title: Complete genome of Hainan papaya ringspot virus using small RNA deep sequencing.
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.
authors: Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
authors: Yuliang
authors: Y
authors: Zhang
authors: Naitong
authors: N
authors: Yu
authors: Qixing
authors: Q
authors: Huang
authors: Guohua
authors: G
authors: Yin
authors: Anping
authors: A
authors: Guo
authors: Xiangfeng
authors: X
authors: Wang
authors: Zhongguo
authors: Z
authors: Xiong
authors: Zhixin
authors: Z
authors: Liu
mesh_terms: D001483:Base Sequence; D029441:Carica / Q000821:virology*; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008969:Molecular Sequence Data; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D017800:Potyvirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D012367:RNA, Viral / Q000235:genetics; D017423:Sequence Analysis, RNA
chemical_list: D012367:RNA, Viral