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Genomic sequencing and analysis of Chilli ringspot virus, a novel potyvirus

Abstract

Chilli ringspot virus (ChiRSV), a novel potyvirus, was recently found in Hainan, China with high prevalence. The genomic sequence of the ChiRSV-HN/14 isolate was determined by sequencing overlapping cDNA segments generated by reverse transcription polymerase chain reaction with degenerate and/or specific primers. ChiRSV genome (GenBank Acc. no. JN008909) comprised of 9,571 nucleotides (nt) excluding the 3′-terminal poly (A) tail and contained a large open reading frame of 9,240 nt encoding a large polyprotein of 3,079 amino acids with predicted Mr of 349.1 kDa. A small, overlapping PIPO coding region was also found to span from nt 2,913 to 3,095, with a capacity to encode a peptide of 60 amino acids. ChiRSV shares sequence identities of only 48.5–65.4 and 42.9–68.7% with closely related potyviruses at the nucleotide and the amino acid levels, respectively. Phylogenetic analysis of the genomic sequences provided further evidence that ChiRSV is a distinct species of the Potyvirus genus. ChiRSV-HN/14 is most closely related to Tobacco vein banding mosaic virus and two other pepper-infecting potyviruses.

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Correspondence to Zhongguo Xiong or Zhi-Xin Liu.

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Zhongguo Xiong and Zhi-Xin Liu contributed equally to this research.

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Gong, D., Wang, JH., Lin, ZS. et al. Genomic sequencing and analysis of Chilli ringspot virus, a novel potyvirus. Virus Genes 43, 439–444 (2011). https://doi.org/10.1007/s11262-011-0652-2

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Keywords

  • ChiRSV
  • Potyvirus
  • Genome
  • Phylogeny
  • Motif