Programa de Pós-Graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Brazil.
Genome Biol Evol. 2012;4(8):689-99. doi: 10.1093/gbe/evs055. Epub 2012 Jul 12.
The genetic similarity observed among species is normally attributed to the existence of a common ancestor. However, a growing body of evidence suggests that the exchange of genetic material is not limited to the transfer from parent to offspring but can also occur through horizontal transfer (HT). Transposable elements (TEs) are DNA fragments with an innate propensity for HT; they are mobile and possess parasitic characteristics that allow them to exist and proliferate within host genomes. However, horizontal transposon transfer (HTT) is not easily detected, primarily because the complex TE life cycle can generate phylogenetic patterns similar to those expected for HTT events. The increasingly large number of new genome projects, in all branches of life, has provided an unprecedented opportunity to evaluate the TE content and HTT events in these species, although a standardized method of HTT detection is required before trends in the HTT rates can be evaluated in a wide range of eukaryotic taxa and predictions about these events can be made. Thus, we propose a straightforward hypothesis test that can be used by TE specialists and nonspecialists alike to discriminate between HTT events and natural TE life cycle patterns. We also discuss several plausible explanations and predictions for the distribution and frequency of HTT and for the inherent biases of HTT detection. Finally, we discuss some of the methodological concerns for HTT detection that may result in the underestimation and overestimation of HTT rates during eukaryotic genome evolution.
在物种间观察到的遗传相似性通常归因于共同祖先的存在。然而，越来越多的证据表明，遗传物质的交换不仅限于从亲代到后代的转移，还可以通过水平转移（HT）发生。转座元件（TEs）是具有固有 HT 倾向的 DNA 片段；它们是移动的，具有寄生特性，使它们能够在宿主基因组中存在和增殖。然而，水平转座子转移（HTT）不易被检测到，主要是因为复杂的 TE 生命周期可以产生与 HTT 事件相似的系统发育模式。越来越多的新基因组计划，在生命的所有分支中，提供了一个前所未有的机会来评估这些物种中的 TE 含量和 HTT 事件，尽管需要一种标准化的 HTT 检测方法，才能在广泛的真核分类群中评估 HTT 率的趋势，并对这些事件进行预测。因此，我们提出了一个简单的假设检验，可以供 TE 专家和非专家使用，以区分 HTT 事件和自然 TE 生命周期模式。我们还讨论了 HTT 的分布和频率以及 HTT 检测固有偏差的几种可能的解释和预测。最后，我们讨论了一些可能导致在真核基因组进化过程中低估和高估 HTT 率的 HTT 检测方法学问题。
