Ongoing transposition in cell culture reveals the phylogeny of diverse Drosophila S2 sublines.

IF 3.3 3区 生物学
Genetics Pub Date : 2022-07-04 DOI:10.1093/genetics/iyac077
Shunhua Han, Guilherme B Dias, Preston J Basting, Michael G Nelson, Sanjai Patel, Mar Marzo, Casey M Bergman
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引用次数: 0

Abstract

Cultured cells are widely used in molecular biology despite poor understanding of how cell line genomes change in vitro over time. Previous work has shown that Drosophila cultured cells have a higher transposable element content than whole flies, but whether this increase in transposable element content resulted from an initial burst of transposition during cell line establishment or ongoing transposition in cell culture remains unclear. Here, we sequenced the genomes of 25 sublines of Drosophila S2 cells and show that transposable element insertions provide abundant markers for the phylogenetic reconstruction of diverse sublines in a model animal cell culture system. DNA copy number evolution across S2 sublines revealed dramatically different patterns of genome organization that support the overall evolutionary history reconstructed using transposable element insertions. Analysis of transposable element insertion site occupancy and ancestral states support a model of ongoing transposition dominated by episodic activity of a small number of retrotransposon families. Our work demonstrates that substantial genome evolution occurs during long-term Drosophila cell culture, which may impact the reproducibility of experiments that do not control for subline identity.

细胞培养中的持续换位揭示了不同果蝇S2亚系的系统发育
尽管对细胞系基因组在体外随时间变化的了解甚少,但培养细胞广泛应用于分子生物学。先前的研究表明,果蝇培养的细胞具有比整只果蝇更高的转座因子(TE)含量,但TE含量的增加是由于细胞系建立过程中最初的转座爆发还是细胞培养过程中持续的转座,目前尚不清楚。本研究对果蝇S2细胞的25个亚系进行了基因组测序,发现TE插入为模型动物细胞培养系统中不同亚系的系统发育重建提供了丰富的标记。对S2亚系DNA拷贝数进化的分析揭示了基因组组织模式的显著差异,这支持了利用TE插入重建的整体进化史。对TE插入位点占用和祖先状态的分析支持一种由少数反转录转座子家族的偶发性活动主导的持续转座子模型。我们的工作表明,大量的基因组进化发生在长期的果蝇细胞培养过程中,这可能会影响不控制子系身份的实验的可重复性。
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来源期刊
Genetics
Genetics 生物-遗传学
CiteScore
6.20
自引率
6.10%
发文量
177
期刊介绍: GENETICS is published by the Genetics Society of America, a scholarly society that seeks to deepen our understanding of the living world by advancing our understanding of genetics. Since 1916, GENETICS has published high-quality, original research presenting novel findings bearing on genetics and genomics. The journal publishes empirical studies of organisms ranging from microbes to humans, as well as theoretical work. While it has an illustrious history, GENETICS has changed along with the communities it serves: it is not your mentor''s journal. The editors make decisions quickly – in around 30 days – without sacrificing the excellence and scholarship for which the journal has long been known. GENETICS is a peer reviewed, peer-edited journal, with an international reach and increasing visibility and impact. All editorial decisions are made through collaboration of at least two editors who are practicing scientists. GENETICS is constantly innovating: expanded types of content include Reviews, Commentary (current issues of interest to geneticists), Perspectives (historical), Primers (to introduce primary literature into the classroom), Toolbox Reviews, plus YeastBook, FlyBook, and WormBook (coming spring 2016). For particularly time-sensitive results, we publish Communications. As part of our mission to serve our communities, we''ve published thematic collections, including Genomic Selection, Multiparental Populations, Mouse Collaborative Cross, and the Genetics of Sex.
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