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Eur J Wildl Res
2023 Jan 01;694:81. doi: 10.1007/s10344-023-01709-8.
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Consequences of polyploidy and divergence as revealed by cytogenetic mapping of tandem repeats in African clawed frogs (Xenopus, Pipidae).
Fornaini NR
,
Bergelová B
,
Gvoždík V
,
Černohorská H
,
Krylov V
,
Kubíčková S
,
Fokam EB
,
Badjedjea G
,
Evans BJ
,
Knytl M
.
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Repetitive elements 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 used fluorescence in situ hybridization and genomic data to map the U1 and U2 small nuclear RNAs and histone H3 in six species of African clawed frog (genus Xenopus), including, from subgenus Silurana, the diploid Xenopus tropicalis and its close allotetraploid relative X. calcaratus and, from subgenus Xenopus, the allotetraploid species X. pygmaeus, X. allofraseri, X. laevis, and X. muelleri. 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 that is relatively young that gave rise to X. calcaratus and another that is older that gave rise to the other (older) allotetraploids. Our results demonstrated conserved loci number and position of signals in the species from subgenus Silurana; allotetraploid X. calcaratus has twice as many signals as diploid X. tropicalis. However, the content of repeats varied among the other allotetraploid species. We detected almost same number of signals in X. muelleri as in X. calcaratus and same number of signals in X. pygmaeus, X. allofraseri, X. laevis as in the diploid X. tropicalis. Overall, these results are consistent with the proposal that allopolyploidization duplicated these tandem repeats and that variation in their copy number was accumulated over time through reduction and expansion in a subset of the older allopolyploids.
Fig. 1
Inferred phylogenetic relationships and approximate divergence times among our focal taxa based on Evans et al. (2015), Session et al. (2016), and Feng et al. (2017). Allotetraploidization (depicted as reticulating lineages) occurred independently in each subgenus; inferred diploid lineages with no known extant diploid descendants are indicated with daggers. Time scale is in millions of years ago; chromosome numbers are shown in parentheses
Fig. 2
Double-color FISH with U1 and U2 snDNA probes. The U1 probe (red) reveals one clear signal (= a pair of homologous chromosomes) in a X. tropicalis, c X. pygmaeus, d X. allofraseri, and e X. laevis, while the same FISH shows two signals, each within homoeologous chromosomes in b X. calcaratus and f X. muelleri. The U2 (green) probe shows one signal in a X. tropicalis, c X. pygmaeus, d X. allofraseri, and e X. laevis, while the U2 probe shows two signals, each of them within homoeologous chromosomes in b X. calcaratus and f X. muelleri. Green and red arrows correspond to the U2 and U1 repeat loci, respectively. Painting probes were used for identification of chromosomes 1 (green) and 8 (red) in a X. tropicalis. Chromosomes were counterstained with DAPI in blue/gray. Scale bars represent 10 µM
FIg. 3
Sequential FISH in X. calcaratus chromosomes. Cross-species painting FISH experiments with the whole chromosome painting probes from X. tropicalis a chromosome 1 (XTR 1) and b XTR 8 highlight chromosome-bearing U1 and U2 snRNA loci, respectively. c snDNA FISH illustrates that the U1 locus (in red) is localized on X. calcaratus chromosomes 1 (XCA 1a and 1b) and the U2 locus (in green) on XCA 8a and 8b. a and b are shown in the red channel, c is merged in the red-green-blue (RGB) channels. c chromosomes were counterstained with DAPI in gray. Scale bars represent 10 µM
Fig. 4
Sequential FISH in X. laevis chromosomes. Cross-species painting FISH experiments with whole chromosome painting probes from a XTR 1 (in red) and XTR 8 (in green) illustrate that b the U1 locus (in red) is localized on X. laevis chromosomes 1S (XLA 1S), and the U2 locus (in green) on XLA 8L. Both a and b are merged in the RGB channels. Chromosomes were counterstained with DAPI in blue. Scale bars represent 10 µM
Fig. 5
FISH with histone H3 probe. The probe (green) shows multiple signals in a X. tropicalis, b X. calcaratus, c X. pygmaeus, d X. allofraseri, e X. laevis, and f X. muelleri. Chromosomes were counterstained with DAPI in blue/gray. Scale bars represent 10 µM
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