Transposable element (TE) sequences are classified into families based on the reconstructed history of replication, and into subfamilies based on more fine-grained features that are often intended to capture family history. We evaluate the reliability of annotation with common subfamilies by assessing the extent to which subfamily annotation is reproducible in replicate copies created by segmental duplications in the human genome, and in homologous copies shared by human and chimpanzee. We find that standard methods annotate over 10% of replicates as belonging to different subfamilies, despite the fact that they are expected to be annotated as belonging to the same subfamily. Point mutations and homologous recombination appear to be responsible for some of this discordant annotation (particularly in the young Alu family), but are unlikely to fully explain the annotation unreliability. The surprisingly high level of disagreement in subfamily annotation of homologous sequences highlights a need for further research into definition of TE subfamilies, methods for representing subfamily annotation confidence of TE instances, and approaches to better utilizing such nuanced annotation data in downstream analysis.

中文翻译：

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转座因子亚族注释存在重现性问题

转座因子 (TE) 序列根据重建的复制历史分为家族，并根据通常旨在捕获家族史的更细粒度的特征分为亚家族。我们通过评估亚科注释在人类基因组中由节段重复创建的复制副本以及人类和黑猩猩共享的同源副本中的可再现程度来评估具有常见亚科的注释的可靠性。我们发现标准方法将超过 10% 的复制品注释为属于不同的亚科，尽管它们预计会被注释为属于同一个亚科。点突变和同源重组似乎是造成这种不一致注释的原因（尤其是在年轻的 Alu 家族中），但不太可能完全解释注释的不可靠性。同源序列的亚科注释中令人惊讶的高度分歧突出表明需要进一步研究 TE 亚科的定义、表示 TE 实例的亚科注释置信度的方法以及在下游分析中更好地利用这种细微的注释数据的方法。