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

Therese Mitros; Jessica B Lyons; Adam M Session; Jerry Jenkins; Shengquiang Shu; Taejoon Kwon; Maura Lane; Connie Ng; Timothy C Grammer; Mustafa K Khokha; Jane Grimwood; Jeremy Schmutz; Richard M Harland; Daniel S Rokhsar

doi:10.1016/j.ydbio.2019.03.015

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

Dev Biol. 2019 Aug 1;452(1):8-20. doi: 10.1016/j.ydbio.2019.03.015. Epub 2019 Apr 10.

Authors

Affiliations

¹ University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA. Electronic address: tmitros@berkeley.edu.
² University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA. Electronic address: jblyons@berkeley.edu.
³ Joint Genome Institute, 2800 Mitchell Dr # 100, Walnut Creek, CA 94598, USA. Electronic address: amsession@lbl.gov.
⁴ Joint Genome Institute, 2800 Mitchell Dr # 100, Walnut Creek, CA 94598, USA; HudsonAlpha Institute of Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA. Electronic address: jjenkins@hudsonalpha.org.
⁵ Joint Genome Institute, 2800 Mitchell Dr # 100, Walnut Creek, CA 94598, USA. Electronic address: sqshu@lbl.gov.
⁶ Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea. Electronic address: tkwon@unist.ac.kr.
⁷ Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, FMP 410, 333 Cedar St./LCI 305, New Haven, CT 06520, USA. Electronic address: maura.lane@yale.edu.
⁸ University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA. Electronic address: connie.ng@berkeley.edu.
⁹ University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA. Electronic address: timgrammer@gmail.com.
¹⁰ Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, FMP 410, 333 Cedar St./LCI 305, New Haven, CT 06520, USA. Electronic address: mustafa.khokha@yale.edu.
¹¹ Joint Genome Institute, 2800 Mitchell Dr # 100, Walnut Creek, CA 94598, USA; HudsonAlpha Institute of Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA. Electronic address: jgrimwood@hudsonalpha.org.
¹² Joint Genome Institute, 2800 Mitchell Dr # 100, Walnut Creek, CA 94598, USA; HudsonAlpha Institute of Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA. Electronic address: jschmutz@hudsonalpha.org.
¹³ University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA. Electronic address: harland@berkeley.edu.
¹⁴ University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA; Joint Genome Institute, 2800 Mitchell Dr # 100, Walnut Creek, CA 94598, USA; Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 9040495, Japan. Electronic address: dsrokhsar@gmail.com.

PMID: 30980799
DOI: 10.1016/j.ydbio.2019.03.015

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.

Keywords: Comparative genomics; Gene expression analysis; Genetic mapping; Genome assembly; Pigmentation; Sex determination.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Chromosome Mapping*
Chromosomes / genetics*
Gene Expression Profiling*
Genome*
Humans
Molecular Sequence Annotation*
Xenopus

Abstract

Publication types

MeSH terms

Grants and funding