Complete genome of Hainan papaya ringspot virus using small RNA deep sequencing

Yuliang Zhang, Naitong Yu, Qixing Huang, Guohua Yin, Anping Guo, Xiangfeng Wang, Zhongguo Xiong, Zhixin Liu

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Small RNA deep sequencing allows for virus identification, virus genome assembly, and strain differentiation. In this study, papaya plants with virus-like symptoms collected in Hainan province were used for deep sequencing and small RNA library construction. After in silicon subtraction of the papaya sRNAs, small RNA reads were used to in the viral genome assembly using a reference-guided, iterative assembly approach. A nearly complete genome was assembled for a Hainan isolate of papaya ringspot virus (PRSV-HN-2). The complete PRSV-HN-2 genome (accession no.: KF734962) was obtained after a 15-nucleotide gap was filled by direct sequencing of the amplified genomic region. Direct sequencing of several random genomic regions of the PRSV isolate did not find any sequence discrepancy with the sRNA-assembled genome. The newly sequenced PRSV-HN-2 genome shared a nucleotide identity of 96 and 94% to that of the PRSV-HN (EF183499) and PRSV-HN-1 (HQ424465) isolates, and together with these two isolates formed a new PRSV clade. These data demonstrate that the small RNA deep sequencing technology provides a viable and rapid mean to assemble complete viral genomes in plants.

Original languageEnglish (US)
Pages (from-to)502-508
Number of pages7
JournalVirus Genes
Volume48
Issue number3
DOIs
StatePublished - 2014

Fingerprint

RNA Sequence Analysis
Carica
High-Throughput Nucleotide Sequencing
Genome
Viruses
Virus Assembly
Viral Genome
Nucleotides
RNA
Plant Viruses
Silicon
Technology

Keywords

  • Genome
  • Papaya ringspot virus
  • RT-PCR
  • Small RNA sequencing

ASJC Scopus subject areas

  • Virology
  • Genetics
  • Molecular Biology
  • Medicine(all)

Cite this

Zhang, Y., Yu, N., Huang, Q., Yin, G., Guo, A., Wang, X., ... Liu, Z. (2014). Complete genome of Hainan papaya ringspot virus using small RNA deep sequencing. Virus Genes, 48(3), 502-508. https://doi.org/10.1007/s11262-014-1042-3

Complete genome of Hainan papaya ringspot virus using small RNA deep sequencing. / Zhang, Yuliang; Yu, Naitong; Huang, Qixing; Yin, Guohua; Guo, Anping; Wang, Xiangfeng; Xiong, Zhongguo; Liu, Zhixin.

In: Virus Genes, Vol. 48, No. 3, 2014, p. 502-508.

Research output: Contribution to journalArticle

Zhang, Y, Yu, N, Huang, Q, Yin, G, Guo, A, Wang, X, Xiong, Z & Liu, Z 2014, 'Complete genome of Hainan papaya ringspot virus using small RNA deep sequencing', Virus Genes, vol. 48, no. 3, pp. 502-508. https://doi.org/10.1007/s11262-014-1042-3
Zhang, Yuliang ; Yu, Naitong ; Huang, Qixing ; Yin, Guohua ; Guo, Anping ; Wang, Xiangfeng ; Xiong, Zhongguo ; Liu, Zhixin. / Complete genome of Hainan papaya ringspot virus using small RNA deep sequencing. In: Virus Genes. 2014 ; Vol. 48, No. 3. pp. 502-508.
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