CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
Commun Biol. 2021 Feb 11;4(1):186. doi: 10.1038/s42003-021-01716-y.
Simple sequence repeats (SSRs) are rare (approximately 1%) in most genomes and are generally considered to have no function. However, penaeid shrimp genomes have a high proportion of SSRs (>23%), raising the question of whether these SSRs play important functional and evolutionary roles in these SSR-rich species. Here, we show that SSRs drive genome plasticity and adaptive evolution in two penaeid shrimp species, Fenneropenaeus chinensis and Litopenaeus vannamei. Assembly and comparison of genomes of these two shrimp species at the chromosome-level revealed that transposable elements serve as carriers for SSR expansion, which is still occurring. The remarkable genome plasticity identified herein might have been shaped by significant SSR expansions. SSRs were also found to regulate gene expression by multi-omics analyses, and be responsible for driving adaptive evolution, such as the variable osmoregulatory capacities of these shrimp under low-salinity stress. These data provide strong evidence that SSRs are an important driver of the adaptive evolution in penaeid shrimp.
简单序列重复（SSRs）在大多数基因组中较为罕见（约 1%），通常被认为没有功能。然而，对虾基因组中 SSR 的比例较高（>23%），这引发了一个问题，即在这些富含 SSR 的物种中，这些 SSR 是否发挥了重要的功能和进化作用。在这里，我们展示了 SSRs 在两种对虾物种，中国明对虾和凡纳滨对虾中驱动基因组可塑性和适应性进化。对这两个虾物种的染色体水平基因组组装和比较表明，转座元件作为 SSR 扩展的载体，这一过程仍在发生。本文中鉴定的显著的基因组可塑性可能是由显著的 SSR 扩展所塑造的。多组学分析还发现 SSRs 可以调节基因表达，并负责驱动适应性进化，例如这些虾在低盐度胁迫下可变的渗透压调节能力。这些数据为 SSRs 是对虾适应性进化的重要驱动因素提供了有力证据。
