Detection of a New Luteovirus in Imported Nectarine Trees: A Case Study to Propose Adoption of Metagenomics in Post-Entry Quarantine
Detection of a New Luteovirus in Imported Nectarine Trees: A Case Study to Propose Adoption of Metagenomics in Post-Entry Quarantine
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DOI：
10.1094/phyto-09-14-0262-r
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发表时间：
2015-06-01
期刊：
影响因子：
3.2
通讯作者：
Sudarshana, Mysore R.
中科院分区：
文献类型：
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作者：
Bag, Sudeep;Al Rwahnih, Maher;Sudarshana, Mysore R.
2013年春季，在加州的一个繁殖区，5年生油桃（Prunus persica）树嫁接在桃砧木Nemaguard上，被发现发育不良。这些油桃是从法国进口的三个油桃品种的芽体繁殖而来，并通过入境后检疫程序。对天篷的检查没有发现任何明显的症状。然而，在剥去树皮后对树干进行检查，发现木质圆柱体上有广泛的点蚀。为了研究病原体，从接穗和砧木部分的树皮碎屑中提取双链RNA，并使用Illumina平台制备cDNA文库并测序。通过重新组装序列读数产生的重叠群的BLAST分析表明存在新的黄病毒。通过对逆转录-聚合酶链反应（RT-PCR）和快速扩增59-和39-末端产生的三个重叠cDNA克隆进行测序，确定病毒基因组的完整序列。该病毒基因组由4，991个核苷酸组成，其基因结构与黄病毒属（黄病毒科）成员相似。病毒的存在，暂命名为油桃茎痘相关病毒，证实在症状树的RT-PCR。在入境检疫后油桃树中发现一种新病毒，表明包括（i）通过下一代测序方法进行宏基因组分析作为评估植物健康状况的重要工具，以及（ii）检查木质圆柱体作为索引过程的一部分的重要性。
In spring 2013, 5-year-old nectarine (Prunus persica) trees, grafted on peach rootstock Nemaguard, were found stunted in a propagation block in California. These trees had been propagated from budwood of three nectarine cultivars imported from France and cleared through the post-entry quarantine procedure. Examination of the canopy failed to reveal any obvious symptoms. However, examination of the trunks, after stripping the bark, revealed extensive pitting on the woody cylinder. To investigate the etiological agent, double-stranded RNA was extracted from bark scrapings from the scion and rootstock portions, and a cDNA library was prepared and sequenced using the Illumina platform. BLAST analysis of the contigs generated by the de novo assembly of sequence reads indicated the presence of a novel luteovirus. Complete sequence of the viral genome was determined by sequencing of three overlapping cDNA clones generated by reverse transcription-polymerase chain reaction (RT-PCR) and by rapid amplification of the 59- and 39-termini. The virus genome was comprised of 4,991 nucleotides with a gene organization similar to members of the genus Luteovirus (family Luteoviridae). The presence of the virus, tentatively named Nectarine stem pitting-associated virus, was confirmed in symptomatic trees by RT-PCR. Discovery of a new virus in nectarine trees after post-entry quarantine indicates the importance of including (i) metagenomic analysis by next-generation sequencing approach as an essential tool to assess the plant health status, and (ii) examination of the woody cylinders as part of the indexing process.