Colpoda是世界性的单细胞真核生物,主要居住在土壤中并有益于植物生长,但是它们仍然是纤毛原生动物领域中遗传学和基因组学中了解最少的分类单元之一。这里,我们研究了六个Colpoda物种的从头组装的有丝分裂基因组的结构,使用长读数测序,总共涉及36个新分离的天然菌株。有丝分裂基因组的大小从43到63kbp,通常包含28-33个蛋白质编码基因。它们具有可变的端粒和中心重复序列的线性结构,从西藏分离出的一种Colpodaelliotti菌株在所有研究的纤毛虫中具有最长的端粒。系统学分析表明,Colpoda物种在3.26亿年前开始分化,最终演变成两个不同的群体。共线性分析还揭示了显著的基因组差异和缺乏长的共线块。最显着的特征之一是不同Colpoda物种的线粒体基因组之间异常高水平的基因重排,以基因丢失事件为主。对天然菌株的群体水平有丝分裂基因组学分析也显示出高度的序列差异,无论地理距离如何,但是基因序列在物种中仍然高度保守,为Colpoda物种提供了新的物种鉴定标准。此外,我们在三种Colpoda物种的大多数菌株中确定了潜在的异质位点,尽管没有明显的重组信号来解释这种异质性。这项全面的研究系统地揭示了这些古老且具有生态意义的Colpoda纤毛虫的有丝分裂基因组结构和进化,从而为更深入地了解单细胞真核生物的进化奠定了基础。IMPORTANCEColpoda,土壤中最普遍的纤毛原生动物之一,对他们的遗传学和进化知之甚少。我们的研究揭示了由基因丢失事件主导的极端线粒体基因重排,可能导致Colpoda有丝分裂基因组的精简。令人惊讶的是,虽然种间重排比比皆是,我们的种群水平的有丝分裂基因组学研究揭示了物种内保守的基因顺序,提供了一个潜在的新的识别标准。系统基因组分析追踪了他们超过3.26亿年的血统,揭示了两个不同的群体。大量的基因组差异可能与缺乏延伸的共线嵌段和宽松的纯化选择有关。本研究系统地揭示了Colpoda纤毛虫丝裂原的结构和进化,提供对这些重要土壤微生物的生存和进化的见解。
Colpoda are cosmopolitan unicellular eukaryotes primarily inhabiting soil and benefiting plant growth, but they remain one of the least understood taxa in genetics and genomics within the realm of ciliated protozoa. Here, we investigate the architecture of de novo assembled mitogenomes of six Colpoda species, using long-read sequencing and involving 36 newly isolated natural strains in total. The mitogenome sizes span from 43 to 63 kbp and typically contain 28-33 protein-coding genes. They possess a linear structure with variable telomeres and central repeats, with one Colpoda elliotti strain isolated from Tibet harboring the longest telomeres among all studied ciliates. Phylogenomic analyses reveal that Colpoda species started to diverge more than 326 million years ago, eventually evolving into two distinct groups. Collinearity analyses also reveal significant genomic divergences and a lack of long collinear blocks. One of the most notable features is the exceptionally high level of gene rearrangements between mitochondrial genomes of different Colpoda species, dominated by gene loss events. Population-level mitogenomic analysis on natural strains also demonstrates high sequence divergence, regardless of geographic distance, but the gene order remains highly conserved within species, offering a new species identification criterion for Colpoda species. Furthermore, we identified underlying heteroplasmic sites in the majority of strains of three Colpoda species, albeit without a discernible recombination signal to account for this heteroplasmy. This comprehensive study systematically unveils the mitogenomic structure and evolution of these ancient and ecologically significant Colpoda ciliates, thus laying the groundwork for a deeper understanding of the evolution of unicellular eukaryotes.IMPORTANCEColpoda, one of the most widespread ciliated protozoa in soil, are poorly understood in regard to their genetics and evolution. Our research revealed extreme mitochondrial gene rearrangements dominated by gene loss events, potentially leading to the streamlining of Colpoda mitogenomes. Surprisingly, while interspecific rearrangements abound, our population-level mitogenomic study revealed a conserved gene order within species, offering a potential new identification criterion. Phylogenomic analysis traced their lineage over 326 million years, revealing two distinct groups. Substantial genomic divergence might be associated with the lack of extended collinear blocks and relaxed purifying selection. This study systematically reveals Colpoda ciliate mitogenome structures and evolution, providing insights into the survival and evolution of these vital soil microorganisms.