Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs

作者：Jessen V. Bredeson, Austin B. Mudd, Sofía Medina-Ruiz, Therese Mitros, Owen K. Smith, Kelly E. Miller, Jessica B. Lyons, Sanjit Singh Batra, Joseph Park, Kodiak C. Berkoff, Christopher B. Plott, Jane Grimwood, Jeremy Schmutz, Guadalupe Aguirre-Figueroa, Mustafa Kezar 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 Daniel Denton, John H. Malone, John B. Wallingford, Aaron F. Straight, Rebecca Heald, Dirk F. Hockemeyer, Richard M. Harland, Daniel S. Rokhsar · 发表于：Nature Communications · 年份：2024 · DOI：10.1038/s41467-023-43012-9 · 被引用次数：44 · 研究领域：Chromosomal and Genetic Variations、Genomics and Phylogenetic Studies、Plant Virus Research Studies

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.