title: Genome evolution in the allotetraploid frog Xenopus laevis.
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.
authors.affiliation: University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA.|US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.
authors.forename: Adam M
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authors.affiliation: Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
authors.forename: Yoshinobu
authors.initials: Y
authors.lastname: Uno
authors.affiliation: Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, USA.|Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 689-798, Republic of Korea.
authors.forename: Taejoon
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authors.lastname: Kwon
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.
authors.forename: Jarrod A
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authors.lastname: Chapman
authors.affiliation: Center for Information Biology, and Advanced Genomics Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan.
authors.forename: Atsushi
authors.initials: A
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authors.affiliation: Amphibian Research Center, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
authors.forename: Shuji
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authors.lastname: Takahashi
authors.affiliation: Laboratory of Tissue and Polymer Sciences, Faculty of Advanced Life Science, Hokkaido University, N10W8, Kita-ku, Sapporo 060-0810, Japan.
authors.forename: Akimasa
authors.initials: A
authors.lastname: Fukui
authors.affiliation: Division of Human Sciences, Graduate School of Integrated Arts and Sciences, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan.
authors.forename: Akira
authors.initials: A
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authors.forename: Atsushi
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authors.forename: Mariko
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authors.forename: Simon J
authors.initials: SJ
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authors.forename: Sven
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authors.affiliation: Department of Animal Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan.
authors.forename: Hajime
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authors.affiliation: Institute for Promotion of Medical Science Research, Yamagata University Faculty of Medicine, 2-2-2 Iida-Nishi, Yamagata, Yamagata 990-9585, Japan.
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authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.
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authors.initials: JB
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authors.affiliation: Radboud University, Faculty of Science, Department of Molecular Developmental Biology, 259 RIMLS, M850/2.97, Geert Grooteplein 28, Nijmegen 6525 GA, the Netherlands.
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authors.initials: G
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authors.forename: Ila
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authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.
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authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.
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authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.|HudsonAlpha Institute of Biotechnology, Huntsville, Alabama 35806, USA.
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authors.affiliation: Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, USA.
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authors.affiliation: Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, USA.
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authors.initials: M
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authors.affiliation: Division of Morphogenesis, Department of Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan.|Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan.
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authors.forename: Gert Jan C
authors.initials: GJ
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authors.affiliation: Center for Information Biology, and Advanced Genomics Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan.|Principles of Informatics, National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo 101-8430, Japan.|Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizoka 411-8540, Japan.
authors.forename: Asao
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authors.affiliation: University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA.
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authors.initials: RM
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authors.affiliation: Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Masanori
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authors.lastname: Taira
authors.affiliation: University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA.|US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.|Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
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mesh_terms: D000818:Animals; D002875:Chromosomes / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D004171:Diploidy; D019143:Evolution, Molecular; D005260:Female; D017353:Gene Deletion; D020869:Gene Expression Profiling; D016678:Genome / Q000235:genetics*; D059785:Karyotype; D058977:Molecular Sequence Annotation; D016296:Mutagenesis / Q000235:genetics; D010802:Phylogeny; D011544:Pseudogenes; D057891:Tetraploidy; D014981:Xenopus / Q000235:genetics; D014982:Xenopus laevis / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements