Characterization of Potato Virus Y Isolates and Assessment of Nanopore Sequencing to Detect and Genotype Potato Viruses
Characterization of Potato Virus Y Isolates and Assessment of Nanopore Sequencing to Detect and Genotype Potato Viruses
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DOI：
10.3390/v12040478
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发表时间：
2020-04-01
期刊：
影响因子：
4.7
通讯作者：
Mullins, Ewen
中科院分区：
文献类型：
--
作者：
Della Bartola, Michele;Byrne, Stephen;Mullins, Ewen
马铃薯Y病毒（Potato virus Y， PVY）是马铃薯（Solanum tuberosum L.）上最重要的经济病毒。准确的诊断对规范块茎贸易和卫生选择繁殖材料至关重要。然而，PVY的高遗传多样性给分离株的检测和分类带来了挑战。本文采用传统的分子和血清学技术，对来自种质收集和商业站点的爱尔兰PVY分离株的多样性进行了研究。重组PVY菌株普遍存在，PVYNTNa为主要基因型。此外，我们利用纳米孔测序技术检测并重建了8株马铃薯亚群中4种病毒（PVY、PVX、PVS、PLRV）和5种PVY基因型的全基因组序列。重新组装纳米孔测序reads产生的单个contigs覆盖了90%以上的病毒基因组，并且与Illumina测序获得的共识序列具有99.5%以上的一致性。有趣的是，共感染同一株植物的PVY的不同分离株获得了单个接近全基因组的contigs。对可用参考病毒基因组的映射读取使我们能够生成接近完整的基因组序列，与illumina衍生的共识具有99.90%以上的一致性。这是第一份描述使用牛津纳米孔公司的MinION检测土豆病毒并进行基因分型的报告。我们重建了PVY和其他RNA病毒的基因组；指出了在马铃薯生产系统中检测病毒的技术潜力，以及研究PVY等高度异质病毒的遗传多样性的技术潜力。
Potato virus Y (PVY) is the most economically important virus infecting cultivated potato (Solanum tuberosum L.). Accurate diagnosis is crucial to regulate the trade of tubers and for the sanitary selection of plant material for propagation. However, high genetic diversity of PVY represents a challenge for the detection and classification of isolates. Here, the diversity of Irish PVY isolates from a germplasm collection and commercial sites was investigated using conventional molecular and serological techniques. Recombinant PVY isolates were prevalent, with PVYNTNa being the predominant genotype. In addition, we evaluated Nanopore sequencing to detect and reconstruct the whole genome sequence of four viruses (PVY, PVX, PVS, PLRV) and five PVY genotypes in a subset of eight potato plants. De novo assembly of Nanopore sequencing reads produced single contigs covering greater than 90% of the viral genome and sharing greater than 99.5% identity to the consensus sequences obtained with Illumina sequencing. Interestingly, single near full genome contigs were obtained for different isolates of PVY co-infecting the same plant. Mapping reads to available reference viral genomes enabled us to generate near complete genome sequences sharing greater than 99.90% identity to the Illumina-derived consensus. This is the first report describing the use of Oxford Nanopore's MinION to detect and genotype potato viruses. We reconstructed the genome of PVY and other RNA viruses; indicating the technologies potential for virus detection in potato production systems, and for the study of genetic diversity of highly heterogeneous viruses such as PVY.