Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome
- University of California, Santa Barbara, United States
- University of Utah School of Medicine, United States
- Southern Illinois University, United States
- J. Craig Venter Institute, United States
- Eli and Edythe L. Broad Institute of Harvard and MIT, United States
- Broad Institute, United States
- Institute of Molecular Biotechnology, Austria
- The Johns Hopkins University School of Medicine, United States
- MRC Laboratory of Molecular Biology, United Kingdom
- Cornell University, United States
- Chinese Academy of Sciences, China
Abstract
The germline genome of the binucleated ciliate Tetrahymena thermophila undergoes programmed chromosome breakage and massive DNA elimination to generate the somatic genome. Here we present a complete sequence assembly of the germline genome and analyze multiple features of its structure and its relationship to the somatic genome, shedding light on the mechanisms of genome rearrangement as well as the evolutionary history of this remarkable germline/soma differentiation. Our results strengthen the notion that a complex, dynamic, and ongoing interplay between mobile DNA elements and the host genome have shaped Tetrahymena chromosome structure, locally and globally. Non-standard outcomes of rearrangement events, including the generation of short-lived somatic chromosomes and excision of DNA interrupting protein-coding regions, may represent novel forms of developmental gene regulation. We also compare Tetrahymena's germline/soma differentiation to that of other characterized ciliates, illustrating the wide diversity of adaptations that have occurred within this phylum.
Data availability
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Micronuclear Genome AssemblyPublicly available at NCBI Nucleotide (accession no: AFSS00000000).
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Tetrahymena thermophila SB210 micronuclear genome sequencingPublicly available at NCBI BioProject (accession no: PRJNA51571).
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Macronuclear Genome AssemblyPublicly available at NCBI Nucleotide (accession no: AAGF03000000).
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Tetrahymena thermophila Transcriptome SequencingPublicly available at NCBI BioProject (accession no: PRJNA177770).
Article and author information
Author details
Vivek Krishnakumar
Kazufumi Mochizuki
Funding
National Human Genome Research Institute (U54 HG003067)
- Chad Nusbaum
National Science Foundation (MCB-1158346)
- Robert S Coyne
Natural Science Foundation of Hubei Province (31525021)
- Wei Miao
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Kathleen Collins, University of California, Berkeley, United States
Version history
- Received: June 24, 2016
- Accepted: November 14, 2016
- Accepted Manuscript published: November 28, 2016 (version 1)
- Version of Record published: December 23, 2016 (version 2)
Copyright
This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
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Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome
eLife 5:e19090.
https://doi.org/10.7554/eLife.19090
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