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Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs.
Bredeson, Jessen V; Mudd, Austin B; Medina-Ruiz, Sofia; Mitros, Therese; Smith, Owen Kabnick; Miller, Kelly E; Lyons, Jessica B; Batra, Sanjit S; Park, Joseph; Berkoff, Kodiak C; Plott, Christopher; Grimwood, Jane; Schmutz, Jeremy; Aguirre-Figueroa, Guadalupe; Khokha, Mustafa K; Lane, Maura; Philipp, Isabelle; Laslo, Mara; Hanken, James; Kerdivel, Gwenneg; Buisine, Nicolas; Sachs, Laurent M; Buchholz, Daniel R; Kwon, Taejoon; Smith-Parker, Heidi; Gridi-Papp, Marcos; Ryan, Michael J; Denton, Robert D; Malone, John H; Wallingford, John B; Straight, Aaron F; Heald, Rebecca; Hockemeyer, Dirk; Harland, Richard M; Rokhsar, Daniel S.
Afiliação
  • Bredeson JV; Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA.
  • Mudd AB; DOE-Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
  • Medina-Ruiz S; Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA.
  • Mitros T; Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA.
  • Smith OK; Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA.
  • Miller KE; Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA.
  • Lyons JB; Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA.
  • Batra SS; Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA.
  • Park J; Computer Science Division, University of California Berkeley, 2626 Hearst Avenue, Berkeley, CA, 94720, USA.
  • Berkoff KC; Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA.
  • Plott C; Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA.
  • Grimwood J; HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.
  • Schmutz J; HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.
  • Aguirre-Figueroa G; HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.
  • Khokha MK; Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA.
  • Lane M; Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA.
  • Philipp I; Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA.
  • Laslo M; Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA.
  • Hanken J; Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA.
  • Kerdivel G; Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA.
  • Buisine N; Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France.
  • Sachs LM; Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France.
  • Buchholz DR; Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France.
  • Kwon T; Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA.
  • Smith-Parker H; Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
  • Gridi-Papp M; Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea.
  • Ryan MJ; Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas, Austin, TX, 78712, USA.
  • Denton RD; Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA.
  • Malone JH; Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas, Austin, TX, 78712, USA.
  • Wallingford JB; Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut, 181 Auditorium Road, Unit 3197, Storrs, CT, 06269, USA.
  • Straight AF; Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut, 181 Auditorium Road, Unit 3197, Storrs, CT, 06269, USA.
  • Heald R; Department of Molecular Biosciences, Patterson Labs, 2401 Speedway, The University of Texas at Austin, Austin, TX, 78712, USA.
  • Hockemeyer D; Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA.
  • Harland RM; Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA.
  • Rokhsar DS; Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA.
Nat Commun ; 15(1): 579, 2024 Jan 17.
Article em En | MEDLINE | ID: mdl-38233380
ABSTRACT
Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus, and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., arm-preserving) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding surrounded by pericentromeric LINE/L1 elements. This work explores the structure of chromosomes across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible associations of centromeric chromatin and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Cromatina / Evolução Molecular Limite: Animals Idioma: En Ano de publicação: 2024 Tipo de documento: Article
Texto completo
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XML
PubMed Links
Buscar no Google

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Cromatina / Evolução Molecular Limite: Animals Idioma: En Ano de publicação: 2024 Tipo de documento: Article