School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA.
Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.
Genome Biol Evol. 2024 Aug 5;16(8). doi: 10.1093/gbe/evae157.
Transposable elements (TEs) are repetitive DNA sequences which create mutations and generate genetic diversity across the tree of life. In amniote vertebrates, TEs have been mainly studied in mammals and birds, whose genomes generally display low TE diversity. Squamates (Order Squamata; including ∼11,000 extant species of lizards and snakes) show as much variation in TE abundance and activity as they do in species and phenotypes. Despite this high TE activity, squamate genomes are remarkably uniform in size. We hypothesize that novel, lineage-specific genome dynamics have evolved over the course of squamate evolution. To understand the interplay between TEs and host genomes, we analyzed the evolutionary history of the chicken repeat 1 (CR1) retrotransposon, a TE family found in most tetrapod genomes which is the dominant TE in most reptiles. We compared 113 squamate genomes to the genomes of turtles, crocodilians, and birds and used ancestral state reconstruction to identify shifts in the rate of CR1 copy number evolution across reptiles. We analyzed the repeat landscapes of CR1 in squamate genomes and determined that shifts in the rate of CR1 copy number evolution are associated with lineage-specific variation in CR1 activity. We then used phylogenetic reconstruction of CR1 subfamilies across amniotes to reveal both recent and ancient CR1 subclades across the squamate tree of life. The patterns of CR1 evolution in squamates contrast other amniotes, suggesting key differences in how TEs interact with different host genomes and at different points across evolutionary history.
转座元件 (TEs) 是重复的 DNA 序列，它们在生命之树上产生突变并产生遗传多样性。在羊膜动物脊椎动物中，TEs 主要在哺乳动物和鸟类中进行了研究，它们的基因组通常显示出低的 TE 多样性。有鳞目动物（包括蜥蜴和蛇的约 11000 种现存物种）在 TE 丰度和活性方面的变化与它们在物种和表型方面的变化一样多。尽管 TE 活性很高，但有鳞目动物的基因组大小却非常均匀。我们假设，在有鳞目动物的进化过程中，出现了新的、谱系特异性的基因组动态。为了了解 TE 与宿主基因组之间的相互作用，我们分析了鸡重复 1 (CR1) 反转录转座子的进化历史，这是一种在大多数四足动物基因组中发现的 TE 家族，也是大多数爬行动物中的主要 TE。我们比较了 113 种有鳞目动物的基因组与龟鳖目动物、鳄目动物和鸟类的基因组，并利用祖先状态重建来确定 CR1 拷贝数进化率在爬行动物中的变化。我们分析了 CR1 在有鳞目动物基因组中的重复景观，并确定 CR1 拷贝数进化率的变化与 CR1 活性的谱系特异性变化有关。然后，我们使用 CR1 亚科在羊膜动物中的系统发育重建，揭示了有鳞目动物生命之树上的近期和古代 CR1 亚科。有鳞目动物中 CR1 的进化模式与其他羊膜动物形成对比，这表明 TE 与不同宿主基因组相互作用的方式以及在进化历史的不同时期存在关键差异。
