转座因子（TEs）的基因组景观在不同物种中变化巨大，有些TEs表现出比其他物种更容易在特定谱系上定殖的成功。 在哺乳动物中，LINE逆转录转座子通常比任何其他TE更常见。在这里，我们报告了鹿鼠Peromyscus maniculatus中TEs的异常基因组景观。与先前检查过的其他哺乳动物相比，LTR元素占鹿鼠基因组的比例更高（分别为11％和10％）。这种模式反映了相对较低的LINE活性和一次大规模的特定谱系内源性逆转录病毒（ERVs）入侵。鹿鼠ERVs具有各种起源，涵盖逆转录病毒分类学，表明它们一直是广泛的外源性逆转录病毒的宿主。值得注意的是，我们追溯了一条ERV谱系的起源，它约在5-18百万年前，源于猫白血病病毒的近亲，揭示了亚目间的水平传播。几个特定谱系的ERV亚科族群具有非常高的拷贝数，其中前五个最丰富的约占基因组的2％。我们还观察到Kruppel相关盒结构域含锌指基因（KZNFs）的大规模扩增，这些基因可能控制ERV活性，其扩张可能得到ERV之间的异位重组的促进。最后，我们发现ERV直接影响了LINE的进化轨迹，通过与它们竞争基因组位点并频繁破坏自主LINE拷贝。总之，我们的结果阐明了塑造独特鹿鼠TE景观的基因组生态学，揭示了导致哺乳动物基因组结构变异的进化过程。©作者（2023）。由牛津大学出版社代表分子生物与进化学会出版。

The genomic landscape of transposable elements (TEs) varies dramatically across species, with some TEs demonstrating greater success in colonizing particular lineages than others. In mammals, LINE retrotransposons are typically more common than any other TE. Here, we report an unusual genomic landscape of TEs in the deer mouse, Peromyscus maniculatus. In contrast to other previously examined mammals, LTR elements occupy more of the deer mouse genome than LINEs (11% and 10% respectively). This pattern reflects a combination of relatively low LINE activity and a massive invasion of lineage-specific endogenous retroviruses (ERVs). Deer mouse ERVs exhibit diverse origins spanning the retroviral phylogeny suggesting they have been host to a wide range of exogenous retroviruses. Notably, we trace the origin of one ERV lineage, which arose ∼5-18 million years ago, to a close relative of feline leukemia virus, revealing inter-ordinal horizontal transmission. Several lineage-specific ERV subfamilies have very high copy numbers, with the top five most abundant accounting for ∼2% of the genome. We also observe a massive amplification of Kruppel-associated box domain-containing zinc finger genes (KZNFs), which likely control ERV activity and whose expansion may have been facilitated by ectopic recombination between ERVs. Finally, we find evidence that ERVs directly impacted the evolutionary trajectory of LINEs by outcompeting them for genomic sites and frequently disrupting autonomous LINE copies. Together, our results illuminate the genomic ecology that shaped the unique deer mouse TE landscape, shedding light on the evolutionary processes that give rise to variation in mammalian genome structure.© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.