Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
Department of Biology, University of Rochester, Rochester, NY 14627, USA.
Mob DNA. 2013 Sep 23;4(1):20. doi: 10.1186/1759-8753-4-20.
Only a few transposable elements are known to exhibit site-specific insertion patterns, including the well-studied R-element retrotransposons that insert into specific sites within the multigene rDNA. The only known rDNA-specific DNA transposon, Pokey (superfamily: piggyBac) is found in the freshwater microcrustacean, Daphnia pulex. Here, we present a genome-wide analysis of Pokey based on the recently completed whole genome sequencing project for D. pulex.
Phylogenetic analysis of Pokey elements recovered from the genome sequence revealed the presence of four lineages corresponding to two divergent autonomous families and two related lineages of non-autonomous miniature inverted repeat transposable elements (MITEs). The MITEs are also found at the same 28S rRNA gene insertion site as the Pokey elements, and appear to have arisen as deletion derivatives of autonomous elements. Several copies of the full-length Pokey elements may be capable of producing an active transposase. Surprisingly, both families of Pokey possess a series of 200 bp repeats upstream of the transposase that is derived from the rDNA intergenic spacer (IGS). The IGS sequences within the Pokey elements appear to be evolving in concert with the rDNA units. Finally, analysis of the insertion sites of Pokey elements outside of rDNA showed a target preference for sites similar to the specific sequence that is targeted within rDNA.
Based on the target site preference of Pokey elements and the concerted evolution of a segment of the element with the rDNA unit, we propose an evolutionary path by which the ancestors of Pokey elements have invaded the rDNA niche. We discuss how specificity for the rDNA unit may have evolved and how this specificity has played a role in the long-term survival of these elements in the subgenus Daphnia.
只有少数转座元件表现出特定的插入模式，包括研究得很好的 R 元件逆转录转座子，它们插入多基因 rDNA 中的特定位点。唯一已知的 rDNA 特异性 DNA 转座子 Pokey（超家族：piggyBac）存在于淡水微型甲壳动物 Daphnia pulex 中。在这里，我们根据最近完成的 D. pulex 全基因组测序项目，对 Pokey 进行了全基因组分析。
从基因组序列中回收的 Pokey 元件的系统发育分析显示，存在四个谱系，对应于两个不同的自主家族和两个相关的非自主微型反向重复转座元件（MITE）谱系。这些 MITE 也存在于 Pokey 元件相同的 28S rRNA 基因插入位点，并且似乎是自主元件缺失衍生而来的。几个全长 Pokey 元件的副本可能能够产生活性转座酶。令人惊讶的是， Pokey 的两个家族都在转座酶上游有一系列 200bp 的重复序列，这些重复序列来自 rDNA 基因间区（IGS）。 Pokey 元件内的 IGS 序列似乎与 rDNA 单元协同进化。最后，分析 Pokey 元件在 rDNA 之外的插入位点表明，它们对类似于 rDNA 内靶序列的靶序列具有偏好性。
基于 Pokey 元件的靶位点偏好性和元件的一个片段与 rDNA 单元的协同进化，我们提出了一个进化路径，即 Pokey 元件的祖先已经入侵了 rDNA 生态位。我们讨论了 rDNA 单元的特异性是如何进化的，以及这种特异性如何在这些元素在 Daphnia 亚属中的长期生存中发挥作用。
