Session_2016_Nature_538_336

Reference

Title : Genome evolution in the allotetraploid frog Xenopus laevis - Session_2016_Nature_538_336
Author(s) : 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
Ref : Nature , 538 :336 , 2016
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.

PubMedSearch : Session_2016_Nature_538_336
PubMedID: 27762356
Gene_locus related to this paper: xenla-a0a1l8f4t7 , xenla-a0a1l8fbc6 , xenla-a0a1l8fct2 , xenla-q2tap9 , xenla-q4klb6 , xenla-q5xh09 , xenla-q6ax59 , xenla-q6dcw6 , xenla-q6irp4 , xenla-q6pad5 , xenla-q7sz70 , xenla-Q7ZXQ6 , xenla-q66kx1 , xenla-q640y7 , xenla-q642r3 , xenla-Q860X9 , xenla-BCHE2 , xenla-a0a1l8g7v4 , xenla-a0a1l8g1u7 , xenla-a0a1l8fmc5 , xenla-a0a1l8g467 , xenla-a0a1l8g4e4 , xenla-a0a1l8ga66 , xenla-a0a1l8gaw4 , xenla-a0a1l8gt68 , xenla-a0a1l8h0b2 , xenla-a0a1l8fdr1 , xenla-a0a1l8fdt7 , xenla-a0a1l8fi72 , xenla-a0a1l8fi73 , xenla-a0a1l8fi77 , xenla-a0a1l8fi96 , xenla-a0a1l8hc38 , xenla-a0a1l8hn27 , xenla-a0a1l8hry6 , xenla-a0a1l8hw96 , xenla-a0a1l8i2x6 , xenla-a0a1l8hei7 , xenla-a0a1l8gnd1 , xenla-a0a1l8i2g3 , xenla-a0a1l8hdn0 , xenla-a0a1l8h622

Related information

Gene_locus xenla-a0a1l8f4t7    xenla-a0a1l8fbc6    xenla-a0a1l8fct2    xenla-q2tap9    xenla-q4klb6    xenla-q5xh09    xenla-q6ax59    xenla-q6dcw6    xenla-q6irp4    xenla-q6pad5    xenla-q7sz70    xenla-Q7ZXQ6    xenla-q66kx1    xenla-q640y7    xenla-q642r3    xenla-Q860X9    xenla-BCHE2    xenla-a0a1l8g7v4    xenla-a0a1l8g1u7    xenla-a0a1l8fmc5    xenla-a0a1l8g467    xenla-a0a1l8g4e4    xenla-a0a1l8ga66    xenla-a0a1l8gaw4    xenla-a0a1l8gt68    xenla-a0a1l8h0b2    xenla-a0a1l8fdr1    xenla-a0a1l8fdt7    xenla-a0a1l8fi72    xenla-a0a1l8fi73    xenla-a0a1l8fi77    xenla-a0a1l8fi96    xenla-a0a1l8hc38    xenla-a0a1l8hn27    xenla-a0a1l8hry6    xenla-a0a1l8hw96    xenla-a0a1l8i2x6    xenla-a0a1l8hei7    xenla-a0a1l8gnd1    xenla-a0a1l8i2g3    xenla-a0a1l8hdn0    xenla-a0a1l8h622
Gene_locus_frgt xenla-a0a1l8f4t7    xenla-a0a1l8fbc6    xenla-a0a1l8fct2    xenla-q2tap9    xenla-q4klb6    xenla-q5xh09    xenla-q6ax59    xenla-q6dcw6    xenla-q6irp4    xenla-q6pad5    xenla-q7sz70    xenla-Q7ZXQ6    xenla-q66kx1    xenla-q640y7    xenla-q642r3    xenla-Q860X9    xenla-BCHE2    xenla-a0a1l8g7v4    xenla-a0a1l8g1u7    xenla-a0a1l8fmc5    xenla-a0a1l8g467    xenla-a0a1l8g4e4    xenla-a0a1l8ga66    xenla-a0a1l8gaw4    xenla-a0a1l8gt68    xenla-a0a1l8h0b2    xenla-a0a1l8fdr1    xenla-a0a1l8fdt7    xenla-a0a1l8fi72    xenla-a0a1l8fi73    xenla-a0a1l8fi77    xenla-a0a1l8fi96    xenla-a0a1l8hc38    xenla-a0a1l8hn27    xenla-a0a1l8hry6    xenla-a0a1l8hw96    xenla-a0a1l8i2x6    xenla-a0a1l8hei7    xenla-a0a1l8gnd1    xenla-a0a1l8i2g3    xenla-a0a1l8hdn0    xenla-a0a1l8h622    xenla-a0a1l8g407    xenla-a0a1l8g4b7    xenla-a0a1l8ghq4    xenla-a0a1l8fdq0    xenla-a0a1l8fi79    xenla-a0a1l8hgg1

Citations formats

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 (2016)
Genome evolution in the allotetraploid frog Xenopus laevis
Nature 538 :336

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 (2016)
Nature 538 :336