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Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs

Authors :
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
Source :
Nature Communications, Vol 15, Iss 1, Pp 1-18 (2024)
Publication Year :
2024
Publisher :
Nature Portfolio, 2024.

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.

Subjects

Subjects :
Science

Details

Language :
English
ISSN :
20411723
Volume :
15
Issue :
1
Database :
Directory of Open Access Journals
Journal :
Nature Communications
Publication Type :
Academic Journal
Accession number :
edsdoj.9f0d24ceb42e45d88c1f3bffc99c544b
Document Type :
article
Full Text :
https://doi.org/10.1038/s41467-023-43012-9