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Open Access Publications from the University of California

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

  • Author(s): 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
  • et al.
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.

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