TY - JOUR
T1 - Complete genome of Hainan papaya ringspot virus using small RNA deep sequencing
AU - Zhang, Yuliang
AU - Yu, Naitong
AU - Huang, Qixing
AU - Yin, Guohua
AU - Guo, Anping
AU - Wang, Xiangfeng
AU - Xiong, Zhongguo
AU - Liu, Zhixin
N1 - Funding Information:
Acknowledgments The authors thank Professor J. S. Hu, Department of Plant and Environmental Protection Sciences, University of Hawaii, USA, Professor H. P. Li, South China Agricultural University, China and Dr. R. Z. Jia, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences for technical guide. This work was partially funded by National Natural Science Foundation of China (31201486) and Major Science and Technology Program of Hainan Province (ZDZX2013010-3 and ZDZX2013023-1).
PY - 2014/6
Y1 - 2014/6
N2 - 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.
AB - 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.
KW - Genome
KW - Papaya ringspot virus
KW - RT-PCR
KW - Small RNA sequencing
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U2 - 10.1007/s11262-014-1042-3
DO - 10.1007/s11262-014-1042-3
M3 - Article
C2 - 24510356
AN - SCOPUS:84901607383
SN - 0920-8569
VL - 48
SP - 502
EP - 508
JO - Virus Genes
JF - Virus Genes
IS - 3
ER -