Consequences of polyploidy and divergence as revealed by cytogenetic mapping of repetitive elements in African clawed frogs (Xenopus, Pipidae)

Abstract

Repetitive elements have multiple copies in a genome and have been identified in several amphibian genomes using whole genome sequencing, but few studies have used cytogenetic mapping to visualize these elements in this vertebrate group. Here we compared the numbers and positions of repetitive elements in diploid and tetraploid species of the genus Xenopus, specifically between the diploid Xenopus tropicalis and its close allotetraploid relative X. calcaratus (both from Silurana subgenus), and also in more phylogenetically distant allotetraploids from the amieti, muelleri, and laevis species groups (all from subgenus Xenopus). Results allowed us to qualitatively evaluate the relative roles of polyploidization and divergence in the evolution of repetitive elements because our focal species include allotetraploid species derived from two independent polyploidization events – one closely related to the diploid species and one that is more distant. We used fluorescence in situ hybridization (FISH) to map the U1 and U2 small nuclear RNA (snRNA), histone H3, and retroelement Rex3 repeat loci. Our results demonstrated that U1 and U2 snRNA loci were conserved in copy number and position in the Silurana genomes, with one copy of U1 and U2 snRNA in diploid genome and one copy in each subgenome of allotetraploid species in subgenus Silurana and the muelleri species group. However, snRNA content varied among allotetraploid species in the amieti and laevis species groups, with only one U1 and U2 snRNA copy present in the entire allotetraploid genome of three species. Probes interrogating repetitive H3 and Rex3 loci were present on all chromosomes in diploid and allotetraploid species in subgenus Silurana, and in the muelleri species group. In the amieti and laevis species groups, H3 and Rex3 repeats were present on about half of all chromosomes. Overall, the results indicated that variation in the position and copy number of repetitive elements increases with phylogenetic distance, with high conservation in diploid and tetraploid Silurana species but more variation between Xenopus subgenera and among species groups in the subgenus Xenopus. In general and as expected, the effect of allotetraploidization was to increase the copy number of repetitive elements relative to diploid species, with the exception of the amieti and laevis species groups.