Jack Birch Unit for Molecular Carcinogenesis, The Department of Biology and York Biomedical Research Institute, The University of York, York, YO10 5DD, UK.
Retrovirology. 2021 Apr 20;18(1):10. doi: 10.1186/s12977-021-00555-3.
High quality reference genomes have facilitated the study of endogenous retroviruses (ERVs). However, there are an increasing number of published works which assume the ERVs in reference genomes are universal; even those of evolutionarily recent integrations. Consequently, these studies fail to properly characterise polymorphic ERVs, and even propose biological functions for ERVs that may not actually be present in the genomes of interest. Here, I outline the pitfalls of three studies of chicken endogenous Avian Leukosis Viruses (ALVEs or "ev genes": the "original" ERVs), all confounded by the assumption that the reference genome provides a representative ALVE baseline.
高质量的参考基因组促进了内源性逆转录病毒（ERVs）的研究。然而，越来越多的已发表的研究假设参考基因组中的 ERVs 是普遍存在的；即使是那些进化上最近整合的 ERVs 也是如此。因此，这些研究未能正确描述多态性 ERVs，甚至为 ERVs 提出了可能实际上不存在于感兴趣的基因组中的生物学功能。在这里，我概述了三项关于鸡内源性禽白血病病毒（ALVEs 或“ev 基因”：“原始”ERVs）的研究的陷阱，所有这些研究都因假设参考基因组提供了一个代表性的 ALVE 基线而受到混淆。
