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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.
Afiliação
  • Mitros T; University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA. Electronic address: tmitros@berkeley.edu.
  • Lyons JB; University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA. Electronic address: jblyons@berkeley.edu.
  • Session AM; Joint Genome Institute, 2800 Mitchell Dr # 100, Walnut Creek, CA 94598, USA. Electronic address: amsession@lbl.gov.
  • Jenkins J; 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.
  • Shu S; Joint Genome Institute, 2800 Mitchell Dr # 100, Walnut Creek, CA 94598, USA. Electronic address: sqshu@lbl.gov.
  • Kwon T; 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.
  • Lane M; 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.
  • Ng C; University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA. Electronic address: connie.ng@berkeley.edu.
  • Grammer TC; University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA. Electronic address: timgrammer@gmail.com.
  • Khokha MK; 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.
  • Grimwood J; 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.
  • Schmutz J; 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.
  • Harland RM; University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA. Electronic address: harland@berkeley.edu.
  • Rokhsar DS; 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, O
Dev Biol ; 452(1): 8-20, 2019 08 01.
Article em En | MEDLINE | ID: mdl-30980799
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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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Mapeamento Cromossômico / Cromossomos / Genoma / Perfilação da Expressão Gênica / Anotação de Sequência Molecular Limite: Animals / Humans Idioma: En Revista: Dev Biol Ano de publicação: 2019 Tipo de documento: Article País de publicação: Estados Unidos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Mapeamento Cromossômico / Cromossomos / Genoma / Perfilação da Expressão Gênica / Anotação de Sequência Molecular Limite: Animals / Humans Idioma: En Revista: Dev Biol Ano de publicação: 2019 Tipo de documento: Article País de publicação: Estados Unidos