A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis

The Western clawed frog Xenopus tropicalis is a diploid model system for both frog genetics and developmental biology, complementary to the paleotetraploid X. laevis. Here we report a chromosome-scale assembly of the X. tropicalis genome, improving the previously published draft genome assembly thro...

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Published inDevelopmental biology Vol. 452; no. 1; pp. 8 - 20
Main Authors Mitros, Therese, Lyons, Jessica B., Session, Adam M., Jenkins, Jerry, Shu, Shengquiang, Kwon, Taejoon, Lane, Maura, Ng, Connie, Grammer, Timothy C., Khokha, Mustafa K., Grimwood, Jane, Schmutz, Jeremy, Harland, Richard M., Rokhsar, Daniel S.
Format Journal Article
LanguageEnglish
Published United States Elsevier Inc 01.08.2019
Elsevier
Subjects
algorithms
Animals
BASIC BIOLOGICAL SCIENCES
Chromosome Mapping
Chromosomes - genetics
Comparative genomics
diploidy
frogs
gene expression
Gene expression analysis
Gene Expression Profiling
gene order
genes
Genetic mapping
Genome
Genome assembly
Humans
loci
Molecular Sequence Annotation
mutants
Pigmentation
Sex determination
tissues
Xenopus
Xenopus laevis
Xenopus tropicalis
Genetic mapping
Comparative genomics
Gene expression analysis
Genome assembly
Sex determination
Pigmentation
Online AccessGet full text
ISSN0012-1606
1095-564X
1095-564X
DOI10.1016/j.ydbio.2019.03.015

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Abstract The Western clawed frog Xenopus tropicalis is a diploid model system for both frog genetics and developmental biology, complementary to the paleotetraploid X. laevis. Here we report a chromosome-scale assembly of the X. tropicalis genome, improving the previously published draft genome assembly through the use of new assembly algorithms, additional sequence data, and the addition of a dense genetic map. The improved genome enables the mapping of specific traits (e.g., the sex locus or Mendelian mutants) and the characterization of chromosome-scale synteny with other tetrapods. We also report an improved annotation of the genome that integrates deep transcriptome sequence from diverse tissues and stages. The exon-intron structures of these genes are highly conserved relative to both X. laevis and human, as are chromosomal linkages (“synteny”) and local gene order. A network analysis of developmental gene expression will aid future studies. •X. tropicalis genome assembly v9 is chromosome scale and facilitates new analyses.•The enhanced proteome is more complete compared to human.•This proteome enables novel findings when compared with the related frog X. laevis.•Genetic map was used for genome assembly, and mapping sex and a pigmentation mutant.
AbstractList The Western clawed frog Xenopus tropicalis is a diploid model system for both frog genetics and developmental biology, complementary to the paleotetraploid X. laevis. Here we report a chromosome-scale assembly of the X. tropicalis genome, improving the previously published draft genome assembly through the use of new assembly algorithms, additional sequence data, and the addition of a dense genetic map. The improved genome enables the mapping of specific traits (e.g., the sex locus or Mendelian mutants) and the characterization of chromosome-scale synteny with other tetrapods. We also report an improved annotation of the genome that integrates deep transcriptome sequence from diverse tissues and stages. The exon-intron structures of these genes are highly conserved relative to both X. laevis and human, as are chromosomal linkages ("synteny") and local gene order. A network analysis of developmental gene expression will aid future studies.The Western clawed frog Xenopus tropicalis is a diploid model system for both frog genetics and developmental biology, complementary to the paleotetraploid X. laevis. Here we report a chromosome-scale assembly of the X. tropicalis genome, improving the previously published draft genome assembly through the use of new assembly algorithms, additional sequence data, and the addition of a dense genetic map. The improved genome enables the mapping of specific traits (e.g., the sex locus or Mendelian mutants) and the characterization of chromosome-scale synteny with other tetrapods. We also report an improved annotation of the genome that integrates deep transcriptome sequence from diverse tissues and stages. The exon-intron structures of these genes are highly conserved relative to both X. laevis and human, as are chromosomal linkages ("synteny") and local gene order. A network analysis of developmental gene expression will aid future studies.
The Western clawed frog Xenopus tropicalis is a diploid model system for both frog genetics and developmental biology, complementary to the paleotetraploid X. laevis. Here we report a chromosome-scale assembly of the X. tropicalis genome, improving the previously published draft genome assembly through the use of new assembly algorithms, additional sequence data, and the addition of a dense genetic map. The improved genome enables the mapping of specific traits (e.g., the sex locus or Mendelian mutants) and the characterization of chromosome-scale synteny with other tetrapods. We also report an improved annotation of the genome that integrates deep transcriptome sequence from diverse tissues and stages. The exon-intron structures of these genes are highly conserved relative to both X. laevis and human, as are chromosomal linkages (“synteny”) and local gene order. A network analysis of developmental gene expression will aid future studies. •X. tropicalis genome assembly v9 is chromosome scale and facilitates new analyses.•The enhanced proteome is more complete compared to human.•This proteome enables novel findings when compared with the related frog X. laevis.•Genetic map was used for genome assembly, and mapping sex and a pigmentation mutant.
The Western clawed frog Xenopus tropicalis is a diploid model system for both frog genetics and developmental biology, complementary to the paleotetraploid X. laevis. Here we report a chromosome-scale assembly of the X. tropicalis genome, improving the previously published draft genome assembly through the use of new assembly algorithms, additional sequence data, and the addition of a dense genetic map. The improved genome enables the mapping of specific traits (e.g., the sex locus or Mendelian mutants) and the characterization of chromosome-scale synteny with other tetrapods. We also report an improved annotation of the genome that integrates deep transcriptome sequence from diverse tissues and stages. The exon-intron structures of these genes are highly conserved relative to both X. laevis and human, as are chromosomal linkages ("synteny") and local gene order. A network analysis of developmental gene expression will aid future studies.
The Western clawed frog Xenopus tropicalis is a diploid model system for both frog genetics and developmental biology, complementary to the paleotetraploid X. laevis. Here we report a chromosome-scale assembly of the X. tropicalis genome, improving the previously published draft genome assembly through the use of new assembly algorithms, additional sequence data, and the addition of a dense genetic map. The improved genome enables the mapping of specific traits (e.g., the sex locus or Mendelian mutants) and the characterization of chromosome-scale synteny with other tetrapods. We also report an improved annotation of the genome that integrates deep transcriptome sequence from diverse tissues and stages. The exon-intron structures of these genes are highly conserved relative to both X. laevis and human, as are chromosomal linkages (“synteny”) and local gene order. A network analysis of developmental gene expression will aid future studies.
Author Grammer, Timothy C.
Schmutz, Jeremy
Jenkins, Jerry
Rokhsar, Daniel S.
Grimwood, Jane
Mitros, Therese
Harland, Richard M.
Khokha, Mustafa K.
Session, Adam M.
Shu, Shengquiang
Kwon, Taejoon
Ng, Connie
Lyons, Jessica B.
Lane, Maura
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  givenname: Shengquiang
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  email: maura.lane@yale.edu
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  organization: University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA
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Issue 1
Keywords Genetic mapping
Comparative genomics
Gene expression analysis
Genome assembly
Sex determination
Pigmentation
Language English
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Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.
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Snippet The Western clawed frog Xenopus tropicalis is a diploid model system for both frog genetics and developmental biology, complementary to the paleotetraploid...
The Western clawed frog Xenopus tropicalis is a diploid model system for both frog genetics and developmental biology, complementary to the paleotetraploid X....
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SubjectTerms algorithms
Animals
BASIC BIOLOGICAL SCIENCES
Chromosome Mapping
Chromosomes - genetics
Comparative genomics
diploidy
frogs
gene expression
Gene expression analysis
Gene Expression Profiling
gene order
genes
Genetic mapping
Genome
Genome assembly
Humans
loci
Molecular Sequence Annotation
mutants
Pigmentation
Sex determination
tissues
Xenopus
Xenopus laevis
Xenopus tropicalis
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Title A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis
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