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Title: 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 Lab. (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. 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., & 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}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1016/j.ydbio.2019.03.015

Citation Metrics:
Cited by: 3 works
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