Genome of sea anemone Exaiptasia pallida and microRNA-messenger RNA interactome of tentacle regeneration

Cnidarians including sea anemones, corals, hydra, and jellyfishes are a group of animals well known for their regeneration capacity. However, how noncoding RNAs such as microRNAs contribute to the mechanisms underlying in their tissue regeneration in is poorly understood. Here, we sequenced and assembled the genome of a sea anemone Exaiptasia pallida collected in Hong Kong waters. The assembled genome size of E. pallida is 229.21 Mb with a scaffold N50 of 10.58 Mb and BUSCO completeness at 88.2 %. Tenacles of E. pallida were excised and cultured at three temperatures (17°C, 22°C, and 27°C). While tentacles regeneration was slowest for animals cultured at 17 °C, they also experienced highest regeneration and lowest mortality rates. Both mRNA and microRNA were also sequenced at 9 timepoints from regenerating tentacles at 22°C , including 0 hours, 6 hours, 12 hours, 18 hours, 1 day, 2 days, 3 days, 6 days, and 8 days. Based on expression profiles and binding energy, 11 pairs of microRNA:mRNA were predicted to participate during tentacle regeneration. Among them, 3 pairs were also validated by luciferase reporter assays, including miR-2037:TFAP2E, miR-2037:RBCK1, and a novel microRNA Sc6vya5_7176_790104:RBCK1. The established sea anemone model will be useful for further investigation of cnidarian biology, evolution, and effect under climate change.

刺胞动物（Cnidarians）是一类以卓越再生能力闻名的动物类群，包含海葵、珊瑚、水螅与水母。然而，microRNA（microRNA）这类非编码RNA如何参与其组织再生的分子机制，目前仍有待深入阐释。本研究对采集自香港海域的海葵Exaiptasia pallida（Exaiptasia pallida）进行了基因组测序与组装。该物种的组装基因组大小为229.21 Mb，scaffold N50值达10.58 Mb，BUSCO完整度为88.2%。研究人员切除了E. pallida的触手，并将其分别置于17℃、22℃与27℃三种温度条件下培养。尽管17℃培养组的触手再生速度最慢，但该组的再生成功率最高且死亡率最低。此外，研究人员对22℃培养条件下再生的触手，在9个时间点采集样本并进行了mRNA与microRNA测序，时间点分别为0小时、6小时、12小时、18小时、1天、2天、3天、6天与8天。基于表达谱与结合能分析，本研究预测共有11对microRNA:mRNA调控关系参与触手再生过程。其中3对调控关系通过荧光素酶报告基因实验（luciferase reporter assays）得到验证，分别为miR-2037:TFAP2E、miR-2037:RBCK1以及新型microRNA Sc6vya5_7176_790104:RBCK1。本研究构建的海葵模型将为刺胞动物生物学、演化以及气候变化影响的后续研究提供重要研究工具。