Cheng Yu-Hsuan, Liu Chien-Fu Jeff, Yu Yen-Hsin, Jhou Yu-Ting, Fujishima Masahiro, Tsai Isheng Jason, Leu Jun-Yi
Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, 106, Taiwan.
Institute of Molecular Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan.
BMC Biol. 2020 Nov 30;18(1):180. doi: 10.1186/s12915-020-00912-2.
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.
纤毛虫是一类古老且多样的真核生物群体，存在于各种环境中。纤毛虫的一个独特特征是其核二态性，即同一个细胞质中存在两种类型的细胞核，二倍体生殖系微核（MIC）和多倍体体大核（MAC），它们发挥不同的功能。在每个有性周期中，纤毛虫会发育出一个新的大核，其中新融合的基因组会被广泛重排以产生功能性的微型染色体。有趣的是，每个纤毛虫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样的资源。在这里，我们对草履虫属中一个高度分化的物种——绿草履虫不同菌株的大核基因组进行了测序和分析，该物种能够与绿藻稳定地建立内共生关系。
我们组装了高质量的绿草履虫大核基因组，并通过比较群体基因组数据进一步完善了基因组注释。我们在可能与内共生相关的蛋白质家族和基因谱系中鉴定出了几个物种特异性的扩增。此外，我们观察到一种强烈的染色体断裂模式，这种模式发生在有性生殖期间或之后不久，并导致整个基因组中基因剂量高度可变。然而，拷贝数变异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一些调控机制或自然选择来调节的。进一步分析表明，群体中拷贝数变异低的基因往往在基本细胞途径中发挥作用，而高可变基因则富集于环境响应途径中。
我们报道了绿草履虫大核基因组中的程序性DNA重排，这种重排使细胞能够根据单个基因的功能全局调整基因拷贝数。我们的结果表明，大规模基因拷贝数变异可能代表了细胞适应不同环境的一种古老机制。
