The recent combination of genomics and single cell transcriptomics has allowed to assess a variety of non-conventional model organisms in much more depth. Single cell transcriptomes can uncover hidden cellular complexity and cell lineage relationships within organisms. The recent developmental cell atlases of the sea anemone Nematostella vectensis, a representative of the basally branching Cnidaria, has provided new insights into the development of all cell types (Steger et al Cell Rep 40(12):111370, 2022; Sebé-Pedrós et al. Cell 173(6):1520–1534.e20). However, the mapping of the single cell reads still suffers from relatively poor gene annotations and a draft genome consisting of many scaffolds. Here we present a new wildtype resource of the developmental single cell atlas, by re-mapping of sequence data first published in Steger et al. (2022) and Cole et al. (Nat Commun 14(1):1747, 2023), to the new chromosome-level genome assembly and corresponding gene models in Zimmermann et al. (Nat Commun 14, 8270 (2023). https://doi.org/10.1038/s41467-023-44080-7 ). We expand the pre-existing dataset through the incorporation of additional sequence data derived from the capture and sequencing of cell suspensions from four additional samples: 24 h gastrula, 2d planula, an inter-parietal region of the bodywall from a young unsexed animal, and another adult mesentery from a mature male animal. Our analyses of the full cell-state inventory provide transcriptomic signatures for 127 distinct cell states, of which 47 correspond to neuroglandular subtypes. We also identify two distinct putatively immune-related transcriptomic profiles that segregate between the inner and outer cell layers. Furthermore, the new gene annotation Nv2 has markedly improved the mapping on the single cell transcriptome data and will therefore be of great value for the community and anyone using the dataset.

中文翻译：

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更新了星海葵 Nematostella vectensis 的单细胞参考图集


最近基因组学和单细胞转录组学的结合使得能够更深入地评估各种非传统模式生物。单细胞转录组可以揭示生物体内隐藏的细胞复杂性和细胞谱系关系。海葵 Nematostella vectensis（基底分支刺胞动物的代表）的最新发育细胞图谱为所有细胞类型的发育提供了新的见解（Steger 等 Cell Rep 40(12):111370, 2022；Sebé-Pedrós 等等，细胞 173(6):1520–1534.e20)。然而，单细胞读数的作图仍然受到相对较差的基因注释和由许多支架组成的基因组草案的影响。在这里，我们通过重新映射 Steger 等人首次发表的序列数据，提出了发育单细胞图谱的新野生型资源。 （2022）和科尔等人。 (Nat Commun 14(1):1747, 2023)，Zimmermann 等人的新染色体水平基因组组装和相应的基因模型。 （Nat Commun 14, 8270 (2023)。https://doi.org/10.1038/s41467-023-44080-7）。我们通过合并从四个附加样本的细胞悬液的捕获和测序中获得的附加序列数据来扩展预先存在的数据集：24小时原肠胚、2d浮萍、来自年轻无性动物的体壁顶叶区域，以及来自成熟雄性动物的另一条成年肠系膜。我们对完整细胞状态库存的分析提供了 127 种不同细胞状态的转录组特征，其中 47 种对应于神经腺亚型。我们还鉴定了两种不同的推定免疫相关转录组谱，它们区分内细胞层和外细胞层。 此外，新的基因注释 Nv2 显着改进了单细胞转录组数据的映射，因此对于社区和使用该数据集的任何人都具有巨大价值。