Dichmann DS

References (2)

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.
ESTHER : Session_2016_Nature_538_336
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

Title : The genome of the Western clawed frog Xenopus tropicalis - Hellsten_2010_Science_328_633
Author(s) : Hellsten U , Harland RM , Gilchrist MJ , Hendrix D , Jurka J , Kapitonov V , Ovcharenko I , Putnam NH , Shu S , Taher L , Blitz IL , Blumberg B , Dichmann DS , Dubchak I , Amaya E , Detter JC , Fletcher R , Gerhard DS , Goodstein D , Graves T , Grigoriev IV , Grimwood J , Kawashima T , Lindquist E , Lucas SM , Mead PE , Mitros T , Ogino H , Ohta Y , Poliakov AV , Pollet N , Robert J , Salamov A , Sater AK , Schmutz J , Terry A , Vize PD , Warren WC , Wells D , Wills A , Wilson RK , Zimmerman LB , Zorn AM , Grainger R , Grammer T , Khokha MK , Richardson PM , Rokhsar DS
Ref : Science , 328 :633 , 2010
Abstract : The western clawed frog Xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the African clawed frog Xenopus laevis with more tractable genetics. Here we present a draft genome sequence assembly of X. tropicalis. This genome encodes more than 20,000 protein-coding genes, including orthologs of at least 1700 human disease genes. Over 1 million expressed sequence tags validated the annotation. More than one-third of the genome consists of transposable elements, with unusually prevalent DNA transposons. Like that of other tetrapods, the genome of X. tropicalis contains gene deserts enriched for conserved noncoding elements. The genome exhibits substantial shared synteny with human and chicken over major parts of large chromosomes, broken by lineage-specific chromosome fusions and fissions, mainly in the mammalian lineage.
ESTHER : Hellsten_2010_Science_328_633
PubMedSearch : Hellsten_2010_Science_328_633
PubMedID: 20431018
Gene_locus related to this paper: xenla-q6pcj9 , xentr-a9umk0 , xentr-abhdb , xentr-ACHE , xentr-b0bm77 , xentr-b1h0y7 , xentr-b2guc4 , xentr-b7zt03 , xentr-b7ztj4 , xentr-BCHE1 , xentr-BCHE2 , xentr-cxest2 , xentr-d2x2k4 , xentr-d2x2k6 , xentr-f6rff6 , xentr-f6v0g3 , xentr-f6v2j6 , xentr-f6v3z1 , xentr-f6y4c8 , xentr-f6yve5 , xentr-f7a4y9 , xentr-f7acc5 , xentr-f7e2e2 , xentr-LOC394897 , xentr-ndrg1 , xentr-q0vfb6 , xentr-f7cpl7 , xentr-f6yj44 , xentr-f7ejk4 , xentr-f6q8j8 , xentr-f6z8f0 , xentr-f7d709 , xentr-b0bmb8 , xentr-f7af63 , xentr-a0a1b8y2w9 , xentr-f7d4k9 , xentr-f6r032 , xentr-f6yvq3 , xentr-a0a1b8y2z3 , xentr-f7afg4 , xentr-f6xb15 , xentr-f7e1r2 , xentr-a4ihf1 , xentr-f7eue5 , xentr-f6u7u3 , xentr-f172a , xentr-f7equ8 , xentr-f7dd89 , xentr-a9jtx5