Abstract
Whole genome duplication (WGD) generates new species and genomic redundancy. In African clawed frogs of the genus Xenopus, this phenomenon has been especially important in that (i) all but one extant species are polyploid and (ii) whole genome sequences of some species provide an evidence for genomic rearrangements prior to or after WGD. Within Xenopus in the subgenus Silurana, at least one allotetraploidization event gave rise to three extant tetraploid (2n = 4x = 40) species–Xenopus mellotropicalis, X. epitropicalis, and X. calcaratus–but it is not yet clear the degree to which these tetraploid genomes experienced rearrangements prior to or after allotetraploidization. To explore genome evolution during diversification of these species, we performed cytogenetic analyses of X. mellotropicalis, including assessment of the localization of nucleolar organizer region, chromosome banding, and determination of the p/q arm ratios for each chromosome pair. We compared these data to a previously characterized karyotype of X. epitropicalis. Morphometric, C-banding and Zoo-FISH data support a previously hypothesized common allotetraploid predecessor of these species. Zoo-FISH with whole chromosome painting (WCP) probes derived from the closely related diploid species X. tropicalis confirmed the existence of ten chromosomal quartets in X. mellotropicalis somatic cells, as expected by its ploidy level and tetraploid ancestry. The p/q arm ratio of chromosome 2a was found to be substantially different between X. mellotropicalis (0.81) and X. epitropicalis (0.67), but no substantial difference between these two species was detected in this ratio for the homoeologous chromosome pair 2b, or for other chromosome pairs. Additionally, we identified variation between these two species in the locations of a heterochromatic block on chromosome pair 2a. These results are consistent with a dynamic history of genomic rearrangements before and/or after genome duplication, a surprising finding given the otherwise relatively conserved genomic structure of most frogs.
Highlights
Whole genome duplication (WGD) is an important evolutionary phenomenon that occurs in animals, plants, and several other organisms, and can be associated with chromosomal rearrangements [1,2,3,4]
In addition to a strongly stained heterochromatic block on XME 2a, C-banding in X. mellotropicalis exhibited a faint signal in portions of stained regions on chromosomes 1b, 2b, 6b, 7b, 8a and 10a
C-positive heterochromatic block patterns were consistent within particular homologous pairs of X. tropicalis and X. mellotropicalis, but exhibited some differences between homoeologous pairs of X. mellotropicalis
Summary
Whole genome duplication (WGD) is an important evolutionary phenomenon that occurs in animals, plants, and several other organisms, and can be associated with chromosomal rearrangements [1,2,3,4]. WGD takes place either by allopolyploidization, which is associated with interspecies hybridization, or by autopolyploidization, in which WGD occurs within a single ancestral species [5]. The African clawed frog genus Xenopus [9] includes subgenera Silurana [10] and Xenopus, and contains species with several ploidy levels (diploid, tetraploid, octoploid, or dodecaploid) [11,12,13,14,15]. The genus Xenopus includes 29 species, 28 of which are polyploid, and whose evolutionary relationships bifurcate due to speciation without polyploidization and reticulate due to speciation by allopolyploidization [17]. Octoploid and dodecaploid species in the subgenus Xenopus arose via at least six independent polyploidization events [17]
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