Data from: Small RNAs from a big genome: the piRNA pathway and transposable elements in the salamander species Desmognathus fuscus

Most of the largest vertebrate genomes are found in salamanders, a clade of amphibians that includes 686 species. Salamander genomes range in size from 14 to 120 Gb, reflecting the accumulation of large numbers of transposable element (TE) sequences from all three TE classes. Although DNA loss rates are slow in salamanders relative to other vertebrates, high levels of TE insertion are also likely required to explain such high TE loads. Across the Tree of Life, novel TE insertions are suppressed by several pathways involving small RNA molecules. In most known animals, TE activity in the germline is primarily regulated by the Piwi-interacting RNA (piRNA) pathway. In this study, we test the hypothesis that salamanders’ unusually high TE loads reflect the loss of the ancestral piRNA-mediated TE-silencing machinery. We characterized the small RNA pool in the female and male adult gonads, testing for the presence of small RNA molecules that bear the characteristics of TE-targeting piRNAs. We also analyzed the amino acid sequences of piRNA pathway proteins from salamanders and other vertebrates, testing whether the overall patterns of sequence divergence are consistent with conserved pathway function across the vertebrate clade. Our results do not support the hypothesis of piRNA pathway loss; instead, they suggest that the piRNA pathway is expressed in salamanders. Given these results, we propose hypotheses to explain how the extraordinary TE loads in salamander genomes could have accumulated, despite the expression of TE-silencing machinery.蝾螈（salamander）是两栖动物的一个演化支，共计686个物种，而绝大多数基因组规模最大的脊椎动物基因组均来自该类群。蝾螈的基因组大小跨度为14至120 Gb，这一特征反映出其基因组中积累了大量来自三类转座子（transposable element, TE）的序列。尽管相较于其他脊椎动物，蝾螈的DNA丢失速率较慢，但要解释其基因组中如此高的转座子负载量，仍需借助高水平的转座子插入事件。在整个生命之树中，新型转座子插入事件会被多条涉及小分子RNA的调控通路所抑制。在绝大多数已被研究的动物中，生殖系内的转座子活性主要由Piwi互作RNA（Piwi-interacting RNA, piRNA）通路调控。本研究旨在验证如下假说：蝾螈基因组中异常高的转座子负载量，源于其祖先的Piwi互作RNA介导的转座子沉默机制发生了丢失。我们对成年雌雄个体的性腺中小RNA库进行了表征分析，以检测是否存在具备靶向转座子的Piwi互作RNA特征的小分子RNA。我们还分析了蝾螈及其他脊椎动物的Piwi互作RNA通路蛋白的氨基酸序列，以验证序列分化的整体模式是否符合脊椎动物演化支中该通路功能保守的预期。本研究结果并不支持Piwi互作RNA通路丢失这一假说，反而表明该通路在蝾螈体内得以正常表达。基于上述结果，我们提出了若干假说，以解释尽管蝾螈体内存在转座子沉默机制，其基因组仍能积累如此海量的转座子序列。