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Nature. October 20, 2016; 538 (7625): 336-343.

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: HD065705 , GM086321 , R01 HD069344 NICHD NIH HHS , P41 HD064556 NICHD NIH HHS , HD080708 , R35 GM118183 NIGMS NIH HHS , R01 GM086627 NIGMS NIH HHS , R21 GM119021 NIGMS NIH HHS , R01 HL117164 NHLBI NIH HHS

Genes referenced: actr3 ap3s1 aqp7 arrb1 atp6ap1.2 avd bix1.1 bix1.2 bix1.3 brd2 capza1 ccna1 ccna2 ccnb1.2 ccnb3 ccnd1 ccnd2 ccndx ccne1 ccne2 ccnh ccny cdk1 cdk2 cdk4 cdk6 cdk7 cers1 chrd.1 coil cox7c crb2 crb3 crebbp ctnnb1 cttnbp2 diexf dnase1l1 eda evx1 fam50a foxa1 fubp1 gdf1 gdf3 gdi1 gnao1 gsk3a hhat hhip hoxb2 hoxb4 htt inhba kcnd3 kcnh1 klf2 lats2 lifr lrp5 lypd1 map4k4 mob1a mob1b mst1 myh6 nf2 nodal1 nodal2 nodal3.1 nodal5 nodal6 numbl ptch1 rab11fip4 rcor3 rhoc rnf4 rpl10 rpl13a rps11 sav1 scpep1 scrib sf3b4 shh six6 skp1 slco2b1 smo spcs3 stau1 suz12 sv2a tacc1 tap2 tapbp taz tcf3 tcf4 tcf7 tdrd6 tgfb1 tmem161b trim25 ubxn1 utp6 vdac1 vps41 wnt1 wnt11b wnt2b yap1

Ahn, 2008, Pubmed, Xenbase[+]

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