Institute of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.
Methods Mol Biol. 2021;2250:177-187. doi: 10.1007/978-1-0716-1134-0_17.
Transposable elements (TEs) are an important cause of evolutionary change and functional diversity, yet they are routinely discarded in the first steps of many analyses. In this chapter we show how, given a reference genome, TEs can be incorporated fairly easily into functional and evolutionary studies. We offer a glimpse into a program which detects TE insertion polymorphisms and discuss practical issues arising from the diversity of TEs and genome architectures. Detecting TE polymorphisms relies on a series of ad hoc criteria because, in contrast to single nucleotide polymorphisms, there is no general way to model TE activity. Signatures of TE polymorphisms in reference-aligned reads depend on the type of TE as well as on the complexity of the genomic background. As a consequence, a basic understanding of the limitations imposed by the data and of what the algorithm is doing is important to obtain reliable results. Here, we hope to convey such a basic understanding and help researchers to avoid some of the common pitfalls of TE polymorphism detection.
转座元件（TEs）是进化改变和功能多样性的重要原因，但在许多分析的第一步中，它们通常被丢弃。在本章中，我们展示了如何在给定参考基因组的情况下，相当容易地将 TEs 纳入功能和进化研究中。我们提供了一个程序的概览，该程序可以检测 TE 插入多态性，并讨论了由于 TEs 和基因组结构的多样性而产生的实际问题。检测 TE 多态性依赖于一系列特定的标准，因为与单核苷酸多态性不同，没有通用的方法来模拟 TE 的活性。参考比对读取中 TE 多态性的特征取决于 TE 的类型以及基因组背景的复杂性。因此，基本了解数据所施加的限制以及算法的工作原理对于获得可靠的结果非常重要。在这里，我们希望传达这样的基本理解，并帮助研究人员避免 TE 多态性检测中一些常见的陷阱。
