Krabberød Anders K, Orr Russell J S, Bråte Jon, Kristensen Tom, Bjørklund Kjell R, Shalchian-Tabrizi Kamran
Department of Biosciences, Centre for Integrative Microbial Evolution (CIME) and Centre for Epigenetics Development and Evolution (CEDE), University of Oslo, Oslo, Norway.
Department of Research and Collections, Natural History Museum, University of Oslo, Oslo, Norway.
Mol Biol Evol. 2017 Jul 1;34(7):1557-1573. doi: 10.1093/molbev/msx075.
The innovation of the eukaryote cytoskeleton enabled phagocytosis, intracellular transport, and cytokinesis, and is largely responsible for the diversity of morphologies among eukaryotes. Still, the relationship between phenotypic innovations in the cytoskeleton and their underlying genotype is poorly understood. To explore the genetic mechanism of morphological evolution of the eukaryotic cytoskeleton, we provide the first single cell transcriptomes from uncultured, free-living unicellular eukaryotes: the polycystine radiolarian Lithomelissa setosa (Nassellaria) and Sticholonche zanclea (Taxopodida). A phylogenomic approach using 255 genes finds Radiolaria and Foraminifera as separate monophyletic groups (together as Retaria), while Cercozoa is shown to be paraphyletic where Endomyxa is sister to Retaria. Analysis of the genetic components of the cytoskeleton and mapping of the evolution of these on the revised phylogeny of Rhizaria reveal lineage-specific gene duplications and neofunctionalization of α and β tubulin in Retaria, actin in Retaria and Endomyxa, and Arp2/3 complex genes in Chlorarachniophyta. We show how genetic innovations have shaped cytoskeletal structures in Rhizaria, and how single cell transcriptomics can be applied for resolving deep phylogenies and studying gene evolution in uncultured protist species.
真核生物细胞骨架的创新实现了吞噬作用、细胞内运输和胞质分裂，并且在很大程度上造就了真核生物形态的多样性。然而，细胞骨架的表型创新与其潜在基因型之间的关系仍知之甚少。为了探究真核生物细胞骨架形态进化的遗传机制，我们提供了来自未培养的自由生活单细胞真核生物的首个单细胞转录组：多囊放射虫Lithomelissa setosa（罩笼虫目）和Sticholonche zanclea（分类未定目）。使用255个基因的系统基因组学方法发现，放射虫类和有孔虫类为独立的单系类群（合称为有孔虫界），而丝足虫类显示为并系群，其中内共栖虫类是有孔虫界的姐妹群。对细胞骨架的遗传成分进行分析，并将其进化过程映射到修订后的根足虫类系统发育树上，结果揭示了有孔虫界中α和β微管蛋白、有孔虫界和内共栖虫类中的肌动蛋白以及绿藻虫纲中的Arp2/3复合体基因的谱系特异性基因重复和新功能化。我们展示了遗传创新如何塑造了根足虫类的细胞骨架结构，以及单细胞转录组学如何应用于解析深层系统发育关系和研究未培养原生生物物种的基因进化。
