A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis
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.
- Authors:
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); National Institutes of Health (NIH); National Research Foundation of Korea (NRF)
- OSTI Identifier:
- 1547529
- Alternate Identifier(s):
- OSTI ID: 1615281
- Grant/Contract Number:
- AC02-05CH11231; S10RR029668; S10RR027303; GM66684; HD08070
- Resource Type:
- Published Article
- Journal Name:
- Developmental Biology
- Additional Journal Information:
- Journal Name: Developmental Biology Journal Volume: 452 Journal Issue: 1; Journal ID: ISSN 0012-1606
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Genome assembly; Genetic mapping; Comparative genomics; Pigmentation; Sex determination; Gene expression analysis
Citation Formats
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., and Rokhsar, Daniel S.. A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis. United States: N. p., 2019.
Web. doi:10.1016/j.ydbio.2019.03.015.
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.. A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis. United States. https://doi.org/10.1016/j.ydbio.2019.03.015
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., and Rokhsar, Daniel S.. Thu .
"A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis". United States. https://doi.org/10.1016/j.ydbio.2019.03.015.
@article{osti_1547529,
title = {A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis},
author = {Mitros, Therese and Lyons, Jessica B. and Session, Adam M. and Jenkins, Jerry and Shu, Shengquiang and Kwon, Taejoon and Lane, Maura and Ng, Connie and Grammer, Timothy C. and Khokha, Mustafa K. and Grimwood, Jane and Schmutz, Jeremy and Harland, Richard M. and Rokhsar, Daniel S.},
abstractNote = {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.},
doi = {10.1016/j.ydbio.2019.03.015},
journal = {Developmental Biology},
number = 1,
volume = 452,
place = {United States},
year = {2019},
month = {8}
}
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https://doi.org/10.1016/j.ydbio.2019.03.015
https://doi.org/10.1016/j.ydbio.2019.03.015
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Cited by: 25 works
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Figures / Tables:
Fig. 1: X. tropicalis genetic map. Ten linkage groups were characterized by the analysis of markers in 2219 windows of the X. tropicalis genome assembly. Composite markers were formed for each window. See Supplementary File 2 for a complete list of markers.
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