Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs

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.

Genome Assembly of the Dyeing Poison Frog Provides Insights into the Dynamics of Transposable Element and Genome-Size Evolution

“…Our analysis of synteny between these genomes suggests that the evolution of intrachromosomal rearrangements occurs much more rapidly than the evolution of chromosome structure, despite 2-fold differences in genome size. Recent work comparing eight distantly related anurans supports the idea that the evolution of genome size greatly outpaces chromosomal changes ( Bredeson et al 2024 ).…”

Karyotype Diversification and Chromosome Rearrangements in Squamate Reptiles

“…Karyotype stasis has been defined as the invariability in ploidy, chromosome number, general morphology and genome organization during phylogenetic diversification [ 59 ]. Comparable examples of karyological evolutionary stability have been reported in plants and several clades of the main vertebrate evolutionary lineages, including fish, birds and amphibians (see, e.g., [ 59 , 90 , 91 ]).…”

DNA Damage, Genome Stability and Adaptation: a Question of Chance or Necessity?

“…Mammals first evolved 225 Mya, but experienced a rapid adaptive radiation 65,8 Mya among placentals, much later than the anuran radiation [64]. Hence, salamanders are evolving more slowly than frogs, which are evolving more slowly than mammals [65,66] The question emerges from these and other observations: what are the submicroscopic factors that might explain the correlations between SR and KD and the manifest differences in SR and species evenness in the respective phylogenetic trees-assuming that those cellular and presumably nuclear factors and mechanisms are genuinely associated with the correlations and their respective differences? If that assumption holds true, to what extent then would those yet unidentified factors contribute to-or contrast with-the prevailing view that most if not all speciation and adaptive radiations are attributable to ecological speciation alone instead of to NARs resulting from DNA damage, mutation and diversification?…”