对虾基因组简单重复序列的爆发与适应性进化研究

Environmental adaptive evolution is one of the hot topic in scientific research, and genome decoding is considered to be the major way for the environmental adaptive evolution analysis. As a component of genome, simple sequence repeats (SSRs) only account for less than 1% of genome in most species, and rarely research report for the adaptive evolution of SSRs. Whereas, our recent researches identified highly abundant of SSRs in penaeid shrimps. SSRs represent the most abundant repeat type (23.93%) in the genome of the shrimp Litopenaeus vannamei, which is the highest among the species whose genome are available. However, rare researches reported how can these SSRs retained and significantly expanded, as well as the relationship between SSR expansion and shrimp adaptive evolution during the ancient and present evolutionary history. In this project, in order to investigate the mechanism of the origin and expansion of SSRs, we decide to perform comparative genomics analysis based on the genome of penaeid shrimps and close related species. Then, a series of adaptive evolution analyses will be utilized for the research of the relationship between SSR expansion and shrimp adaptive evolution. Finally, a series of experiments can be implemented to prove the crucial function of these SSRs in shrimps. This study will contribute to the understanding of the essential roles of SSRs in environmental adaptive evolution, which will provide a new way for adaptive evolution analysis.

生物的环境适应性进化是当前科学研究的热点问题，基因组组成和结构的变化则是衡量物种适应环境的重要依据，然而鲜有简单重复序列（SSR）作为物种适应性进化分子证据的报道。绝大多数已测基因组物种SSR含量都低于1%，但最近研究发现对虾科物种基因组SSR含量普遍较高，在凡纳滨对虾中高达23.93%，是已测基因组中含量最高的物种。然而，关于对虾SSR是如何扩增并保留下来的，以及SSR的爆发与地质历史时期海洋环境剧变之间的关系未见报道。本项目拟在对虾基因组基础上，利用生物信息学和比较基因组学建立全基因组尺度SSR分析方法，解析对虾SSR的起源与进化机制；探索SSR的扩增与对虾科祖先起源、以及地质历史时期海洋环境剧变后环境适应性进化之间的关系；通过分子生物学实验解析SSR在环境适应过程中的关键功能。本项目将为阐释SSR与环境适应性进化之间关系提供重要理论基础，为物种环境适应性进化提供新的思路和方法学指导。

简单重复序列（SSR）由于其序列简单化和普遍含量低，关于其功能的研究相对匮乏。对虾基因组高含量的SSR为我们解析SSR扩张机制以及适应性进化提供了重要基础。本课题对凡纳滨对虾、中国明对虾、中华绒螯蟹进行了高深度的三代PacBio测序和全基因组组装，构建了染色体水平的基因组图谱，并对多个十足目物种进行了低深度的二代全基因组测序和组装。通过比较基因组学分析，发现高含量的SSR是对虾科物种共同的显著特征，揭示了SSR的爆发式扩张与对虾科起源与演化的密切关系。首次发现了SSR爆发式扩张的新机制，与传统经验上的复制滑动突变模型不同，我们发现对虾SSR的爆发式扩张主要与转座元件的携带有关。突破了常规的SSR无功能的思维定式，发现SSR在对虾基因组可塑性和环境适应中具有重要作用，SSR能富集于染色体开放可及区，参与基因的表达调控过程。本研究通过多组学测序和比较组学分析，揭示了SSR在对虾起源、演化，以及适应性进化过程中的关键作用，为对虾生物学遗传解析和分子设计育种提供了基础。