Ciliates are an ancient and diverse eukaryotic group found in various environments. A unique feature of ciliates is their nuclear dimorphism, by which two types of nuclei, the diploid germline micronucleus (MIC) and polyploidy somatic macronucleus (MAC), are present in the same cytoplasm and serve different functions. During each sexual cycle, ciliates develop a new macronucleus in which newly fused genomes are extensively rearranged to generate functional minichromosomes. Interestingly, each ciliate species seems to have its way of processing genomes, providing a diversity of resources for studying genome plasticity and its regulation. Here, we sequenced and analyzed the macronuclear genome of different strains of Paramecium bursaria, a highly divergent species of the genus Paramecium which can stably establish endosymbioses with green algae. We assembled a high-quality macronuclear genome of P. bursaria and further refined genome annotation by comparing population genomic data. We identified several species-specific expansions in protein families and gene lineages that are potentially associated with endosymbiosis. Moreover, we observed an intensive chromosome breakage pattern that occurred during or shortly after sexual reproduction and contributed to highly variable gene dosage throughout the genome. However, patterns of copy number variation were highly correlated among genetically divergent strains, suggesting that copy number is adjusted by some regulatory mechanisms or natural selection. Further analysis showed that genes with low copy number variation among populations tended to function in basic cellular pathways, whereas highly variable genes were enriched in environmental response pathways. We report programmed DNA rearrangements in the P. bursaria macronuclear genome that allow cells to adjust gene copy number globally according to individual gene functions. Our results suggest that large-scale gene copy number variation may represent an ancient mechanism for cells to adapt to different environments.

中文翻译：

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人口基因组学揭示草履虫草的基因组可塑性

纤毛虫是在各种环境中发现的古老而多样的真核生物。纤毛虫的独特特征是它们的核二态性，通过它，两种核，即二倍体种系微核（MIC）和多倍体体细胞大核（MAC），存在于同一细胞质中并发挥不同的功能。在每个性周期中，纤毛虫会形成一个新的大核，其中新融合的基因组会被广泛地重排以产生功能性微型染色体。有趣的是，每个纤毛物种似乎都有其处理基因组的方式，为研究基因组可塑性及其调控提供了多种资源。在这里，我们测序和分析了草履虫草（Paramecium bursaria）的不同菌株的大核基因组，草履草属（Paramecium）属的一种高度分化的物种，可以稳定地建立与绿藻的内共生酶。我们组装了优质的法氏假单胞菌大核基因组，并通过比较种群基因组数据进一步完善了基因组注释。我们在蛋白质家族和基因谱系中鉴定了几种可能与内共生相关的物种特异性扩增。此外，我们观察到强烈的染色体断裂模式发生在有性生殖期间或之后不久，并且在整个基因组中导致高度可变的基因剂量。但是，拷贝数变异的模式在遗传上不同的菌株之间高度相关，这表明拷贝数是通过某些调节机制或自然选择来调节的。进一步的分析表明，种群之间拷贝数变异小的基因倾向于在基本细胞途径中起作用，而高度可变的基因则丰富了环境响应途径。我们报告了P​​. bursaria大核基因组中的计划的DNA重排，允许细胞根据单个基因功能全局调整基因拷贝数。我们的结果表明，大规模的基因拷贝数变异可能代表了细胞适应不同环境的古老机制。