Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs

Authors

• Jessen V. Bredeson, University of California, Berkeley
• Austin B. Mudd, University of California, Berkeley
• Sofia Medina-Ruiz, University of California, Berkeley
• Therese Mitros, University of California, Berkeley
• Owen Kabnick Smith, Stanford University School of Medicine
• Kelly E. Miller, University of California, Berkeley
• Jessica B. Lyons, University of California, Berkeley
• Sanjit S. Batra, University of California, Berkeley
• Joseph Park, University of California, Berkeley
• Kodiak C. Berkoff, University of California, Berkeley
• Christopher Plott, HudsonAlpha Institute for Biotechnology
• Jane Grimwood, HudsonAlpha Institute for Biotechnology
• Jeremy Schmutz, HudsonAlpha Institute for Biotechnology
• Guadalupe Aguirre-Figueroa, Stanford University School of Medicine
• Mustafa K. Khokha, Yale School of Medicine
• Maura Lane, Yale School of Medicine
• Isabelle Philipp, University of California, Berkeley
• Mara Laslo, Harvard University
• James Hanken, Harvard University
• Gwenneg Kerdivel, Museum National d'Histoire Naturelle
• Nicolas Buisine, Museum National d'Histoire Naturelle

Document Type

Article

Publication Title

Nature Communications

Department

Biological Sciences

ISSN

20411723

Volume

15

Issue

1

DOI

10.1038/s41467-023-43012-9

First Page

1

Last Page

18

Publication Date

1-17-2024

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.

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Recommended Citation

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; and Buisine, Nicolas, "Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs" (2024). Pacific Faculty Work. 5.
https://scholarlycommons.pacific.edu/all-faculty/5