Genome evolution in the allotetraploid frog Xenopus laevis

Adam M. Session, Yoshinobu Uno, Taejoon Kwon, Jarrod A. Chapman, Atsushi Toyoda, Shuji Takahashi, Akimasa Fukui, Akira Hikosaka, Atsushi Suzuki, Mariko Kondo, Simon J. van Heeringen, Ian Quigley, Sven Heinz, Hajime Ogino, Haruki Ochi, Uffe Hellsten, Jessica B. Lyons, Oleg Simakov, Nicholas Putnam, Jonathan Stites, Yoko Kuroki, Toshiaki Tanaka, Tatsuo Michiue, Minoru Watanabe, Ozren Bogdanovic, Ryan Lister, Georgios Georgiou, Sarita S. Paranjpe, Ila van Kruijsbergen, Shengquiang Shu, Joseph Carlson, Tsutomu Kinoshita, Yuko Ohta, Shuuji Mawaribuchi, Jerry Jenkins, Jane Grimwood, Jeremy Schmutz, Therese Mitros, Sahar V. Mozaffari, Yutaka Suzuki, Yoshikazu Haramoto, Takamasa S. Yamamoto, Chiyo Takagi, Rebecca Heald, Kelly Miller, Christian Haudenschild, Jacob Kitzman, Takuya Nakayama, Yumi Izutsu, Jacques Robert, Joshua Fortriede, Kevin Burns, Vaneet Lotay, Kamran Karimi, Yuuri Yasuoka, Darwin S. Dichmann, Martin F. Flajnik, Douglas W. Houston, Jay Shendure, Louis DuPasquier, Peter D. Vize, Aaron M. Zorn, Michihiko Ito, Edward M. Marcotte, John B. Wallingford, Yuzuru Ito, Makoto Asashima, Naoto Ueno, Yoichi Matsuda, Gert Jan C. Veenstra, Asao Fujiyama, Richard M. Harland (), Masanori Taira () and Daniel S. Rokhsar ()
Additional contact information
Adam M. Session: University of California, Berkeley, Life Sciences Addition #3200
Yoshinobu Uno: Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku
Taejoon Kwon: Center for Systems and Synthetic Biology, University of Texas at Austin
Jarrod A. Chapman: US Department of Energy Joint Genome Institute
Atsushi Toyoda: Center for Information Biology, and Advanced Genomics Center, National Institute of Genetics
Shuji Takahashi: Amphibian Research Center, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama
Akimasa Fukui: Laboratory of Tissue and Polymer Sciences, Faculty of Advanced Life Science, Hokkaido University
Akira Hikosaka: Graduate School of Integrated Arts and Sciences, Hiroshima University
Atsushi Suzuki: Amphibian Research Center, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama
Mariko Kondo: Misaki Marine Biological Station (MMBS), Graduate School of Science, The University of Tokyo, 1024 Koajiro, Misaki
Simon J. van Heeringen: Radboud University, Faculty of Science, 259 RIMLS, M850/2.97
Ian Quigley: Salk Institute, Molecular Neurobiology Laboratory, La Jolla
Sven Heinz: Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla
Hajime Ogino: Nagahama Institute of Bio-Science and Technology
Haruki Ochi: Institute for Promotion of Medical Science Research, Yamagata University Faculty of Medicine
Uffe Hellsten: US Department of Energy Joint Genome Institute
Jessica B. Lyons: University of California, Berkeley, Life Sciences Addition #3200
Oleg Simakov: Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University
Nicholas Putnam: Dovetail Genomics LLC. Santa Cruz
Jonathan Stites: Dovetail Genomics LLC. Santa Cruz
Yoko Kuroki: National Research Institute for Child Health and Development, NCCHD
Toshiaki Tanaka: Tokyo Institute of Technology
Tatsuo Michiue: Graduate School of Arts and Sciences, The University of Tokyo
Minoru Watanabe: Institute of Institution of Liberal Arts and Fundamental Education, Tokushima University
Ozren Bogdanovic: Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia
Ryan Lister: Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia
Georgios Georgiou: Radboud University, Faculty of Science, 259 RIMLS, M850/2.97
Sarita S. Paranjpe: Radboud University, Faculty of Science, 259 RIMLS, M850/2.97
Ila van Kruijsbergen: Radboud University, Faculty of Science, 259 RIMLS, M850/2.97
Shengquiang Shu: US Department of Energy Joint Genome Institute
Joseph Carlson: US Department of Energy Joint Genome Institute
Tsutomu Kinoshita: Faculty of Science, Rikkyo University
Yuko Ohta: University of Maryland
Shuuji Mawaribuchi: Kitasato Institute for Life Sciences, Kitasato University
Jerry Jenkins: US Department of Energy Joint Genome Institute
Jane Grimwood: US Department of Energy Joint Genome Institute
Jeremy Schmutz: US Department of Energy Joint Genome Institute
Therese Mitros: University of California, Berkeley, Life Sciences Addition #3200
Sahar V. Mozaffari: University of Chicago
Yutaka Suzuki: The University of Tokyo
Yoshikazu Haramoto: Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST)
Takamasa S. Yamamoto: National Institute for Basic Biology, 38 Nishigonaka
Chiyo Takagi: National Institute for Basic Biology, 38 Nishigonaka
Rebecca Heald: University of California, Berkeley, Life Sciences Addition #3200
Kelly Miller: University of California, Berkeley, Life Sciences Addition #3200
Christian Haudenschild: Illumina Inc., 25861 Industrial Blvd, Hayward
Jacob Kitzman: University of Washington, Foege Building S-250, Box 355065, 3720 15th Ave NE
Takuya Nakayama: University of Virginia
Yumi Izutsu: Faculty of Science, Niigata University
Jacques Robert: University of Rochester Medical Center, Rochester
Joshua Fortriede: Cincinnati Children's Research Foundation
Kevin Burns: Cincinnati Children's Research Foundation
Vaneet Lotay: University of Calgary
Kamran Karimi: University of Calgary
Yuuri Yasuoka: Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha
Darwin S. Dichmann: University of California, Berkeley, Life Sciences Addition #3200
Martin F. Flajnik: University of Maryland
Douglas W. Houston: The University of Iowa, 257 Biology Building
Jay Shendure: University of Washington, Foege Building S-250, Box 355065, 3720 15th Ave NE
Louis DuPasquier: University of Basel
Peter D. Vize: University of Calgary
Aaron M. Zorn: Cincinnati Children's Research Foundation
Michihiko Ito: School of Science, Kitasato University
Edward M. Marcotte: Center for Systems and Synthetic Biology, University of Texas at Austin
John B. Wallingford: Center for Systems and Synthetic Biology, University of Texas at Austin
Yuzuru Ito: Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST)
Makoto Asashima: Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST)
Naoto Ueno: National Institute for Basic Biology, 38 Nishigonaka
Yoichi Matsuda: Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku
Gert Jan C. Veenstra: Radboud University, Faculty of Science, 259 RIMLS, M850/2.97
Asao Fujiyama: Center for Information Biology, and Advanced Genomics Center, National Institute of Genetics
Richard M. Harland: University of California, Berkeley, Life Sciences Addition #3200
Masanori Taira: Graduate School of Science, The University of Tokyo
Daniel S. Rokhsar: University of California, Berkeley, Life Sciences Addition #3200

Nature, 2016, vol. 538, issue 7625, 336-343

Abstract: Abstract To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of ‘fossil’ transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17–18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.

Date: 2016
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DOI: 10.1038/nature19840

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