Many corals harbour symbiotic dinoflagellate algae. The algae live inside coral cells in a specialized membrane compartment known as the symbiosome, which shares the photosynthetically fixed carbon with coral host cells while host cells provide inorganic carbon to the algae for photosynthesis1. This endosymbiosis—which is critical for the maintenance of coral reef ecosystems—is increasingly threatened by environmental stressors that lead to coral bleaching (that is, the disruption of endosymbiosis), which in turn leads to coral death and the degradation of marine ecosystems2. The molecular pathways that orchestrate the recognition, uptake and maintenance of algae in coral cells remain poorly understood. Here we report the chromosome-level genome assembly of a Xenia species of fast-growing soft coral3, and use this species as a model to investigate coral–alga endosymbiosis. Single-cell RNA sequencing identified 16 cell clusters, including gastrodermal cells and cnidocytes, in Xenia sp. We identified the endosymbiotic cell type, which expresses a distinct set of genes that are implicated in the recognition, phagocytosis and/or endocytosis, and maintenance of algae, as well as in the immune modulation of host coral cells. By coupling Xenia sp. regeneration and single-cell RNA sequencing, we observed a dynamic lineage progression of the endosymbiotic cells. The conserved genes associated with endosymbiosis that are reported here may help to reveal common principles by which different corals take up or lose their endosymbionts. Single-cell RNA sequencing identifies the pattern of gene expression during lineage progression in endosymbiotic cells of the fast-growing soft coral Xenia, revealing principles that underlie uptake and maintenance of endosymbionts by this coral.

中文翻译：

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软珊瑚 Xenia 内共生细胞类型的谱系动力学

许多珊瑚都有共生的甲藻。藻类生活在被称为共生体的特殊膜室中的珊瑚细胞内，共生体与珊瑚宿主细胞共享光合作用固定的碳，而宿主细胞则为藻类提供无机碳以进行光合作用 1。这种对珊瑚礁生态系统的维护至关重要的内共生越来越受到导致珊瑚白化的环境压力因素的威胁（即内共生的破坏），这反过来又导致珊瑚死亡和海洋生态系统退化 2。协调珊瑚细胞中藻类识别、摄取和维持的分子途径仍然知之甚少。在这里，我们报告了一种快速生长的软珊瑚 Xenia 物种的染色体水平基因组组装，并使用该物种作为模型来研究珊瑚藻内共生。单细胞 RNA 测序鉴定了 Xenia sp. 中的 16 个细胞簇，包括胃胚层细胞和刺胞细胞。我们确定了内共生细胞类型，它表达一组不同的基因，这些基因与藻类的识别、吞噬作用和/或内吞作用、维持以及宿主珊瑚细胞的免疫调节有关。通过耦合 Xenia sp。通过再生和单细胞 RNA 测序，我们观察到了内共生细胞的动态谱系进展。此处报告的与内共生相关的保守基因可能有助于揭示不同珊瑚吸收或失去其内共生体的共同原则。