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Science April 30, 2010; 328 (5978): 633-6.

The genome of the Western clawed frog Xenopus tropicalis.

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 .

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.

PubMed ID: 20431018
PMC ID: PMC2994648
Article link: Science
Grant support: U01 HG02155 NHGRI NIH HHS , HHSN261200800001E PHS HHS , R01 AI027877-20 NIAID NIH HHS , R01 DK070858-05 NIDDK NIH HHS , R01 EY018000-03 NEI NIH HHS , R01 GM060572-05 NIGMS NIH HHS , R01 GM086321-03 NIGMS NIH HHS , R01 HD042294-05 NICHD NIH HHS , R01 HD045776-05 NICHD NIH HHS , R01 HD046661-03 NICHD NIH HHS , R01 MH079381-02 NIMH NIH HHS, R24 AI059830-08 NIAID NIH HHS , R24 RR015088-03 NCRR NIH HHS , U01 HG002155-05 NHGRI NIH HHS , R21 HD065713-02 NICHD NIH HHS , HHSN261200800001E NCI NIH HHS , P41 HD064556-01 NICHD NIH HHS , P41 HD064556-02 NICHD NIH HHS , R01 EY018000-04 NEI NIH HHS , MC_U117560482 Medical Research Council , P41 HD064556 NICHD NIH HHS , R01 AI027877 NIAID NIH HHS , R01 DK070858 NIDDK NIH HHS , R01 EY018000 NEI NIH HHS , R01 GM060572 NIGMS NIH HHS , R01 GM086321 NIGMS NIH HHS , R01 HD042294 NICHD NIH HHS , R01 HD045776 NICHD NIH HHS , R01 MH079381 NIMH NIH HHS, R21 HD065713 NICHD NIH HHS , R24 AI059830 NIAID NIH HHS , R24 RR015088 NCRR NIH HHS , Intramural NIH HHS, U01 HG002155 NHGRI NIH HHS , MRC_MC_U117560482 Medical Research Council

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