PDF(Pubmed)
Abstract：
Transposable elements (TEs) and the silencing machinery of their hosts are engaged in a germline arms-race dynamic that shapes TE accumulation and, therefore, genome size. In animal species with extremely large genomes (>10 Gb), TE accumulation has been pushed to the extreme, prompting the question of whether TE silencing also deviates from typical conditions. To address this question, we characterize TE silencing via two pathways-the piRNA pathway and KRAB-ZFP transcriptional repression-in the male and female gonads of Ranodon sibiricus, a salamander species with a ∼21 Gb genome. We quantify 1) genomic TE diversity, 2) TE expression, and 3) small RNA expression and find a significant relationship between the expression of piRNAs and TEs they target for silencing in both ovaries and testes. We also quantified TE silencing pathway gene expression in R. sibiricus and 14 other vertebrates with genome sizes ranging from 1 to 130 Gb and find no association between pathway expression and genome size. Taken together, our results reveal that the gigantic R. sibiricus genome includes at least 19 putatively active TE superfamilies, all of which are targeted by the piRNA pathway in proportion to their expression levels, suggesting comprehensive piRNA-mediated silencing. Testes have higher TE expression than ovaries, suggesting that they may contribute more to the species\' high genomic TE load. We posit that apparently conflicting interpretations of TE silencing and genomic gigantism in the literature, as well as the absence of a correlation between TE silencing pathway gene expression and genome size, can be reconciled by considering whether the TE community or the host is currently \"on the attack\" in the arms race dynamic.
摘要：
可转座元素（TE）及其宿主的沉默机制参与了种系军备竞赛动态，形成了TE的积累，因此,基因组大小。在具有极大基因组（>10Gb）的动物物种中，TE积累已经被推到了极致，提示TE沉默是否也偏离典型条件的问题。为了解决这个问题，我们描述了通过两种途径-piRNA途径和KRAB-ZFP转录抑制-在Ranodonsibiricus的雄性和雌性性腺中的TE沉默，具有21Gb基因组的sal物种。我们量化1)基因组TE多样性，2）TE表达式，和3）小RNA表达，并发现piRNA的表达与它们在卵巢和睾丸中沉默的TEs之间存在显着关系。我们还定量了在基因组大小为1至130Gb的西比氏菌和14种其他脊椎动物中的TE沉默途径基因表达，并且发现途径表达与基因组大小之间没有关联。一起来看,我们的结果表明，巨大的sibiricus基因组包括至少19个假定活跃的TE超家族，所有这些都是piRNA途径的目标，与它们的表达水平成比例，提示piRNA介导的全面沉默。睾丸的TE表达高于卵巢，这表明它们可能对物种的高基因组TE负荷做出更多贡献。我们认为，文献中对TE沉默和基因组巨人症的解释显然是相互矛盾的，以及TE沉默途径基因表达与基因组大小之间缺乏相关性，可以通过考虑TE社区或主机当前是否处于军备竞赛动态中的“攻击中”来调和。
