Lyu Liping, Zhang Xue, Gao Yunyi, Zhang Tengteng, Fu Jinyu, Stover Naomi A, Gao Feng
Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China.
Department of Biology, Bradley University, Peoria, IL 61625 USA.
Mar Life Sci Technol. 2024 Feb 12;6(1):31-49. doi: 10.1007/s42995-023-00213-x. eCollection 2024 Feb.
Genomes are incredibly dynamic within diverse eukaryotes and programmed genome rearrangements (PGR) play important roles in generating genomic diversity. However, genomes and chromosomes in metazoans are usually large in size which prevents our understanding of the origin and evolution of PGR. To expand our knowledge of genomic diversity and the evolutionary origin of complex genome rearrangements, we focus on ciliated protists (ciliates). Ciliates are single-celled eukaryotes with highly fragmented somatic chromosomes and massively scrambled germline genomes. PGR in ciliates occurs extensively by removing massive amounts of repetitive and selfish DNA elements found in the silent germline genome during development of the somatic genome. We report the partial germline genomes of two spirotrich ciliate species, namely cf. and , along with the most compact and highly fragmented somatic genome for cf. . We provide the first insights into the genome rearrangements of these two species and compare these features with those of other ciliates. Our analyses reveal: (1) DNA sequence loss through evolution and during PGR in . cf. has combined to produce the most compact and efficient nanochromosomes observed to date; (2) the compact, transcriptome-like somatic genome in both species results from extensive removal of a relatively large number of shorter germline-specific DNA sequences; (3) long chromosome breakage site motifs are duplicated and retained in the somatic genome, revealing a complex model of chromosome fragmentation in spirotrichs; (4) gene scrambling and alternative processing are found throughout the core spirotrichs, offering unique opportunities to increase genetic diversity and regulation in this group.
The online version contains supplementary material available at 10.1007/s42995-023-00213-x.
基因组在多样的真核生物中具有令人难以置信的动态性，程序化基因组重排（PGR）在产生基因组多样性方面发挥着重要作用。然而，后生动物的基因组和染色体通常体积较大，这阻碍了我们对PGR起源和进化的理解。为了扩展我们对基因组多样性以及复杂基因组重排进化起源的认识，我们聚焦于纤毛原生生物（纤毛虫）。纤毛虫是单细胞真核生物，其体细胞染色体高度碎片化，生殖系基因组大量混乱。纤毛虫中的PGR通过在体细胞基因组发育过程中去除沉默生殖系基因组中大量的重复和自私DNA元件而广泛发生。我们报告了两种旋毛目纤毛虫物种的部分生殖系基因组，即cf. 和 ，以及cf. 最紧凑且高度碎片化的体细胞基因组。我们首次深入了解了这两个物种的基因组重排情况，并将这些特征与其他纤毛虫的特征进行了比较。我们的分析揭示：（1）在cf. 中，通过进化和PGR过程中的DNA序列丢失共同产生了迄今为止观察到的最紧凑、高效的纳米染色体；（2）这两个物种中紧凑的、类似转录组的体细胞基因组是由于大量去除了相对较多的较短生殖系特异性DNA序列所致；（3）长染色体断裂位点基序在体细胞基因组中被复制并保留，揭示了旋毛目染色体碎片化的复杂模式；（4）在整个核心旋毛目中发现了基因混乱和可变加工现象，为增加该类群的遗传多样性和调控提供了独特机会。
在线版本包含可在10.1007/s42995 - 023 - 00213 - x获取的补充材料。
