University College London, Department of Genetics, Evolution and Environment, London, UK; San Diego State University, Biology Department, San Diego, CA, USA; University of British Columbia, Botany Department, Vancouver, BC, Canada.
University of British Columbia, Botany Department, Vancouver, BC, Canada; Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia.
Curr Biol. 2017 Dec 4;27(23):3717-3724.e5. doi: 10.1016/j.cub.2017.10.051. Epub 2017 Nov 22.
The origin of eukaryotic cells represents a key transition in cellular evolution and is closely tied to outstanding questions about mitochondrial endosymbiosis [1, 2]. For example, gene-rich mitochondrial genomes are thought to be indicative of an ancient divergence, but this relies on unexamined assumptions about endosymbiont-to-host gene transfer [3-5]. Here, we characterize Ancoracysta twista, a new predatory flagellate that is not closely related to any known lineage in 201-protein phylogenomic trees and has a unique morphology, including a novel type of extrusome (ancoracyst). The Ancoracysta mitochondrion has a gene-rich genome with a coding capacity exceeding that of all other eukaryotes except the distantly related jakobids and Diphylleia, and it uniquely possesses heterologous, nucleus-, and mitochondrion-encoded cytochrome c maturase systems. To comprehensively examine mitochondrial genome reduction, we also assembled mitochondrial genomes from picozoans and colponemids and re-annotated existing mitochondrial genomes using hidden Markov model gene profiles. This revealed over a dozen previously overlooked mitochondrial genes at the level of eukaryotic supergroups. Analysis of trends over evolutionary time demonstrates that gene transfer to the nucleus was non-linear, that it occurred in waves of exponential decrease, and that much of it took place comparatively early, massively independently, and with lineage-specific rates. This process has led to differential gene retention, suggesting that gene-rich mitochondrial genomes are not a product of their early divergence. Parallel transfer of mitochondrial genes and their functional replacement by new nuclear factors are important in models for the origin of eukaryotes, especially as major gaps in our knowledge of eukaryotic diversity at the deepest level remain unfilled.
真核细胞的起源代表了细胞进化的一个关键转变，与线粒体内共生的一些重要问题密切相关[1,2]。例如，富含基因的线粒体基因组被认为是古老分歧的标志，但这依赖于对内共生体到宿主基因转移的未经检验的假设[3-5]。在这里，我们描述了一种新的捕食性鞭毛虫 Ancoracysta twista，它与 201 种蛋白质系统发育树中任何已知谱系都没有密切关系，具有独特的形态，包括一种新型的挤出体（ancoracyst）。Ancora 线粒体基因组具有丰富的基因，编码能力超过除了遥远相关的 jakobids 和 Diphylleia 之外的所有其他真核生物，并且它独特地拥有异源的、核和线粒体编码的细胞色素 c 成熟酶系统。为了全面研究线粒体基因组的减少，我们还组装了微藻和 colponemids 的线粒体基因组，并使用隐马尔可夫模型基因谱重新注释了现有的线粒体基因组。这揭示了十几个以前在真核超组水平上被忽视的线粒体基因。对进化时间趋势的分析表明，核基因转移是非线性的，它以指数下降的波次发生，并且大部分发生得比较早，大规模地独立发生，并且具有谱系特异性的速率。这个过程导致了基因的差异保留，表明富含基因的线粒体基因组不是它们早期分歧的产物。线粒体基因的平行转移及其在新核因子中的功能替代在真核生物起源的模型中非常重要，尤其是因为我们对最深处的真核生物多样性的知识仍然存在重大空白。
