dwarf fijivirus in maize with rough dwarf disease in China. Arch Virol. 2001;146:167–170. doi: 10.1007/s007050170200. [DOI] [PubMed] [Google Scholar]
  • 7.Guzman F. A., Distefano A. J., Arneodo J. D., et al. Sequencing of the bicistronic genome segments S7 and S9 of Mal de Rio Cuarto virus (Fijivirus, Reoviridae) completes the genome of this virus. Arch Virol. 2007;152:565–573. doi: 10.1007/s00705-006-0864-2. [DOI] [PubMed] [Google Scholar]
  • 8.Harding R. M., Burns P., Geijskes R. J., et al. Molecular analysis of Fiji disease virus segments 2, 4 and 7 completes the genome sequence. Virus Genes. 2006;32:43–47. doi: 10.1007/s11262-006-5844-x. [DOI] [PubMed] [Google Scholar]
  • 9.Isogai M., Uyeda I., Lindsten K. Taxonomic characteristics of fijiviruses based on nucleotide sequences of the oat sterile dwarf virus genome. J Gen Virol. 1998;79:1479–1485. doi: 10.1099/0022-1317-79-6-1479. [DOI] [PubMed] [Google Scholar]
  • 10.Kumar S., Nei M., Dudley J., et al. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform. 2008;9:299–306. doi: 10.1093/bib/bbn017. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11.Larkin M A., Blackshields G., Brown N. P., et al. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23:2947–2948. doi: 10.1093/bioinformatics/btm404. [DOI] [PubMed] [Google Scholar]
  • 12.Marzachì C., Antoniazzi S., d’Aquilio M., et al. The double-stranded RNA genome of maize rough dwarf fijivirus contains both mono and dicistronic segments. Eur J Plant Pathol. 1996;102:601–605. doi: 10.1007/BF01877029. [DOI] [Google Scholar]
  • 13.Marzachi C., Boccardo G., Nuss D. L. Cloning of the maize rough dwarf virus genome: molecular confirmation of the plant-reovirus classification scheme and identification of two large nonoverlapping coding domains within a single genomic segment. Virology. 1991;180:518–526. doi: 10.1016/0042-6822(91)90065-J. [DOI] [PubMed] [Google Scholar]
  • 14.McQualter R. B., Burns P., Smith G. R., et al. Molecular analysis of Fiji disease virus genome segments 5, 6, 8 and 10. Arch Virol. 2004;149:713–721. doi: 10.1007/s00705-003-0243-1. [DOI] [PubMed] [Google Scholar]
  • 15.Milne R. G., del Vas M., Harding R. M., et al. Genus Fijivirus. In: Fauquet C.M., Mayo M.A., Maniloff J., Desselberger U., Ball L.A., et al., editors. Virus Taxomony: Classification and nomenclature of viruses. Eighth Report of the International Committee on the Taxonomy of Viruses. San Diego: Elsevier Academic Press; 2005. pp. 534–542. [Google Scholar]
  • 16.Nakashima N., Koizumi M., Watanabe H., et al. Complete nucleotide sequence of the Nilaparvata lugens reovirus: a putative member of the genus Fijivirus. J Gen Virol. 1996;77:139–146. doi: 10.1099/0022-1317-77-1-139. [DOI] [PubMed] [Google Scholar]
  • 17.Nakashima N., Noda H. Nucleotide sequence of Nilaparvata lugens reovirus genome segment S8 coding for the major outer capsid protein. J Gen Virol. 1994;75:2803–2806. doi: 10.1099/0022-1317-75-10-2803. [DOI] [PubMed] [Google Scholar]
  • 18.Noda H., Nakashima N., Omura T. Cloning of the Nilaparvata lugens reovirus genome: conserved terminal nucleotide sequences and nucleotide sequence of genome segment S10. J Gen Virol. 1994;75:221–225. doi: 10.1099/0022-1317-75-1-221. [DOI] [PubMed] [Google Scholar]
  • 19.Soo H. M., Handley J. A., Maugeri M. M., et al. Molecular characterization of Fiji disease fijivirus genome segment 9. J Gen Virol. 1998;79:3155–61. doi: 10.1099/0022-1317-79-12-3155. [DOI] [PubMed] [Google Scholar]
  • 20.Tamura K., Dudley J., Nei M., et al. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 2007;24:1596–1599. doi: 10.1093/molbev/msm092. [DOI] [PubMed] [Google Scholar]
  • 21.Thompson J. D., Higgins D. G., Gibson T. J. improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucl Acids Res. 1994;22:4673–4680. doi: 10.1093/nar/22.22.4673. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 22.Wang Q., Yang J., Zhou G. H., et al. The complete genome sequence of two isolates of southern rice black-streaked dwarf virus, a new member of the genus Fijivirus. J Phytopathol. 2010;158:733–737. doi: 10.1111/j.1439-0434.2010.01679.x. [DOI] [Google Scholar]
  • 23.Wang Z. H., Fang S. G., Xu J. L., et al. Sequence analysis of the complete genome of rice black-streaked dwarf virus isolated from maize with rough dwarf disease. Virus Genes. 2003;27:163–168. doi: 10.1023/A:1025776527286. [DOI] [PubMed] [Google Scholar]
  • 24.Yu X. Q., Lan Y. F., Wang H. Y., et al. The complete genomic sequence of Tobacco vein banding mosaic virus and its similarities with other potyviruses. Virus Genes. 2007;35:801–806. doi: 10.1007/s11262-007-0135-7. [DOI] [PubMed] [Google Scholar]
  • 25.Zhang H. M., Chen J. P., Adams M. J. Molecular characterisation of segments 1 to 6 of Rice black-streaked dwarf virus from China provides the complete genome. Arch Virol. 2001;146:2331–2339. doi: 10.1007/s007050170006. [DOI] [PubMed] [Google Scholar]
  • 26.Zhang H. M., Chen J. P., Lei J. L., et al. Sequence analysis shows that a dwarfing disease on rice, wheat and maize in China is caused by rice black-streaked dwarf virus. Eur J Plant Pathol. 2001;107:563–567. doi: 10.1023/A:1011204010663. [DOI] [Google Scholar]
  • 27.Zhang H. M., Yang J., Chen J. P., et al. A black-streaked dwarf disease on rice in China is caused by a novel fijivirus. Arch Virol. 2008;153:1893–1898. doi: 10.1007/s00705-008-0209-4. [DOI] [PubMed] [Google Scholar]
  • 28.Zhou G. H., Wen J. J., Cai D. J., et al. Southern rice black-streaked dwarf virus: A new proposed Fijivirus species in the family Reoviridae. Chin Sci Bull. 2008;53:3677–3685. doi: 10.1007/s11434-008-0467-2. [DOI] [Google Scholar]

Articles from Virologica Sinica are provided here courtesy of Wuhan Institute of Virology, Chinese Academy of Sciences

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