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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: Xenopus laevis
Genes referenced: actr3 ap3s1 aqp7 arrb1 atp6ap1.2 avd bix1.1 bix1.2 bix1.3 capza1 ccna1 ccna2 ccnb1.2 ccnb3 ccnd1 ccnd2 ccndx ccne1 ccne2 ccnh ccny cdk1 cdk2 cdk4 cdk6 cdk7 cers1 chrd coil cox7c crb2 crb3 crebbp ctnnb1 cttnbp2 dm-w dnase1l1 dvl2 eda fam50a foxa1 fubp1 gdf1 gdf3 gdi1 gsk3a gsk3b hhat hhatl hhip hoxb2 hoxb4 htt inhba kcnd3 kcnh1 klf2 lats2 lifr lrp1 lrp5 lypd1 map4k4 mhc2-dma mhc2-dmb mob1a mob1b mst1 myh6 nf2 nodal1 nodal2 nodal3.1 nodal5.5 nodal6 numbl ptch1 rab11fip4 rcor3 rhoc rnf4 rpl10 rpl13a rps11 sav1 scpep1 scrib sf3b4 shh six6 skp1 slco2b1 smo spcs3 stau1 suz12 sv2a tacc1 tafazzin tap2 tapbp tcf3 tcf4 tcf7 tmem161b trim25 ubxn1 utp25 utp6 vdac1 vps41 wnt1 wnt11b wnt2b wwtr1 yap1

GEO Series: GSE73419: Xenbase,  NCBI
GSE73430: Xenbase,  NCBI
GSE73431: NCBI
GSE76059: Xenbase,  NCBI
GSE76247: NCBI

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