Central Veterinary Institute of Wageningen UR, Lelystad, The Netherlands.
J Virol. 2012 Sep;86(18):10150-61. doi: 10.1128/JVI.01271-12. Epub 2012 Jul 11.
We used deep sequencing of poly(A) RNA to characterize the transcriptome of an economically important eel virus, anguillid herpesvirus 1 (AngHV1), at a stage during the lytic life cycle when infectious virus was being produced. In contrast to the transcription of mammalian herpesviruses, the overall level of antisense transcription from the 248,526-bp genome was low, amounting to only 1.5% of transcription in predicted protein-coding regions, and no abundant, nonoverlapping, noncoding RNAs were identified. RNA splicing was found to be more common than had been anticipated previously. Counting the 10,634-bp terminal direct repeat once, 100 splice junctions were identified, of which 58 were considered likely to be involved in the expression of functional proteins because they represent splicing between protein-coding exons or between 5' untranslated regions and protein-coding exons. Each of the 30 most highly represented of these 58 splice junctions was confirmed by RT-PCR. We also used deep sequencing to identify numerous putative 5' and 3' ends of AngHV1 transcripts, confirming some and adding others by rapid amplification of cDNA ends (RACE). The findings prompted a revision of the AngHV1 genome map to include a total of 129 protein-coding genes, 5 of which are duplicated in the terminal direct repeat. Not counting duplicates, 11 genes contain integral, spliced protein-coding exons, and 9 contain 5' untranslated exons or, because of alternative splicing, 5' untranslated and 5' translated exons. The results of this study sharpen our understanding of AngHV1 genomics and provide the first detailed view of a fish herpesvirus transcriptome.
我们使用聚腺苷酸（poly(A)）RNA 深度测序技术，在传染性病毒产生的裂解生命周期阶段，对经济上重要的鳗鲡疱疹病毒 1（AngHV1）的转录组进行了特征分析。与哺乳动物疱疹病毒的转录不同，来自 248526bp 基因组的反义转录总体水平较低，仅占预测蛋白编码区转录的 1.5%，并且未鉴定出大量、不重叠的非编码 RNA。发现 RNA 剪接比以前预期的更为常见。如果将 10634bp 的末端直接重复计算一次，共鉴定出 100 个剪接接头，其中 58 个可能与功能性蛋白的表达有关，因为它们代表蛋白编码外显子之间或 5'非翻译区与蛋白编码外显子之间的剪接。这 58 个剪接接头中最具代表性的 30 个，每个都通过 RT-PCR 进行了验证。我们还使用深度测序技术鉴定了大量 AngHV1 转录物的假定 5'和 3'末端，通过快速扩增 cDNA 末端 (RACE) 证实了一些，并添加了其他末端。这些发现促使我们对 AngHV1 基因组图谱进行了修订，共包括 129 个蛋白编码基因，其中 5 个在末端直接重复中重复。不包括重复，11 个基因包含完整的、拼接的蛋白编码外显子，9 个基因包含 5'非翻译外显子或由于选择性剪接，包含 5'非翻译和 5'翻译外显子。这项研究的结果加深了我们对 AngHV1 基因组学的理解，并提供了鱼类疱疹病毒转录组的第一个详细视图。
