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

文献类型: 外文期刊

作者: Zhang, Yuliang 1 ; Yu, Naitong 1 ; Huang, Qixing 1 ; Yin, Guohua 2 ; Guo, Anping 1 ; Wang, Xiangfeng 3 ; Xiong, Zhongg 1 ;

作者机构: 1.Chinese Acad Trop Agr Sci, Inst Trop Biosci & Biotechnol, Key Lab Biol & Genet Resources Trop Crops, Minist Agr, Haikou 571101, Hainan, Peoples R China

2.Univ Arizona, Coll Agr & Life Sci, Tucson, AZ 85721 USA

3.Univ Arizona, Inst BIO5, Tucson, AZ 85721 USA

4.Univ Arizona, Sch Plant Sci, Tucson, AZ 85721 USA

关键词: Genome;Papaya ringspot virus;RT-PCR;Small RNA sequencing

期刊名称:VIRUS GENES ( 影响因子:2.332; 五年影响因子:2.0 )

ISSN:

年卷期:

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收录情况: SCI

摘要: 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.

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