Single Cell Transcriptomics, Mega-Phylogeny, and the Genetic Basis of Morphological Innovations in Rhizaria.
Single Cell Transcriptomics, Mega-Phylogeny, and the Genetic Basis of Morphological Innovations in Rhizaria.
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DOI：
10.1093/molbev/msx075
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发表时间：
2017-07-01
影响因子：
10.7
通讯作者：
Shalchian-Tabrizi K
中科院分区：
文献类型：
--
作者：
Krabberød AK;Orr RJS;Bråte J;Kristensen T;Bjørklund KR;Shalchian-Tabrizi K
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，并在很大程度上造成了真核生物形态的多样性。尽管如此，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。为了探索真核细胞骨架形态进化的遗传机制，我们提供了来自未培养的、自由生活的单细胞真核生物的第一个单细胞转录组：多胱氨酸放射虫 Lithomelissa setosa (Nassellaria) 和 Sticholonche zanclea (Taxopodida)。使用 255 个基因的系统发育学方法发现放射虫和有孔虫为单独的单系类群（统称为 Retaria），而尾虫则显示为并系群，其中 Endomyxa 是 Retaria 的姐妹。对细胞骨架遗传成分的分析以及这些在修订后的根属系统发育学上的进化图谱揭示了 Retaria 中 α 和 β 微管蛋白、Retaria 和 Endomyxa 中肌动蛋白以及 Chlorarachniophyta 中 Arp2/3 复合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根茎的细胞骨架结构，以及如何应用单细胞转录组学来解决深层系统发育和研究未培养的原生生物物种的基因进化。
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.