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.

中文翻译：

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鸡参考基因组的落脚鸡：研究多态性内源性逆转录病毒的陷阱

高质量的参考基因组促进了内源性逆转录病毒 (ERV) 的研究。然而，越来越多的已发表作品假设参考基因组中的 ERV 是通用的；甚至那些进化上最近的集成。因此，这些研究未能正确表征多态性 ERV，甚至提出 ERV 的生物学功能，而这些功能实际上可能不存在于感兴趣的基因组中。在这里，我概述了鸡内源性禽白血病病毒（ALVE 或“ev 基因”：“原始”ERV）的三项研究的陷阱，所有这些研究都被参考基因组提供了具有代表性的 ALVE 基线的假设所混淆。