European Journal of Plant Pathology

, Volume 135, Issue 2, pp 335–349 | Cite as

Complete genome characterization of Sugarcane yellow leaf virus from India: Evidence for RNA recombination

  • C. Chinnaraja
  • R. Viswanathan
  • R. Karuppaiah
  • K. Bagyalakshmi
  • P. Malathi
  • B. Parameswari
Article
First Online:
Accepted:

Abstract

Yellow leaf (YL) caused by Sugarcane yellow leaf virus (SCYLV) has become a serious constraint for sugarcane production in different countries. Worldwide seven genotypes have been reported, with five based on complete and two based on partial genome characterization. We have previously reported the occurrence of three different SCYLV genotypes in India based on their partial genome sequences. A further four SCYLV isolates from sugarcane from Coimbatore (in India) were characterized after complete genome sequencing (~ 5,875 nt). These isolates (SCYLV-IND) exhibited amino acid (aa) sequence differences of 29.2–31.8, 28.1–34.4 and 30.7–33.4 % with REU, HAW-PER and BRA in partial ORF0 sequences, respectively. Similarly IND isolates have 21.4–23.7, 22.5–25.0 and 21.4–23.9 % aa sequence differences with REU, HAW-PER and BRA, respectively in partial ORF1. However, the difference was found to be least in ORF5. The genotype reported from China, CHN1 shared a very close relationship with IND isolates with minimum differences of 4.3–5.3 %, 4.8–5.8 % and 2.5–3.0 % in ORF0, 1 and 5 in aa sequences, respectively and 4.4–5.3 % in complete nucleotide sequences. Phylogenetic analyses showed a separate lineage for IND isolates. Evidence of recombination was found in ORF1 to ORF5 with the maximum number of sites occurring in ORF2. The high incidence of SCYLV recombination suggests that recombination plays an important role in SCYLV evolution.

Keywords

Molecular variation Sugarcane Sugarcane yellow leaf virus Virus genotypes Virus recombination 
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Notes

Acknowledgments

The authors are grateful to Dr. N. Vijayan Nair, the Director of the Institute for providing necessary facilities and support to carry out the work.

Supplementary material

10658_2012_90_MOESM1_ESM.jpg (1 mb)
Supplementary Fig. 1 Yellow leaf (SCYLV-IND isolate) affected field showing severe symptoms of the disease in the cv Co 86032 in Erode district, Tamil Nadu, India (JPEG 1046kb)

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Copyright information

© KNPV 2012

Authors and Affiliations

  • C. Chinnaraja
    • 1
  • R. Viswanathan
    • 1
    • 3
  • R. Karuppaiah
    • 1
  • K. Bagyalakshmi
    • 1
  • P. Malathi
    • 1
  • B. Parameswari
    • 2
  1. 1.Plant Pathology section, Sugarcane Breeding InstituteIndian Council of Agricultural ResearchCoimbatoreIndia
  2. 2.Sugarcane Breeding Institute Regional CentreIndian Council of Agricultural ResearchKarnalIndia
  3. 3.Division of Crop Protection, Sugarcane Breeding InstituteIndian Council of Agricultural ResearchCoimbatoreIndia

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