Divergent subgenome evolution in the allotetraploid frog Xenopus calcaratus

Allopolyploid genomes are divided into compartments called subgenomesthat are derived from lower ploidy ancestors. In African clawed frogsof the subgenus Xenopus (genus Xenopus), allotetraploid species havetwo subgenomes (L and S) with morphologically distinct homoeol-ogous chromosomes. In allotetraploid species of the sister subgenusSilurana, independently evolved subgenomes also exist, but their cytogenetics have not been investigated in detail. We used an allotetraploid species in Silurana—Xenopus calcaratus—to explore evolutionary dynamics of chromosome morphology and rearrangements. We find that the subgenomes of X. calcaratus have distinctive characteristics, with a more conserved a-subgenome resembling the closelyrelated genome of the diploid species X. tropicalis, and a more rapidlyevolving b-subgenome having more pronounced changes in chromosome structure, including diverged heterochromatic blocks, repetitivesequences, and deletion of a nucleolar secondary constriction. Basedon these cytogenetic differences, we propose a chromosome nomenclature for X. calcaratus that may apply to other allotetraploids insubgenus Silurana, depending on as yet unresolved details of theirevolutionary origins. These findings highlight the potential for large-scale asymmetry in subgenome evolution following allopolyploidization.