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Nature 2016 Oct 20;5387625:336-343. doi: 10.1038/nature19840.
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Genome evolution in the allotetraploid frog Xenopus laevis.

Session AM , Uno Y , Kwon T , Chapman JA , Toyoda A , Takahashi S , Fukui A , Hikosaka A , Suzuki A , Kondo M , van Heeringen SJ , Quigley I , Heinz S , Ogino H , Ochi H , Hellsten U , Lyons JB , Simakov O , Putnam N , Stites J , Kuroki Y , Tanaka T , Michiue T , Watanabe M , Bogdanovic O , Lister R , Georgiou G , Paranjpe SS , van Kruijsbergen I , Shu S , Carlson J , Kinoshita T , Ohta Y , Mawaribuchi S , Jenkins J , Grimwood J , Schmutz J , Mitros T , Mozaffari SV , Suzuki Y , Haramoto Y , Yamamoto TS , Takagi C , Heald R , Miller K , Haudenschild C , Kitzman J , Nakayama T , Izutsu Y , Robert J , Fortriede J , Burns K , Lotay V , Karimi K , Yasuoka Y , Dichmann DS , Flajnik MF , Houston DW , Shendure J , DuPasquier L , Vize PD , Zorn AM , Ito M , Marcotte EM , Wallingford JB , Ito Y , Asashima M , Ueno N , Matsuda Y , Veenstra GJ , Fujiyama A , Harland RM , Taira M , Rokhsar DS .

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.

PubMed ID: 27762356
PMC ID: PMC5313049
Article link: Nature
Grant support: [+]

Species referenced: Echinodermata
Genes referenced: ago1b apc btaf1 chrd gli3 gsk3a hh hhat irak1bp1 LOC100888955 LOC100892350 LOC100893907 LOC105441174 LOC115918936 LOC115919910 LOC115921693 LOC115925415 LOC576611 LOC578583 LOC579717 LOC581699 LOC583082 LOC588471 LOC589947 LOC594261 LOC594488 LOC752814 polr3a ptch1 rpl13a taz Tcf/Lef

Article Images: [+] show captions
References [+] :
Ahn, MMTS, a new subfamily of Tc1-like transposons. 2008, Pubmed