Nature Communications (Jan 2024)
Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs
- Jessen V. Bredeson,
- Austin B. Mudd,
- Sofia Medina-Ruiz,
- Therese Mitros,
- Owen Kabnick Smith,
- Kelly E. Miller,
- Jessica B. Lyons,
- Sanjit S. Batra,
- Joseph Park,
- Kodiak C. Berkoff,
- Christopher Plott,
- Jane Grimwood,
- Jeremy Schmutz,
- Guadalupe Aguirre-Figueroa,
- Mustafa K. Khokha,
- Maura Lane,
- Isabelle Philipp,
- Mara Laslo,
- James Hanken,
- Gwenneg Kerdivel,
- Nicolas Buisine,
- Laurent M. Sachs,
- Daniel R. Buchholz,
- Taejoon Kwon,
- Heidi Smith-Parker,
- Marcos Gridi-Papp,
- Michael J. Ryan,
- Robert D. Denton,
- John H. Malone,
- John B. Wallingford,
- Aaron F. Straight,
- Rebecca Heald,
- Dirk Hockemeyer,
- Richard M. Harland,
- Daniel S. Rokhsar
Affiliations
- Jessen V. Bredeson
- Department of Molecular and Cell Biology, Weill Hall, University of California
- Austin B. Mudd
- Department of Molecular and Cell Biology, Weill Hall, University of California
- Sofia Medina-Ruiz
- Department of Molecular and Cell Biology, Weill Hall, University of California
- Therese Mitros
- Department of Molecular and Cell Biology, Weill Hall, University of California
- Owen Kabnick Smith
- Department of Biochemistry, Stanford University School of Medicine
- Kelly E. Miller
- Department of Molecular and Cell Biology, Weill Hall, University of California
- Jessica B. Lyons
- Department of Molecular and Cell Biology, Weill Hall, University of California
- Sanjit S. Batra
- Computer Science Division, University of California Berkeley
- Joseph Park
- Department of Molecular and Cell Biology, Weill Hall, University of California
- Kodiak C. Berkoff
- Department of Molecular and Cell Biology, Weill Hall, University of California
- Christopher Plott
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology
- Jane Grimwood
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology
- Jeremy Schmutz
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology
- Guadalupe Aguirre-Figueroa
- Department of Biochemistry, Stanford University School of Medicine
- Mustafa K. Khokha
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine
- Maura Lane
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine
- Isabelle Philipp
- Department of Molecular and Cell Biology, Weill Hall, University of California
- Mara Laslo
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University
- James Hanken
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University
- Gwenneg Kerdivel
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d’Histoire Naturelle
- Nicolas Buisine
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d’Histoire Naturelle
- Laurent M. Sachs
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d’Histoire Naturelle
- Daniel R. Buchholz
- Department of Biological Sciences, University of Cincinnati
- Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology
- Heidi Smith-Parker
- Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas
- Marcos Gridi-Papp
- Department of Biological Sciences, University of the Pacific
- Michael J. Ryan
- Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas
- Robert D. Denton
- Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut
- John H. Malone
- Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut
- John B. Wallingford
- Department of Molecular Biosciences, Patterson Labs, 2401 Speedway, The University of Texas at Austin
- Aaron F. Straight
- Department of Biochemistry, Stanford University School of Medicine
- Rebecca Heald
- Department of Molecular and Cell Biology, Weill Hall, University of California
- Dirk Hockemeyer
- Department of Molecular and Cell Biology, Weill Hall, University of California
- Richard M. Harland
- Department of Molecular and Cell Biology, Weill Hall, University of California
- Daniel S. Rokhsar
- Department of Molecular and Cell Biology, Weill Hall, University of California
- DOI
- https://doi.org/10.1038/s41467-023-43012-9
- Journal volume & issue
-
Vol. 15,
no. 1
pp. 1 – 18
Abstract
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.
