Institute of Fisheries Science, National Taiwan University, Taipei, 10617, Taiwan.
Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, 277-0882, Japan.
Mar Biotechnol (NY). 2024 Nov 26;27(1):8. doi: 10.1007/s10126-024-10391-z.
Octocorals, vital components of reef ecosystems, inhabit various marine environments across diverse climate zones, spanning from tropical shallows to frigid deep-sea regions. Certain octocoral species, notably Lobophytum and Sinularia, are particularly intriguing due to their production of diverse metabolites, warranting continuous investigation. Although octocorals played the roles in coral ecosystems, the studies are rare in comparison to scleractinian corals, especially in transcriptomic and genomic data. However, RNA extraction was massively interfered by the polysaccharides and secondary metabolites produced from octocoral holobiont. For this purpose, five lysis buffer systems and two extraction processes were examined for the RNA extraction efficiency in octocorals. We found CTAB/10%SDS as a new method for RNA extraction from six different octocoral genera. Furthermore, our new method is enable to extract RNA with good quality for downstream application such as quantitative PCR and RNA sequencing. Finally, comparative transcriptomic analysis between healthy octocorals and those dark-induced bleaching corals in Lobophytum hsiehi revealed extracellular matrix and immunity-related genes may play the important roles in coral-symbiodinium symbiosis. We believe that this study's findings and the developed RNA extraction method will serve as valuable references for future research, particularly in octocorals.
八放珊瑚，作为珊瑚礁生态系统的重要组成部分，栖息于各种海洋环境中，涵盖了从热带浅海到严寒深海的多样气候带。某些八放珊瑚物种，特别是 Lobophytum 和 Sinularia，因其产生多样化的代谢产物而备受关注，值得持续研究。尽管八放珊瑚在珊瑚生态系统中发挥着重要作用，但与石珊瑚相比，相关研究相对较少，尤其是在转录组和基因组数据方面。然而，八放珊瑚的整体共生体产生的多糖和次生代谢产物极大地干扰了 RNA 的提取。为此，我们研究了五种裂解缓冲液系统和两种提取方法，以评估其在八放珊瑚中的 RNA 提取效率。我们发现 CTAB/10%SDS 是从六种不同八放珊瑚属中提取 RNA 的新方法。此外，我们的新方法能够提取出质量良好的 RNA，可用于下游应用，如定量 PCR 和 RNA 测序。最后，对健康的 Lobophytum hsiehi 八放珊瑚和受暗诱导白化的八放珊瑚进行比较转录组分析，结果表明细胞外基质和免疫相关基因可能在珊瑚-共生藻共生关系中发挥重要作用。我们相信，本研究的结果和开发的 RNA 提取方法将为未来的研究提供有价值的参考，特别是在八放珊瑚领域。
