PDF(Pubmed)
Abstract：
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.
摘要：
转座因子（TE）是重复的DNA序列，可在整个生命树中产生突变并产生遗传多样性。在羊膜脊椎动物中，TEs主要在哺乳动物和鸟类中进行研究，其基因组通常表现出低TE多样性。Squamates（秩序Squamata；包括〜11,000种现存的蜥蜴和蛇）在TE丰度和活性上的变化与在物种和表型上的变化一样多。尽管TE活性很高，鳞状细胞的基因组大小非常均匀。我们假设那本小说，谱系特定的基因组动力学在squamate进化过程中已经进化。为了理解TEs和宿主基因组之间的相互作用，我们分析了CR1反转录转座子的进化史,在大多数四足动物基因组中发现的TE家族，是大多数爬行动物中的显性TE。我们比较了113个鳞状细胞基因组和海龟的基因组，鳄鱼,和鸟,并使用祖先状态重建来确定爬行动物之间CR1拷贝数进化速率的变化。我们分析了鳞状基因组中CR1的重复景观，并确定CR1拷贝数进化速率的变化与CR1活性的谱系特异性变化有关。然后，我们使用跨羊膜的CR1亚科的系统发育重建来揭示跨角化生命树的近期和古代CR1亚进化。鳞茎中CR1的进化模式与其他羊膜相反，提示TEs如何与不同宿主基因组以及在进化史上的不同点相互作用的关键差异。
