Reconstructing 50 million years of Xenopus borealis evolution: three temporal strata of DNA rearrangements and persistent sex chromosome homomorphism

Genomic rearrangements are fundamental drivers of biodiversity, yet dynamics of structural evolution following polyploidization remain poorly understood. Genus Xenopus provides a valuable tool to study these phenomena. Utilizing the diploid X. tropicalis as a reference, we employed cytogenetic and genomic mapping to track the structural evolution of the allotetraploids X. borealis and X. laevis across a 50-million-year timeline. Based on chromosome morphometrics and C-banding patterns, we characterized the X. borealis pseudotetraploid karyotype (2n = 4x = 36), localizing the nucleolus organizer region (NOR) to chromosome 5L, U1 and U2 small nuclear DNAs to 1S and 8L, and 5S rDNA to nearly all chromosomes. Our analysis revealed 17 genomic rearrangements distributed within three temporal strata: ancestral (50-35 Mya), intermediate (35-15 Mya), and recent (< 15 Mya). Although we categorized chromosome 9/10 fusion as an ancestral rearrangement, the 2/9 translocation previously identified in X. mellotropicalis was absent in both studied allotetraploids. Furthermore, we tested for sex-specific structural polymorphism on the X. borealis W chromosome. Despite a large region of recombination suppression between the W and Z, no inversions were detected, indicating persistent sex chromosome homomorphism. Results are consistent with the expectation that tandem repeats such as NORs follow an asymmetric trajectory driven by a jumping mechanism and biased deletion, whereas small nuclear DNA loci are governed by copy number reduction-expansion dynamics. These findings indicate that structural rearrangements in Xenopus were not limited to punctuated bursts immediately following whole-genome duplication; rather, they accumulated over a prolonged evolutionary history, affecting the entire polyploid complement.