The completed macronuclear genome of a model ciliate Tetrahymena thermophila and its application in genome scrambling an
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e completed macronuclear genome of a model ciliate Tetrahymena thermophila and its application in genome scrambling and copy number analyses 1,2
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Yalan Sheng , Lili Duan , Ting Cheng , Yu Qiao , Naomi A. Stover & Shan Gao
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Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 3
Qingdao 266003, China; Department of Biology, Bradley University, Peoria, Illinois 61625, USA
Received February 8, 2020; accepted March 26, 2020; published online April 13, 2020
The ciliate Tetrahymena thermophila has been a powerful model system for molecular and cellular biology. However, some investigations have been limited due to the incomplete closure and sequencing of the macronuclear genome assembly, which for many years has been stalled at 1,158 scaffolds, with large sections of unknown sequences (available in Tetrahymena Genome Database, TGD, http://ciliate.org/). Here we completed the first chromosome-level Tetrahymena macronuclear genome assembly, with approximately 300× long Single Molecule, Real-Time reads of the wild-type SB210 cells—the reference strain for the initial macronuclear genome sequencing project. All 181 chromosomes were capped with two telomeres and gaps were entirely closed. The completed genome shows significant improvements over the current assembly (TGD 2014) in both chromosome structure and sequence integrity. The majority of previously identified gene models shown in TGD were retained, with the addition of 36 new genes and 883 genes with modified gene models. The new genome and annotation were incorporated into TGD. This new genome allows for pursuit in some underexplored areas that were far more challenging previously; two of them, genome scrambling and chromosomal copy number, were investigated in this study. We expect that the completed macronuclear genome will facilitate many studies in Tetrahymena biology, as well as multiple lines of research in other eukaryotes. Tetrahymena thermophila, macronuclear genome, 181 chromosomes, DNA scrambling, copy number Citation:
Sheng, Y., Duan, L., Cheng, T., Qiao, Y., Stover, N.A., and Gao, S. (2020). The completed macronuclear genome of a model ciliate Tetrahymena thermophila and its application in genome scrambling and copy number analyses. Sci China Life Sci 63, https://doi.org/10.1007/s11427-020-1689-4
INTRODUCTION As a unicellular eukaryote model organism, Tetrahymena thermophila is the most well-studied of all protozoa and has contributed to fundamental biological discoveries in multiple aspects (Cervantes et al., 2013; Feng et al., 2017; Gao et al., 2013; Mochizuki et al., 2002; Mochizuki and Gorovsky, 2004a, 2005; Orias et al., 2017; Wang et al., 2017b; Wang et
al., 2019b; Xiong et al., 2016; Xu et al., 2019; Zhao et al., 2019). Like other ciliates, Tetrahymena possess two types of nuclei in a single cell, distinct in their appearance and function (Cheng et al., 2019; Colli
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