一个警告:内源性病毒元素如何影响转录基因数据中的病毒发现.
Nadja Brait1, Thomas Hackl, Côme Morel2
1Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen 9747 AG, The Netherlands.
Virus evolution
|March 22, 2024
概括
宿主基因组中的内源性病毒元素 (EVE) 在RNA-Seq数据中可以被误认为是活跃的病毒感染. 这项研究表明,EVE影响病毒发现的准确性,需要更好的方法来区分它们与真正的病毒序列.
科学领域:
- 病毒学 病毒学
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
背景情况:
- 大基因组和转录组研究扩大了对病毒多样性的知识.
- 嵌入宿主基因组的内源性病毒元素 (EVE) 在病毒发现中经常被忽视,特别是在RNA-Seq数据中.
- 将EVE与活跃病毒感染区分开来是一项重大挑战,可能会影响分析和分类.
研究的目的:
- 系统地评估EVE对病毒发现管道的影响.
- 评估EVE如何影响数据完整性和分类准确性.
- 为从转录基因数据中发现病毒提供改善实践的建议.
主要方法:
- 对EVE和与Orthomyxoviridae相关的外源性病毒序列的分析.
- 对来自Culicinae蚊子的13个基因组和538个转录组数据集的检查.
- 在EVE的存在下评估原型病毒发现管道的性能.
主要成果:
- 在转录基因数据中检测到的大量病毒序列被确定为EVE的转录,而不是活跃的病毒.
- 从外源病毒中区分转录EVE是具有挑战性的,特别是在病毒丰度较低的样本中.
- 映射读取主机基因组与EVE减少了EVE负担,但减少了病毒命中数量和组装质量.
结论:
- 存在EVE可以改变感知到的病毒遗传多样性,导致假阳性和不准确的序列信息.
- 准确识别和管理EVE对于可靠的病毒发现和理解病毒多样性至关重要.
- 需要改进的生物信息学策略来区分EVE转录与转录基因数据集中的真实病毒序列.
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