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The completed macronuclear genome of a model ciliate Tetrahymena thermophila and its application in genome scrambling and copy number analyses

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Abstract

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.

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Acknowledgements

This work was supported by the Natural Science Foundation of Shandong Province (JQ201706), The Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology (Qingdao) (2018SDKJ0406-2), Fundamental Research Funds for the Central Universities (201841005), the Blue Life Breakthrough Program of LMBB of Qingdao National Laboratory for Marine Science and Technology (MS2018NO04), and National Institutes of Health (2P40OD010964). The authors would like to thank the following people for assistance with this study: Dr. Weibo Zheng (Ocean University of China) for providing advice during data analysis; Mr. Bo Pan (OUC) for helping revise the manuscript; and Dr. Mingjian Liu (OUC) for taking photos of T. thermophila. Our special thanks are given to Dr. Weibo Song (OUC) and Dr. Yifan Liu (University of Michigan) for their helpful suggestions during drafting the manuscript. We also acknowledge the computing resources provided on IEMB-1, a high-performance computing cluster operated by the Institute of Evolution and Marine Biodiversity.

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Authors and Affiliations

  1. Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China

    Yalan Sheng, Lili Duan, Ting Cheng, Yu Qiao & Shan Gao

  2. Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China

    Yalan Sheng, Lili Duan, Ting Cheng, Yu Qiao & Shan Gao

  3. Department of Biology, Bradley University, Peoria, Illinois, 61625, USA

    Naomi A. Stover

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  1. Yalan Sheng
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  2. Lili Duan
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Correspondence to Shan Gao.

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Supporting Information

Figure S1 Gel electrophoresis results in this study.

Figure S2 qPCR analysis confirmed that the copy number of the rDNA minichromosome increases in replication-deficient ΔTXR1 cells.

Table S1 Primers used in this study

Table S2 TGD genes BLAST to the predicted genes

Table S3 TGD proteins BLAST to the predicted proteins

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Sheng, Y., Duan, L., Cheng, T. et al. 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, 1534–1542 (2020). https://doi.org/10.1007/s11427-020-1689-4

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