@article{47af0447f0094e3f9a8b6eb83e152d5e,
title = "Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome",
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{\textquoteright}s germline/soma differentiation to that of other characterized ciliates, illustrating the wide diversity of adaptations that have occurred within this phylum.",
author = "Hamilton, {Eileen P.} and Aur{\'e}lie Kapusta and Huvos, {Piroska E.} and Bidwell, {Shelby L.} and Nikhat Zafar and Haibao Tang and Michalis Hadjithomas and Vivek Krishnakumar and Badger, {Jonathan H.} and Caler, {Elisabet V.} and Carsten Russ and Qiandong Zeng and Lin Fan and Levin, {Joshua Z.} and Terrance Shea and Young, {Sarah K.} and Ryan Hegarty and Riza Daza and Sharvari Gujja and Wortman, {Jennifer R.} and Birren, {Bruce W.} and Chad Nusbaum and Jainy Thomas and Carey, {Clayton M.} and Pritham, {Ellen J.} and C{\'e}dric Feschotte and Tomoko Noto and Kazufumi Mochizuki and Romeo Papazyan and Taverna, {Sean D.} and Dear, {Paul H.} and Cassidy-Hanley, {Donna M.} and Jie Xiong and Wei Miao and Eduardo Orias and Coyne, {Robert S.}",
note = "Funding Information: We thank the Broad Genomics Platform for their contribution and support. We thank James Bochicchio for project coordination, Margaret Priest for annotation and Lucia Alvarado-Balderrama for data release. This work was supported by the National Human Genome Research Institute grant U54 HG003067 (to Eric S Lander and Stacey Gabriel), by award MCB-1158346 from the National Science Foundation to RSC, and by award 31525021 from the Natural Science Foundation of China to WM, and by the National Institutes of Health grant GM077582 to CF. We thank the following Southern Illinois University students for technical assistance (listed in chronological order of their contributions): Courtney Taylor, Kylie Corry, Logan Roberts, Benjamin Clevenger, Nicole Szczepanik, Brian Pinkins, and Aparajita Rajamahanty. We thank the following University of California at Santa Barbara students for technical assistance (listed in alphabetical order): Sergio Alvarez, Brian Argueta, Justin Kanerva, Gavriel Matt, Veronica Munoz, Atul Saini, Richard Sanchez, and Leinah Tran, as well as technician Judith Orias. We thank the following Cornell University students: Francis Chen, Shanique Alabi, Kacey Solotoff, and Gary Tan, as well as technician Mozzamal Hossain. We gratefully acknowledge Chris Town for administrative management and helpful discussions, Heather B. McDonald for scientific illustration, and the Next Generation Sequencing unit of Campus Support Facility, Vienna Bio-Center, for sequencing small RNAs. Publisher Copyright: {\textcopyright} 2016, eLife Sciences Publications Ltd. All rights reserved.",
year = "2016",
month = nov,
day = "28",
doi = "10.7554/eLife.19090.001",
language = "English (US)",
volume = "5",
journal = "eLife",
issn = "2050-084X",
publisher = "eLife Sciences Publications",
number = "NOVEMBER2016",
}