逆转录病毒可以整合到宿主基因组中形成内源性逆转录病毒。内源性逆转录病毒可为研究逆转录病毒的宏进化及逆转录病毒与宿主之间互作的机制提供重要的“分子化石”。迄今为止，有关内源性逆转录病毒的系统研究主要集中在哺乳类和鸟类中，而对鱼类、两栖类和爬行类等低等脊椎动物内源性逆转录病毒的研究较为缺乏。本项目拟采用大规模比较基因组学的方法，在低等脊椎动物基因组中系统地挖掘内源性逆转录病毒，揭示低等脊椎动物逆转录病毒多样性和进化的时间尺度。通过对低等脊椎动物内源性逆转录病毒以及其它代表性逆转录病毒的比较分析来完善逆转录病毒分类系统，探讨逆转录病毒不同传播模式（与宿主共进化或跨物种传播）及其相对频率，解析起源于远古鱼类的逆转录病毒“登陆”感染陆生脊椎动物的模式，从而有助于全面了解逆转录病毒的起源、进化和多样性。

Retroviruses could be integrated into the host genomes, forming endogenous retroviruses (ERVs). ERVs provide “molecular fossils” for studying the macroevolution of retroviruses and the mechanism of retrovirus-host interaction. While ERVs have been mainly studied in mammals and birds, little is known about ERVs in lower vertebrates, such as fishes, amphibians, and reptiles. This project is to use large-scale comparative genomics approaches to mine ERVs within the genomes of lower vertebrates and reveal the diversity and evolutionary time scale of retroviruses in lower vertebrates. Through analyzing ERVs of lower vertebrates and other representative retroviruses, this project aims to refine the classification system of retroviruses, explore the relative frequency of different transmission modes (co-divergence and cross-species transmission) of retroviruses, and reveal the terrestrialization modes of retroviruses that have an ancient marine origin. This project has important implications in understanding the origin, evolution, and diversity of retroviruses.