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

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.

doi:10.1016/j.ydbio.2019.03.015

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

Journal Article · 01 August 2019 · Developmental Biology

DOI: https://doi.org/10.1016/j.ydbio.2019.03.015 · OSTI ID:1547529

Mitros, Therese ^[1]; Lyons, Jessica B. ^[1]; Session, Adam M. ^[2]; Jenkins, Jerry ^[3]; Shu, Shengquiang ^[2]; Kwon, Taejoon ^[4]; Lane, Maura ^[5]; Ng, Connie ^[1]; Grammer, Timothy C. ^[1]; Khokha, Mustafa K. ^[5]; Grimwood, Jane ^[3]; Schmutz, Jeremy ^[3]; Harland, Richard M. ^[1]; Rokhsar, Daniel S. ^[6]

Univ. of California, Berkeley, CA (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Inst. of Biotechnology, Huntsville, AL (United States)
Ulsan National Inst. of Science and Technology, Ulsan (Korea)
Yale Univ., New Haven, CT (United States). School of Medicine
Univ. of California, Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Okinawa Inst. of Science and Technology Graduate Univ., Onna, Okinawa (Japan)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); National Institutes of Health (NIH); National Research Foundation of Korea (NRF)

Grant/Contract Number:: AC02-05CH11231; S10RR029668; S10RR027303; GM66684; HD08070

OSTI ID:: 1547529

Alternate ID(s):: OSTI ID: 1615281

Journal Information:: Developmental Biology, Vol. 452, Issue 1; ISSN 0012-1606

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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