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The first complete genome sequence of iris severe mosaic virus

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Abstract

The first complete genome sequence of ISMV was determined by deep sequencing of a small RNA library constructed from ISMV-infected samples and rapid amplification of cDNA ends (RACE) PCR. The ISMV genome consists of 10,403 nucleotides excluding the poly(A) tail and contains a large open reading frame encoding a polyprotein of 3316 amino acids. Putative proteolytic cleavage sites were identified by BLAST analysis. The ISMV polyprotein showed highest amino acid sequence identity to that encoded by onion yellow dwarf virus. Phylogenetic analysis of the polyprotein amino acid sequence confirmed that ISMV forms a cluster with shallot yellow stripe virus, Cyrtanthus elatus virus A, narcissus degeneration virus and onion yellow dwarf virus. These results confirm that ISMV is a distinct member of the genus Potyvirus.

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References

  1. Adams MJ, Antoniw JF, Beaudoin F (2005) Overview and analysis of the polyprotein cleavage sites in the family Potyviridae. Mol Plant Pathol 6:471–487

    Article  CAS  PubMed  Google Scholar 

  2. Alper M, Salomon R, Loebenstein G (1984) Gel electrophoresis of virus-associated polypeptides for detecting viruses in bulbous irises. Phytopathology 74:960–962

    Article  CAS  Google Scholar 

  3. Asjes CJ (1979) Viruses and virus diseases in Dutch bulbous irises (Iris hollandica) in the Netherlands. Neth J Plant Pathol 85:269–279

    Article  Google Scholar 

  4. Atreya CD, Raccah B, Pirone TP (1990) A point mutation in the coat protein abolishes aphid transmissibility of a potyvirus. Virology 178:161–165

    Article  CAS  PubMed  Google Scholar 

  5. Atreya PL, Lopez-Moya JJ, Chu MH, Atreya CD, Pirone TP (1995) Mutational analysis of the coat protein N-terminal amino-acids involved in potyvirus transmission by aphids. J Gen Virol 76:265–270

    Article  CAS  PubMed  Google Scholar 

  6. Brierley P, McWhorter FP (1936) A mosaic disease of iris. J Agric Res 53:621–635

    Google Scholar 

  7. Brunt AA, Phillips S (1980) The detection, separation from naturally occurring complexes, and partial characterisation of four aphid-borne viruses infecting bulbous iris. ISHS Acta Hortic 109:503–508

    Article  Google Scholar 

  8. Chung BY, Miller WA, Atkins JF, Firth AE (2008) An overlapping essential gene in the Potyviridae. Proc Natl Acad Sci USA 105:5897–5902

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Derks AFLM (1985) Recent advances in bulb virus research. Acta Hortic 164:281–289

    Article  Google Scholar 

  10. Derks AFLM, Hollinger TC (1986) Similarities of and differences between potyviruses from bulbous and rhizomatous irises. ISHS Acta Hortic 177:555–561

    Article  Google Scholar 

  11. Derks AFLM, Vink-van den Abeele JL, Muller PJ (1980) Bean yellow mosaic virus in some iridaceous plants. ISHS Acta Hortic 110:31–37

    Article  Google Scholar 

  12. Hammond J, Derks AFLM, Barnett OW, Lawson RH, Brunt AA, Inouye N, Allen TC (1985) Viruses infecting bulbous iris: a clarification of nomenclature. ISHS Acta Hortic 164:395–397

    Article  Google Scholar 

  13. Inouye N, Mitsuhata K (1978) Turnip mosaic virus isolated from Iris. Nogaku Kenkyu 57:1–16 (in Japanese)

    Google Scholar 

  14. Kulshrestha S, Hallan V, Raikhy G, Kumar A, Ram R, Garg ID, Zaidi AA (2004) Molecular characterization of an Iris severe mosaic virus isolate from India. Acta Virol 48:65–67

    CAS  PubMed  Google Scholar 

  15. Lucinda N, Rocha WB, Inoue-Nagata AK, Nagata T (2012) Complete genome sequence of pepper yellow mosaic virus, a potyvirus, occurring in Brazil. Arch Virol 157:1397–1401

    Article  CAS  PubMed  Google Scholar 

  16. Nateqi M, Habibi MK, Dizadji A, Parizad S (2015) Detection and molecular characterization of the Iris severe mosaic virus-Ir isolate from Iran. J Plant Prot Res. doi:10.1515/jppr-2015-0032

    Google Scholar 

  17. Park WM, Lee SS, Park SH, Ryu KH (2000) Sequence analysis of the coat protein gene of a Korean isolate of Iris severe mosaic potyvirus from Iris plant. Plant Pathol J16:36–42

    Google Scholar 

  18. Revers F, Le Gall O, Candresse T, Maule AJ (1999) New advances in understanding the molecular biology of plant/potyvirus interactions. Mol Plant Microbe Interact 12:367–376

    Article  CAS  Google Scholar 

  19. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Urcuqui-Inchima S, Haenni AL, Bernardi F (2001) Potyvirus proteins: a wealth of functions. Virus Res 74:157–175

    Article  CAS  PubMed  Google Scholar 

  21. Van der Vlugt CIM (1994) Distribution and multiplication of Iris severe mosaic potyvirus in bulbous Iris in relation to metabolic activity: implications for ISMV detection, Ph.D. thesis. Bulb Research Centre Lisse, Dutch Flower bulb Industry, The Netherlands

  22. Van der Vlugt CIM, Langeveld SA, Goldbach RW (1994) Molecular cloning and sequence analysis of the 3’-terminal region of iris severe mosaic virus RNA. Arch Virol 136:397–406

    Article  PubMed  Google Scholar 

  23. Wu QF, Wang Y, Cao MJ, Pantaleo V, Burgyan J, Li WX, Ding SW (2012) Homology-independent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm. Proc Natl Acad Sci USA 109:3938–3943

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Yan SJ, Qin ZD, Jin LL, Chen JS (2010) A new isolate of Iris severe mosaic virus causing yellow mosaic in Iris ensata Thunb. J Nanosci Nanotechnol 10:726–730

    Article  CAS  PubMed  Google Scholar 

  25. Zerbino DR, Birney E (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

This work was supported by a Special Fund for the Detecting for Plant Virus (201310068, 2012BAK11B02) from General Administration of Quality Supervision, Inspection and Quarantine of the People’s Republic of China and National Natural Science Foundation of China (Grant No. 31401711) and the Comprehensive Reforming Project to Promote Talents Training of BUA (BNRC&YX201415).

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Authors and Affiliations

  1. College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China

    Yongqiang Li & Qiaoxia Shang

  2. Plant Laboratory of Beijing Entry-Exit Inspection and Quarantine Bureau, Beijing, 100026, China

    Yongqiang Li, Congliang Deng, Xiaoli Zhao & Xingliang Liu

  3. Chinese Society of Inspection and Quarantine, Beijing, 101312, China

    Qi Zhou

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  1. Yongqiang Li
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  2. Congliang Deng
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  3. Qiaoxia Shang
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  4. Xiaoli Zhao
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  5. Xingliang Liu
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  6. Qi Zhou
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Correspondence to Yongqiang Li or Qi Zhou.

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Li, Y., Deng, C., Shang, Q. et al. The first complete genome sequence of iris severe mosaic virus. Arch Virol 161, 1069–1072 (2016). https://doi.org/10.1007/s00705-015-2743-1

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  • DOI: https://doi.org/10.1007/s00705-015-2743-1

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