Sookdeo Akash, Hepp Crystal M, Boissinot Stéphane
1Department of Biology, New York University, New York, NY USA.
2School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ USA.
Mob DNA. 2018 Mar 28;9:12. doi: 10.1186/s13100-018-0117-4. eCollection 2018.
LINE-1 (L1) is the dominant autonomously replicating non-LTR retrotransposon in mammals. Although our knowledge of L1 evolution across the tree of life has considerably improved in recent years, what we know of L1 evolution in mammals is biased and comes mostly from studies in primates (mostly human) and rodents (mostly mouse). It is unclear if patterns of evolution that are shared between those two groups apply to other mammalian orders. Here we performed a detailed study on the evolution of L1 in perissodactyls by making use of the complete genome of the domestic horse and of the white rhinoceros. This mammalian order offers an excellent model to study the extinction of L1 since the rhinoceros is one of the few mammalian species to have lost active L1.
We found that multiple L1 lineages, carrying different 5'UTRs, have been simultaneously active during the evolution of perissodactyls. We also found that L1 has continuously amplified and diversified in horse. In rhinoceros, L1 was very prolific early on. Two successful families were simultaneously active until ~20my ago but became extinct suddenly at exactly the same time.
The general pattern of L1 evolution in perissodactyls is very similar to what was previously described in mouse and human, suggesting some commonalities in the way mammalian genomes interact with L1. We confirmed the extinction of L1 in rhinoceros and we discuss several possible mechanisms.
LINE-1（L1）是哺乳动物中主要的自主复制非长末端重复逆转座子。尽管近年来我们对L1在整个生命树中的进化的了解有了显著提高，但我们对L1在哺乳动物中的进化的了解存在偏差，且大多来自灵长类动物（主要是人类）和啮齿动物（主要是小鼠）的研究。尚不清楚这两组动物共有的进化模式是否适用于其他哺乳动物目。在这里，我们利用家马和白犀牛的完整基因组对奇蹄目动物中L1的进化进行了详细研究。这个哺乳动物目为研究L1的灭绝提供了一个极好的模型，因为犀牛是少数失去活跃L1的哺乳动物物种之一。
我们发现，在奇蹄目动物的进化过程中，携带不同5'非翻译区的多个L1谱系同时活跃。我们还发现L1在马中持续扩增并多样化。在犀牛中，L1早期非常活跃。两个成功的家族在约2000万年前同时活跃，但在同一时间突然灭绝。
奇蹄目动物中L1进化的总体模式与之前在小鼠和人类中描述的非常相似，这表明哺乳动物基因组与L1相互作用的方式存在一些共性。我们证实了犀牛中L1的灭绝，并讨论了几种可能的机制。
