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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.

SUBMITTER: Session AM 

PROVIDER: S-EPMC5313049 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature

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Genome evolution in the allotetraploid frog Xenopus laevis.

Session Adam M AM   Uno Yoshinobu Y   Kwon Taejoon T   Chapman Jarrod A JA   Toyoda Atsushi A   Takahashi Shuji S   Fukui Akimasa A   Hikosaka Akira A   Suzuki Atsushi A   Kondo Mariko M   van Heeringen Simon J SJ   Quigley Ian I   Heinz Sven S   Ogino Hajime H   Ochi Haruki H   Hellsten Uffe U   Lyons Jessica B JB   Simakov Oleg O   Putnam Nicholas N   Stites Jonathan J   Kuroki Yoko Y   Tanaka Toshiaki T   Michiue Tatsuo T   Watanabe Minoru M   Bogdanovic Ozren O   Lister Ryan R   Georgiou Georgios G   Paranjpe Sarita S SS   van Kruijsbergen Ila I   Shu Shengquiang S   Carlson Joseph J   Kinoshita Tsutomu T   Ohta Yuko Y   Mawaribuchi Shuuji S   Jenkins Jerry J   Grimwood Jane J   Schmutz Jeremy J   Mitros Therese T   Mozaffari Sahar V SV   Suzuki Yutaka Y   Haramoto Yoshikazu Y   Yamamoto Takamasa S TS   Takagi Chiyo C   Heald Rebecca R   Miller Kelly K   Haudenschild Christian C   Kitzman Jacob J   Nakayama Takuya T   Izutsu Yumi Y   Robert Jacques J   Fortriede Joshua J   Burns Kevin K   Lotay Vaneet V   Karimi Kamran K   Yasuoka Yuuri Y   Dichmann Darwin S DS   Flajnik Martin F MF   Houston Douglas W DW   Shendure Jay J   DuPasquier Louis L   Vize Peter D PD   Zorn Aaron M AM   Ito Michihiko M   Marcotte Edward M EM   Wallingford John B JB   Ito Yuzuru Y   Asashima Makoto M   Ueno Naoto N   Matsuda Yoichi Y   Veenstra Gert Jan C GJ   Fujiyama Asao A   Harland Richard M RM   Taira Masanori M   Rokhsar Daniel S DS  

Nature 20161001 7625

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  ...[more]

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