The genome of the Western clawed frog Xenopus tropicalis

Uffe Hellsten; Richard M Harland; Michael J Gilchrist; David Hendrix; Jerzy Jurka; Vladimir Kapitonov; Ivan Ovcharenko; Nicholas H Putnam; Shengqiang Shu; Leila Taher; Ira L Blitz; Bruce Blumberg; Darwin S Dichmann; Inna Dubchak; Enrique Amaya; John C Detter; Russell Fletcher; Daniela S Gerhard; David Goodstein; Tina Graves; Igor V Grigoriev; Jane Grimwood; Takeshi Kawashima; Erika Lindquist; Susan M Lucas; Paul E Mead; Therese Mitros; Hajime Ogino; Yuko Ohta; Alexander V Poliakov; Nicolas Pollet; Jacques Robert; Asaf Salamov; Amy K Sater; Jeremy Schmutz; Astrid Terry; Peter D Vize; Wesley C Warren; Dan Wells; Andrea Wills; Richard K Wilson; Lyle B Zimmerman; Aaron M Zorn; Robert Grainger; Timothy Grammer; Mustafa K Khokha; Paul M Richardson; Daniel S Rokhsar

doi:10.1126/science.1183670

The genome of the Western clawed frog Xenopus tropicalis

Uffe Hellsten^*, Richard M Harland, Michael J Gilchrist, David Hendrix, Jerzy Jurka, Vladimir Kapitonov, Ivan Ovcharenko, Nicholas H Putnam, Shengqiang Shu, Leila Taher, Ira L Blitz, Bruce Blumberg, Darwin S Dichmann, Inna Dubchak, Enrique Amaya, John C Detter, Russell Fletcher, Daniela S Gerhard, David Goodstein, Tina GravesIgor V Grigoriev, Jane Grimwood, Takeshi Kawashima, Erika Lindquist, Susan M Lucas, Paul E Mead, Therese Mitros, Hajime Ogino, Yuko Ohta, Alexander V Poliakov, Nicolas Pollet, Jacques Robert, Asaf Salamov, Amy K Sater, Jeremy Schmutz, Astrid Terry, Peter D Vize, Wesley C Warren, Dan Wells, Andrea Wills, Richard K Wilson, Lyle B Zimmerman, Aaron M Zorn, Robert Grainger, Timothy Grammer, Mustafa K Khokha, Paul M Richardson, Daniel S Rokhsar

^*Corresponding author for this work

Institute of Biomedical Informatics (7200)

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	633-6
Number of pages	4
Journal	Science
Volume	328
Issue number	5978
DOIs	https://doi.org/10.1126/science.1183670
Publication status	Published - 30 Apr 2010

Keywords

Animals
Chickens/genetics
Chromosome Mapping
Chromosomes/genetics
Computational Biology
Conserved Sequence
DNA Transposable Elements
DNA, Complementary
Embryo, Nonmammalian/metabolism
Evolution, Molecular
Expressed Sequence Tags
Gene Duplication
Genes
Genome
Humans
Phylogeny
Sequence Analysis, DNA
Synteny
Vertebrates/genetics
Xenopus/embryology
Xenopus Proteins/genetics

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1126/science.1183670

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Hellsten, U., Harland, R. M., Gilchrist, M. J., Hendrix, D., Jurka, J., Kapitonov, V., Ovcharenko, I., Putnam, N. H., Shu, S., Taher, L., Blitz, I. L., Blumberg, B., Dichmann, D. S., Dubchak, I., Amaya, E., Detter, J. C., Fletcher, R., Gerhard, D. S., Goodstein, D., ... Rokhsar, D. S. (2010). The genome of the Western clawed frog Xenopus tropicalis. Science, 328(5978), 633-6. https://doi.org/10.1126/science.1183670

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 2010, 'The genome of the Western clawed frog Xenopus tropicalis', Science, vol. 328, no. 5978, pp. 633-6. https://doi.org/10.1126/science.1183670

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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.",

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AU - Hellsten, Uffe

AU - Harland, Richard M

AU - Gilchrist, Michael J

AU - Hendrix, David

AU - Jurka, Jerzy

AU - Kapitonov, Vladimir

AU - Ovcharenko, Ivan

AU - Putnam, Nicholas H

AU - Shu, Shengqiang

AU - Taher, Leila

AU - Blitz, Ira L

AU - Blumberg, Bruce

AU - Dichmann, Darwin S

AU - Dubchak, Inna

AU - Amaya, Enrique

AU - Detter, John C

AU - Fletcher, Russell

AU - Gerhard, Daniela S

AU - Goodstein, David

AU - Graves, Tina

AU - Grigoriev, Igor V

AU - Grimwood, Jane

AU - Kawashima, Takeshi

AU - Lindquist, Erika

AU - Lucas, Susan M

AU - Mead, Paul E

AU - Mitros, Therese

AU - Ogino, Hajime

AU - Ohta, Yuko

AU - Poliakov, Alexander V

AU - Pollet, Nicolas

AU - Robert, Jacques

AU - Salamov, Asaf

AU - Sater, Amy K

AU - Schmutz, Jeremy

AU - Terry, Astrid

AU - Vize, Peter D

AU - Warren, Wesley C

AU - Wells, Dan

AU - Wills, Andrea

AU - Wilson, Richard K

AU - Zimmerman, Lyle B

AU - Zorn, Aaron M

AU - Grainger, Robert

AU - Grammer, Timothy

AU - Khokha, Mustafa K

AU - Richardson, Paul M

AU - Rokhsar, Daniel S

PY - 2010/4/30

Y1 - 2010/4/30

N2 - 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.

AB - 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.

KW - Animals

KW - Chickens/genetics

KW - Chromosome Mapping

KW - Chromosomes/genetics

KW - Computational Biology

KW - Conserved Sequence

KW - DNA Transposable Elements

KW - DNA, Complementary

KW - Embryo, Nonmammalian/metabolism

KW - Evolution, Molecular

KW - Expressed Sequence Tags

KW - Gene Duplication

KW - Genes

KW - Genome

KW - Humans

KW - Phylogeny

KW - Sequence Analysis, DNA

KW - Synteny

KW - Vertebrates/genetics

KW - Xenopus/embryology

KW - Xenopus Proteins/genetics

U2 - 10.1126/science.1183670

DO - 10.1126/science.1183670

M3 - Article

C2 - 20431018

SN - 0036-8075

VL - 328

SP - 633

EP - 636

JO - Science

JF - Science

IS - 5978

ER -

The genome of the Western clawed frog Xenopus tropicalis

Abstract

Keywords

UN SDGs

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