Dinoflagellates possess many cellular characteristics with unresolved evolutionary histories. These include nuclei with greatly expanded genomes and chromatin packaged using histone-like proteins and dinoflagellate-viral nucleoproteins instead of histones, highly reduced mitochondrial genomes with extensive RNA editing, a mix of photosynthetic and cryptic secondary plastids, and tertiary plastids. Resolving the evolutionary origin of these traits requires understanding their ancestral states and early intermediates. Several early-branching dinoflagellate lineages are good candidates for such reconstruction, however these cells tend to be delicate and environmentally sparse, complicating such analyses. Here, we employ transcriptome sequencing from manually isolated and microscopically documented cells to resolve the placement of two cells of one such genus, Abedinium, collected by remotely operated vehicle in deep waters off the coast of Monterey Bay, CA. One cell corresponds to the only described species, Abedinium dasypus, whereas the second cell is distinct and formally described as Abedinium folium, sp. nov. Abedinium has classically been assigned to the early-branching dinoflagellate subgroup Noctilucales, which is weakly supported by phylogenetic analyses of small subunit ribosomal RNA, the single characterized gene from any member of the order. However, an analysis based on 221 proteins from the transcriptome places Abedinium as a distinct lineage, separate from and basal to Noctilucales and the rest of the core dinoflagellates. The transcriptome also contains evidence of a cryptic plastid functioning in the biosynthesis of isoprenoids, iron–sulfur clusters, and heme, a mitochondrial genome with all three expected protein-coding genes (cob, cox1, and cox3), and the presence of some but not all dinoflagellate-specific chromatin packaging proteins.

中文翻译：

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Abedinium 的单细胞转录组学揭示了一种新的早期分支甲藻谱系

甲藻具有许多细胞特征和未解决的进化历史。这些包括具有极大扩展的基因组和染色质的细胞核，使用组蛋白样蛋白和甲藻病毒核蛋白代替组蛋白包装，高度减少的线粒体基因组具有广泛的 RNA 编辑，光合和隐秘二级质体的混合，以及三级质体。解决这些性状的进化起源需要了解它们的祖先状态和早期中间体。几个早期分支的甲藻谱系是此类重建的良好候选者，但是这些细胞往往很脆弱且环境稀疏，使此类分析复杂化。这里，Abedinium，由远程操作的车辆在加利福尼亚州蒙特雷湾海岸附近的深水中收集。一个细胞对应于唯一描述的物种Abedinium dasypus，而第二个细胞是不同的，正式描述为Abedinium folium，sp。十一月 Abedinium经典地被分配到早期分支的甲藻亚群 Noctilucales，它被小亚基核糖体 RNA 的系统发育分析弱支持，核糖体 RNA 是来自该目任何成员的单一特征基因。然而，基于转录组中 221 种蛋白质的分析将Abedinium作为一个独特的谱系，与夜光藻和其他核心鞭毛藻分开并作为其基础。转录组还包含在类异戊二烯、铁硫簇和血红素的生物合成中发挥作用的神秘质体的证据，血红素是具有所有三个预期蛋白质编码基因（cob、cox1和cox3）的线粒体基因组，并且存在一些但并非所有甲藻特异性染色质包装蛋白。