@article{68826fbf573349a596bcb648f71a1e06,
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.",
author = "Xiao Chen and Bracht, {John R.} and Goldman, {Aaron David} and Egor Dolzhenko and Clay, {Derek M.} and Swart, {Estienne C.} and Perlman, {David H.} and Doak, {Thomas G.} and Andrew Stuart and Amemiya, {Chris T.} and Sebra, {Robert P.} and Landweber, {Laura F.}",
note = "Funding Information: We thank the late David Prescott for suggesting sucrose purification of the Oxytricha micronuclei, Jingmei Wang for laboratory assistance, Jessica Wiggins, Wei Wang, and Donna Storton of the Princeton Sequencing Core Facility for assistance with Illumina library preparation and sequencing, Gintaras Deikus for assistance with PacBio sequencing, Klaas Schotanus, Mariusz Nowacki, Wenwen Fang, and all current laboratory members for discussion. We thank Jue Ruan at Beijing Institute of Genomics for advice on the assembly strategy. We are grateful to National Center for Genome Analysis Support (NCGAS) computing resources (supported by National Science Foundation [NSF] grant ABI-1062432 to Indiana University). This study was supported by NIH grant GM59708 and GM109459 and NSF grants 0900544 and 0923810 to L.F.L.. J.R.B. was supported by NIH fellowship 1F32GM099462 and A.D.G. was a National Aeronautics and Space Administration (NASA) postdoctoral fellow. ",
year = "2014",
month = aug,
day = "28",
doi = "10.1016/j.cell.2014.07.034",
language = "English",
volume = "158",
pages = "1187--1198",
journal = "Cell",
issn = "0092-8674",
publisher = "Cell Press",
number = "5",
}