title: The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development.
abstract: Programmed DNA rearrangements in the single-celled eukaryote Oxytricha trifallax completely rewire its germline into a somatic nucleus during development. This elaborate, RNA-mediated pathway eliminates noncoding DNA sequences that interrupt gene loci and reorganizes the remaining fragments by inversions and permutations to produce functional genes. Here, we report the Oxytricha germline genome and compare it to the somatic genome to present a global view of its massive scale of genome rearrangements. The remarkably encrypted genome architecture contains >3,500 scrambled genes, as well as >800 predicted germline-limited genes expressed, and some posttranslationally modified, during genome rearrangements. Gene segments for different somatic loci often interweave with each other. Single gene segments can contribute to multiple, distinct somatic loci. Terminal precursor segments from neighboring somatic loci map extremely close to each other, often overlapping. This genome assembly provides a draft of a scrambled genome and a powerful model for studies of genome rearrangement.
authors.affiliation: Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
authors.forename: Xiao
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
authors.forename: John R
authors.initials: JR
authors.lastname: Bracht
authors.affiliation: Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
authors.forename: Aaron David
authors.initials: AD
authors.lastname: Goldman
authors.affiliation: Department of Mathematics and Statistics, University of South Florida, Tampa, FL 33620, USA.
authors.forename: Egor
authors.initials: E
authors.lastname: Dolzhenko
authors.affiliation: Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
authors.forename: Derek M
authors.initials: DM
authors.lastname: Clay
authors.affiliation: Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland.
authors.forename: Estienne C
authors.initials: EC
authors.lastname: Swart
authors.affiliation: Collaborative Proteomics and Mass Spectrometry Center, Molecular Biology Department and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
authors.forename: David H
authors.initials: DH
authors.lastname: Perlman
authors.affiliation: Department of Biology, University of Indiana, Bloomington, IN 47405, USA.
authors.forename: Thomas G
authors.initials: TG
authors.lastname: Doak
authors.affiliation: Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Stuart
authors.affiliation: Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA.
authors.forename: Chris T
authors.initials: CT
authors.lastname: Amemiya
authors.affiliation: Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
authors.forename: Robert P
authors.initials: RP
authors.lastname: Sebra
authors.affiliation: Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA. Electronic address: lfl@princeton.edu.
authors.forename: Laura F
authors.initials: LF
authors.lastname: Landweber
mesh_terms: D002467:Cell Nucleus / Q000378:metabolism; D002875:Chromosomes / Q000378:metabolism; D015321:Gene Rearrangement; D018503:Genome, Protozoan; D008969:Molecular Sequence Data; D016813:Oxytricha / Q000166:cytology / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism