University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA 98195, USA.
Western Washington University, Shannon Point Marine Center, Anacortes, WA 98221, USA.
G3 (Bethesda). 2021 Jul 14;11(7). doi: 10.1093/g3journal/jkab148.
Symbiosis with protists is common among cnidarians such as corals and sea anemones and is associated with homeostatic and phenotypic changes in the host that could have epigenetic underpinnings, such as methylation of CpG dinucleotides. We leveraged the sensitivity to base modifications of nanopore sequencing to probe the effect of symbiosis with the chlorophyte Elliptochloris marina on methylation in the sea anemone Anthopleura elegantissima. We first validated the approach by comparison of nanopore-derived methylation levels with CpG depletion analysis of a published transcriptome, finding that high methylation levels are associated with CpG depletion as expected. Next, using reads generated exclusively from aposymbiotic anemones, a largely complete draft genome comprising 243 Mb was assembled. Reads from aposymbiotic and symbiotic sea anemones were then mapped to this genome and assessed for methylation using the program Nanopolish, which detects signal disruptions from base modifications as they pass through the nanopore. Based on assessment of 452,841 CpGs for which there was adequate read coverage (approximately 8% of the CpGs in the genome), symbiosis with E. marina was, surprisingly, associated with only subtle changes in the host methylome. However, we did identify one extended genomic region with consistently higher methylation among symbiotic individuals. The region was associated with a DNA polymerase zeta that is noted for its role in translesion synthesis, which opens interesting questions about the biology of this symbiosis. Our study highlights the power and relative simplicity of nanopore sequencing for studies of nucleic acid base modifications in non-model species.
珊瑚和海葵等刺胞动物与原生生物共生较为常见，与宿主的体内平衡和表型变化有关，这些变化可能具有表观遗传基础，例如 CpG 二核苷酸的甲基化。我们利用纳米孔测序对碱基修饰的敏感性，来探究与绿藻 Elliptochloris marina 的共生对海葵 Anthopleura elegantissima 甲基化的影响。我们首先通过将纳米孔衍生的甲基化水平与已发表转录组的 CpG 耗竭分析进行比较，验证了这种方法的有效性，发现高甲基化水平与预期的 CpG 耗竭有关。接下来，我们仅使用共生海葵的读取数据组装了一个包含 243 Mb 的大部分完整草图基因组。然后，将来自共生和非共生海葵的读取数据映射到这个基因组上，并使用 Nanopolish 程序评估甲基化情况，该程序可以检测碱基修饰通过纳米孔时产生的信号中断。基于对 452,841 个 CpG 进行评估（约占基因组中 CpG 的 8%），出乎意料的是，与 E. marina 的共生仅与宿主甲基组的细微变化有关。然而，我们确实在共生个体中发现了一个具有一致高甲基化的扩展基因组区域。该区域与一种以跨损伤合成作用而闻名的 DNA 聚合酶 zeta 相关，这为这种共生的生物学提出了有趣的问题。我们的研究强调了纳米孔测序在非模式物种中研究核酸碱基修饰的强大功能和相对简单性。
