Ciliated protists are unicellular eukaryotic organisms characterized by their morphological diversity, ubiquitous distribution, and the important roles they play in a wide range of biological studies. The class Litostomatea is a morphologically diverse ciliate group that comprises hundreds of free-living and endosymbiotic species. Here, we sequenced 14 predatory litostomateans, i.e. 12 haptorians and two rhynchostomatians. A comparative analysis was performed with other published omics’ data on litostomateans. Our first phylogenomic analysis of litostomateans showed the monophyly of the subclasses Trichostomatia and Rhynchostomatia, the non-monophyly of the subclass Haptoria, and the monophyly of all orders and families that were analysed. Evolutionary history analysis suggested that Litostomatea diverged during the Late Neoproterozoic, the family Chaeneidae was the earliest diverging haptorian lineage, and the Rhynchostomatia probably separated from the order Lacrymariida (subclass Haptoria) during the Early Palaeozoic. Stop codon usage analysis of 28 litostomateans showed that they use TAA as the biased stop codon and reassign the other two stop codons (TAG and TGA) to code for amino acids. In addition, the preferred codons in the 14 newly sequenced litostomateans are strongly biased towards A/U bases in the third position, very probably due to the comparatively low GC content. Genes encoding carbohydrate-active enzymes (CAZymes) are more diversified in the endosymbiotic Trichostomatia than in the free-living predatory Rhynchostomatia and Haptoria, suggesting that trichostomes have the strongest capability of carbohydrate utilization. Notably, we found that three free-living litostomateans (Didinium sp.1, Myriokaryon sp., and Apodileptus visscheri) exhibit substantial differences from other free-living ciliates in terms of their number of CAZymes. Considering the potency and versatility of CAZymes in the degradation and biotransformation of carbohydates, we propose that the multifarious CAZymes in these three ciliates could be a survival strategy for nutrient acquisition and niche adaptation. Finally, the functional annotation of significantly expanded gene families in these three ciliates revealed their vigorous potency in biochemical metabolism. These findings will facilitate wider omic-scale phylogenetic analyses of Litostomatea and deepen our understanding of this group from an evolutionary standpoint.

中文翻译：

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比较基因组学揭示单细胞真核生物Litostomatea的进化史及其基于生化代谢能力的适应性进化


纤毛原生生物是单细胞真核生物，其特征在于形态多样性、分布广泛以及在广泛的生物学研究中发挥的重要作用。 Litostomatea纲是形态多样的纤毛虫类群，由数百种自由生活和内共生物种组成。在这里，我们对 14 种捕食性石口动物进行了测序，即 12 种触手动物和 2 种喙口动物。与其他已发表的石口动物组学数据进行了比较分析。我们对海口动物的首次系统发育分析表明，毛口亚纲和喙口亚纲是单系的，触口亚纲是非单系的，分析的所有目和科都是单系的。进化历史分析表明，Litostomatea在新元古代晚期分化，Chaeneidae科是最早分化的haptorian谱系，Rhynchostomatia可能在早古生代从Lacrymariida（Haptoria亚纲）中分离出来。对 28 个海口动物的终止密码子使用分析表明，它们使用 TAA 作为有偏向的终止密码子，并重新分配其他两个终止密码子（TAG 和 TGA）来编码氨基酸。此外，14个新测序的石口动物中的首选密码子强烈偏向第三位的A/U碱基，很可能是由于GC含量相对较低。内共生毛口动物中编码碳水化合物活性酶（CAZymes）的基因比自由生活的捕食性喙口动物和弓口动物更加多样化，表明毛口动物具有最强的碳水化合物利用能力。值得注意的是，我们发现了三种自由生活的石口动物（Didinium sp.1、Myriokaryon sp.1）。和 Apodileptus visscheri）在 CAZymes 数量方面与其他自由生活的纤毛虫表现出显着差异。考虑到 CAZymes 在碳水化合物降解和生物转化中的效力和多功能性，我们认为这三种纤毛虫中的多种 CAZymes 可能是营养获取和生态位适应的生存策略。最后，这三种纤毛虫显着扩展的基因家族的功能注释揭示了它们在生化代谢中的强大效力。这些发现将有助于对 Litostomatea 进行更广泛的组学规模的系统发育分析，并从进化的角度加深我们对这个群体的理解。