Deep Sequencing Analysis of Apple Infecting Viruses in Korea.
Deep Sequencing Analysis of Apple Infecting Viruses in Korea.
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DOI：
10.5423/ppj.oa.04.2016.0104
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发表时间：
2016-10
期刊：
影响因子：
--
通讯作者：
Moon JS
中科院分区：
文献类型：
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作者：
Cho IS;Igori D;Lim S;Choi GS;Hammond J;Lim HS;Moon JS
从8个表现出小叶和/或生长迟缓的苹果样品中鉴定出苹果褪绿叶斑病毒(ACLSV)、苹果茎沟病毒(ASGV)、苹果茎痘病毒(ASPV)、苹果绿褶皱相关病毒(AGCaV)和杏潜伏病毒(ApLV)。与5个病毒基因组的参考序列相比，组装的重叠群的核苷酸(NT)序列同源性在68%~99%之间。组装的52个重叠群最丰富地代表了ASPV和ASGV的序列。根据每个组装的重叠群的序列，使用特异性引物进行RT-PCR，证实了这五种病毒在样品中的存在。在三个样本中检测到所有五种病毒，而所有样本都至少与两种病毒混合感染。最常见的病毒是ASPV，其次是ASGV、ApLV、ACLSV和AGCaV，在所检测的样本中未发现混合感染。在组装的重叠群ID 1012480和93549中鉴定到AGCAV，其序列与AGCAV Aurora-1分离物ORF1的核苷酸序列同源性分别为82%和78%。在3个组装的重叠群中检测到ApLV，ID分别为65587、1802365和116777，与ApLV分离物LA2的ORF1的核苷酸序列同源性分别为77%、78%和76%。深度测序技术是检测和鉴定感染苹果树上已知和未知病毒的有效工具，首次在韩国的商业果园中鉴定出ApLV和AGCaV。
Deep sequencing has generated 52 contigs derived from five viruses; Apple chlorotic leaf spot virus (ACLSV), Apple stem grooving virus (ASGV), Apple stem pitting virus (ASPV), Apple green crinkle associated virus (AGCaV), and Apricot latent virus (ApLV) were identified from eight apple samples showing small leaves and/or growth retardation. Nucleotide (nt) sequence identity of the assembled contigs was from 68% to 99% compared to the reference sequences of the five respective viral genomes. Sequences of ASPV and ASGV were the most abundantly represented by the 52 contigs assembled. The presence of the five viruses in the samples was confirmed by RT-PCR using specific primers based on the sequences of each assembled contig. All five viruses were detected in three of the samples, whereas all samples had mixed infections with at least two viruses. The most frequently detected virus was ASPV, followed by ASGV, ApLV, ACLSV, and AGCaV which were withal found in mixed infections in the tested samples. AGCaV was identified in assembled contigs ID 1012480 and 93549, which showed 82% and 78% nt sequence identity with ORF1 of AGCaV isolate Aurora-1. ApLV was identified in three assembled contigs, ID 65587, 1802365, and 116777, which showed 77%, 78%, and 76% nt sequence identity respectively with ORF1 of ApLV isolate LA2. Deep sequencing assay was shown to be a valuable and powerful tool for detection and identification of known and unknown virome in infected apple trees, here identifying ApLV and AGCaV in commercial orchards in Korea for the first time.