title: Structure of the germline genome ofTetrahymena thermophilaand relationship to the massively rearranged somatic genome.
abstract: The germline genome of the binucleated ciliateTetrahymena thermophilaundergoes 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 shapedTetrahymenachromosome 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 compareTetrahymena's germline/soma differentiation to that of other characterized ciliates, illustrating the wide diversity of adaptations that have occurred within this phylum.
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, United States.
authors.forename: Eileen P
authors.initials: EP
authors.lastname: Hamilton
authors.affiliation: Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States.
authors.forename: Aurélie
authors.identifier: 0000-0002-4131-903X
authors.initials: A
authors.lastname: Kapusta
authors.affiliation: Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, United States.
authors.forename: Piroska E
authors.initials: PE
authors.lastname: Huvos
authors.affiliation: J. Craig Venter Institute, Rockville, United States.
authors.forename: Shelby L
authors.initials: SL
authors.lastname: Bidwell
authors.affiliation: J. Craig Venter Institute, Rockville, United States.
authors.forename: Nikhat
authors.initials: N
authors.lastname: Zafar
authors.affiliation: J. Craig Venter Institute, Rockville, United States.
authors.forename: Haibao
authors.initials: H
authors.lastname: Tang
authors.affiliation: J. Craig Venter Institute, Rockville, United States.
authors.forename: Michalis
authors.initials: M
authors.lastname: Hadjithomas
authors.affiliation: J. Craig Venter Institute, Rockville, United States.
authors.forename: Vivek
authors.identifier: 0000-0002-5227-0200
authors.initials: V
authors.lastname: Krishnakumar
authors.affiliation: J. Craig Venter Institute, Rockville, United States.
authors.forename: Jonathan H
authors.initials: JH
authors.lastname: Badger
authors.affiliation: J. Craig Venter Institute, Rockville, United States.
authors.forename: Elisabet V
authors.initials: EV
authors.lastname: Caler
authors.affiliation: Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States.
authors.forename: Carsten
authors.initials: C
authors.lastname: Russ
authors.affiliation: Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States.
authors.forename: Qiandong
authors.initials: Q
authors.lastname: Zeng
authors.affiliation: Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States.
authors.forename: Lin
authors.initials: L
authors.lastname: Fan
authors.affiliation: Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States.
authors.forename: Joshua Z
authors.initials: JZ
authors.lastname: Levin
authors.affiliation: Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States.
authors.forename: Terrance
authors.initials: T
authors.lastname: Shea
authors.affiliation: Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States.
authors.forename: Sarah K
authors.initials: SK
authors.lastname: Young
authors.affiliation: Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States.
authors.forename: Ryan
authors.initials: R
authors.lastname: Hegarty
authors.affiliation: Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States.
authors.forename: Riza
authors.initials: R
authors.lastname: Daza
authors.affiliation: Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States.
authors.forename: Sharvari
authors.initials: S
authors.lastname: Gujja
authors.affiliation: Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States.
authors.forename: Jennifer R
authors.initials: JR
authors.lastname: Wortman
authors.affiliation: Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States.
authors.forename: Bruce W
authors.initials: BW
authors.lastname: Birren
authors.affiliation: Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States.
authors.forename: Chad
authors.initials: C
authors.lastname: Nusbaum
authors.affiliation: Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States.
authors.forename: Jainy
authors.initials: J
authors.lastname: Thomas
authors.affiliation: Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States.
authors.forename: Clayton M
authors.initials: CM
authors.lastname: Carey
authors.affiliation: Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States.
authors.forename: Ellen J
authors.initials: EJ
authors.lastname: Pritham
authors.affiliation: Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States.
authors.forename: Cédric
authors.initials: C
authors.lastname: Feschotte
authors.affiliation: Institute of Molecular Biotechnology, Vienna, Austria.
authors.forename: Tomoko
authors.initials: T
authors.lastname: Noto
authors.affiliation: Institute of Molecular Biotechnology, Vienna, Austria.
authors.forename: Kazufumi
authors.identifier: 0000-0001-7987-9852
authors.initials: K
authors.lastname: Mochizuki
authors.affiliation: Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States.
authors.forename: Romeo
authors.initials: R
authors.lastname: Papazyan
authors.affiliation: Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States.
authors.forename: Sean D
authors.initials: SD
authors.lastname: Taverna
authors.affiliation: MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.
authors.forename: Paul H
authors.initials: PH
authors.lastname: Dear
authors.affiliation: Department of Microbiology and Immunology, Cornell University, Ithaca, United States.
authors.forename: Donna M
authors.initials: DM
authors.lastname: Cassidy-Hanley
authors.affiliation: Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Xiong
authors.affiliation: Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Miao
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, United States.
authors.forename: Eduardo
authors.initials: E
authors.lastname: Orias
authors.affiliation: J. Craig Venter Institute, Rockville, United States.
authors.forename: Robert S
authors.identifier: 0000-0002-7693-3996
authors.initials: RS
authors.lastname: Coyne
mesh_terms: D015321:Gene Rearrangement; D018503:Genome, Protozoan; D017422:Sequence Analysis, DNA; D016808:Tetrahymena thermophila / Q000235:genetics*
keywords: Tetrahymena thermophila; centromere; chromosome breakage; chromosomes; evolutionary biology; genes; genome rearrangement; genomics; intermal eliminated sequence; transposable element