There is massive variation in intron numbers across eukaryotic genomes, yet the major drivers of intron content during evolution remain elusive. Rapid intron loss and gain in some lineages contrast with long-term evolutionary stasis in others. Episodic intron gain could be explained by recently discovered specialized transposons called Introners, but so far Introners are only known from a handful of species. Here, we performed a systematic search across 3,325 eukaryotic genomes and identified 27,563 Introner-derived introns in 175 genomes (5.2%). Species with Introners span remarkable phylogenetic diversity, from animals to basal protists, representing lineages whose last common ancestor dates to over 1.7 billion years ago. Aquatic organisms were 6.5 times more likely to contain Introners than terrestrial organisms. Introners exhibit mechanistic diversity but most are consistent with DNA transposition, indicating that Introners have evolved convergently hundreds of times from nonautonomous transposable elements. Transposable elements and aquatic taxa are associated with high rates of horizontal gene transfer, suggesting that this combination of factors may explain the punctuated and biased diversity of species containing Introners. More generally, our data suggest that Introners may explain the episodic nature of intron gain across the eukaryotic tree of life. These results illuminate the major source of ongoing intron creation in eukaryotic genomes.

中文翻译：

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转座因子驱动多种真核生物中的内含子获得

真核生物基因组中的内含子数量存在巨大差异，但进化过程中内含子含量的主要驱动因素仍然难以捉摸。某些谱系中内含子的快速丢失和获得与其他谱系中的长期进化停滞形成对比。偶发性内含子增益可以用最近发现的称为内含子的特殊转座子来解释，但到目前为止，内含子只存在于少数几个物种中。在这里，我们对 3,325 个真核基因组进行了系统搜索，并在 175 个基因组 (5.2%) 中鉴定了 27,563 个内含子衍生的内含子。具有内含子的物种跨越显着的系统发育多样性，从动物到基础原生生物，代表其最后共同祖先可追溯到 17 亿多年前的谱系。水生生物含有内含子的可能性是陆生生物的 6.5 倍。内含子表现出机制多样性，但大多数与 DNA 转座一致，表明内含子已经从非自主转座因子趋同进化了数百次。转座因子和水生分类群与高水平基因转移率相关，这表明这些因素的组合可以解释含有内含子的物种的间断和有偏见的多样性。更一般地说，我们的数据表明，内含子可以解释真核生命树中内含子获得的偶发性。这些结果阐明了真核基因组中持续产生内含子的主要来源。转座因子和水生分类群与高水平基因转移率相关，这表明这些因素的组合可以解释含有内含子的物种的间断和有偏见的多样性。更一般地说，我们的数据表明，内含子可以解释真核生命树中内含子获得的偶发性。这些结果阐明了真核基因组中持续产生内含子的主要来源。转座因子和水生分类群与高水平基因转移率相关，这表明这些因素的组合可以解释含有内含子的物种的间断和有偏见的多样性。更一般地说，我们的数据表明，内含子可以解释真核生命树中内含子获得的偶发性。这些结果阐明了真核基因组中持续产生内含子的主要来源。