Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome
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 rela...
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2016-11-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/19090 |
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Article |
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DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Eileen P Hamilton Aurélie Kapusta Piroska E Huvos Shelby L Bidwell Nikhat Zafar Haibao Tang Michalis Hadjithomas Vivek Krishnakumar Jonathan H Badger Elisabet V Caler Carsten Russ Qiandong Zeng Lin Fan Joshua Z Levin Terrance Shea Sarah K Young Ryan Hegarty Riza Daza Sharvari Gujja Jennifer R Wortman Bruce W Birren Chad Nusbaum Jainy Thomas Clayton M Carey Ellen J Pritham Cédric Feschotte Tomoko Noto Kazufumi Mochizuki Romeo Papazyan Sean D Taverna Paul H Dear Donna M Cassidy-Hanley Jie Xiong Wei Miao Eduardo Orias Robert S Coyne |
| spellingShingle |
Eileen P Hamilton Aurélie Kapusta Piroska E Huvos Shelby L Bidwell Nikhat Zafar Haibao Tang Michalis Hadjithomas Vivek Krishnakumar Jonathan H Badger Elisabet V Caler Carsten Russ Qiandong Zeng Lin Fan Joshua Z Levin Terrance Shea Sarah K Young Ryan Hegarty Riza Daza Sharvari Gujja Jennifer R Wortman Bruce W Birren Chad Nusbaum Jainy Thomas Clayton M Carey Ellen J Pritham Cédric Feschotte Tomoko Noto Kazufumi Mochizuki Romeo Papazyan Sean D Taverna Paul H Dear Donna M Cassidy-Hanley Jie Xiong Wei Miao Eduardo Orias Robert S Coyne Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome eLife Tetrahymena thermophila chromosome breakage intermal eliminated sequence genome rearrangement transposable element centromere |
| author_facet |
Eileen P Hamilton Aurélie Kapusta Piroska E Huvos Shelby L Bidwell Nikhat Zafar Haibao Tang Michalis Hadjithomas Vivek Krishnakumar Jonathan H Badger Elisabet V Caler Carsten Russ Qiandong Zeng Lin Fan Joshua Z Levin Terrance Shea Sarah K Young Ryan Hegarty Riza Daza Sharvari Gujja Jennifer R Wortman Bruce W Birren Chad Nusbaum Jainy Thomas Clayton M Carey Ellen J Pritham Cédric Feschotte Tomoko Noto Kazufumi Mochizuki Romeo Papazyan Sean D Taverna Paul H Dear Donna M Cassidy-Hanley Jie Xiong Wei Miao Eduardo Orias Robert S Coyne |
| author_sort |
Eileen P Hamilton |
| title |
Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome |
| title_short |
Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome |
| title_full |
Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome |
| title_fullStr |
Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome |
| title_full_unstemmed |
Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome |
| title_sort |
structure of the germline genome of tetrahymena thermophila and relationship to the massively rearranged somatic genome |
| publisher |
eLife Sciences Publications Ltd |
| series |
eLife |
| issn |
2050-084X |
| publishDate |
2016-11-01 |
| description |
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. |
| topic |
Tetrahymena thermophila chromosome breakage intermal eliminated sequence genome rearrangement transposable element centromere |
| url |
https://elifesciences.org/articles/19090 |
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doaj-5b8a3b25eb90453aad49d3598e13d79e2021-05-05T00:43:14ZengeLife Sciences Publications LtdeLife2050-084X2016-11-01510.7554/eLife.19090Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genomeEileen P Hamilton0Aurélie Kapusta1https://orcid.org/0000-0002-4131-903XPiroska E Huvos2Shelby L Bidwell3Nikhat Zafar4Haibao Tang5Michalis Hadjithomas6Vivek Krishnakumar7https://orcid.org/0000-0002-5227-0200Jonathan H Badger8Elisabet V Caler9Carsten Russ10Qiandong Zeng11Lin Fan12Joshua Z Levin13Terrance Shea14Sarah K Young15Ryan Hegarty16Riza Daza17Sharvari Gujja18Jennifer R Wortman19Bruce W Birren20Chad Nusbaum21Jainy Thomas22Clayton M Carey23Ellen J Pritham24Cédric Feschotte25Tomoko Noto26Kazufumi Mochizuki27https://orcid.org/0000-0001-7987-9852Romeo Papazyan28Sean D Taverna29Paul H Dear30Donna M Cassidy-Hanley31Jie Xiong32Wei Miao33Eduardo Orias34Robert S Coyne35https://orcid.org/0000-0002-7693-3996Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, United StatesDepartment of Human Genetics, University of Utah School of Medicine, Salt Lake City, United StatesBiochemistry and Molecular Biology, Southern Illinois University, Carbondale, United StatesJ. Craig Venter Institute, Rockville, United StatesJ. Craig Venter Institute, Rockville, United StatesJ. Craig Venter Institute, Rockville, United StatesJ. Craig Venter Institute, Rockville, United StatesJ. Craig Venter Institute, Rockville, United StatesJ. Craig Venter Institute, Rockville, United StatesJ. Craig Venter Institute, Rockville, United StatesEli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United StatesEli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United StatesEli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United StatesEli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United StatesEli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United StatesEli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United StatesEli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United StatesEli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United StatesEli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United StatesEli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United StatesEli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United StatesEli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United StatesDepartment of Human Genetics, University of Utah School of Medicine, Salt Lake City, United StatesDepartment of Human Genetics, University of Utah School of Medicine, Salt Lake City, United StatesDepartment of Human Genetics, University of Utah School of Medicine, Salt Lake City, United StatesDepartment of Human Genetics, University of Utah School of Medicine, Salt Lake City, United StatesInstitute of Molecular Biotechnology, Vienna, AustriaInstitute of Molecular Biotechnology, Vienna, AustriaDepartment of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United StatesDepartment of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United StatesMRC Laboratory of Molecular Biology, Cambridge, United KingdomDepartment of Microbiology and Immunology, Cornell University, Ithaca, United StatesInstitute of Hydrobiology, Chinese Academy of Sciences, Wuhan, ChinaInstitute of Hydrobiology, Chinese Academy of Sciences, Wuhan, ChinaDepartment of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, United StatesJ. Craig Venter Institute, Rockville, United StatesThe 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.https://elifesciences.org/articles/19090Tetrahymena thermophilachromosome breakageintermal eliminated sequencegenome rearrangementtransposable elementcentromere |