Bredeson JV , Mudd AB , Medina-Ruiz S , Mitros T , Smith OK , Miller KE , Lyons JB , Batra SS , Park J , Berkoff KC , Plott C , Grimwood J , Schmutz J , Aguirre-Figueroa G , Khokha MK , Lane M , Philipp I , Laslo M , Hanken J , Kerdivel G , Buisine N , Sachs LM , Buchholz DR , Kwon T , Smith-Parker H , Gridi-Papp M , Ryan MJ , Denton RD , Malone JH , Wallingford JB , Straight AF , Heald R , Hockemeyer D , Harland RM , Rokhsar DS .

R35 GM118183 NIGMS NIH HHS , R35 GM127069 NIGMS NIH HHS , T32 HG000047 NHGRI NIH HHS , R01 HD065705 NICHD NIH HHS , T32 GM113854 NIGMS NIH HHS , S10 OD018174 NIH HHS , R01 HD080708 NICHD NIH HHS , R01 HD102186 NICHD NIH HHS , S10 OD010786 NIH HHS , T32 GM007127 NIGMS NIH HHS , R01 HD085901 NICHD NIH HHS , R01 GM074728 NIGMS NIH HHS , R01 GM086321 NIGMS NIH HHS , R01 GM104853 NIGMS NIH HHS , R01 GM066684 NIGMS NIH HHS , UL1 TR001863 NCATS NIH HHS

	Fig. 1: Phylogenetic tree and gene ortholog alignment. The phylogenetic tree of the seven analyzed species, calculated from fourfold degenerate sites and divergence time confidence intervals, drawn with FigTree (commit 901211e, https://github.com/rambaut/figtree): Xenopus tropicalis, X. laevis, and Hymenochirus boettgeri (Pipoidea: Pipidae); Leptobrachium (Vibrissaphora) ailaonicum (Pelobatoidea: Megaphrynidae); Engystomops pustulosus (Neobatrachia [Hyloidea]: Leptodactylidae), Eleutherodactylus coqui (Neobatrachia [Hyloidea]: Euleutherodactylidae); and Pyxicephalus adspersus (Neobatrachia [Ranoidea]: Pyxicephalidae). The ancestral karyotype is labeled at each node on the tree. Black circles with white text refer to chromosome changes summarized in Table 1. The alignment plot was generated with JCVI using the 7292 described chromosome one-to-one gene orthologs from OrthoVenn2, followed by manual filtering of single stray orthologs. The Hi-C-derived centromere position is represented with a black circle on each chromosome. Ancestral chromosomes (A to M) are labeled at the top of the alignment based on the corresponding region in P. adspersus. The alignments for each ancestral chromosome are colored uniquely, with those upstream and downstream of the X. tropicalis centromeric satellite repeat colored in dark and light shades of the ancestral chromosome color. Chromosomes labeled with asterisks are shown reverse complemented relative to their orientations in the genome assembly. Mya millions of years ago, n the haploid chromosome number. Source data are provided as a Source Data file.
	Fig. 2: Density of pericentromeric and subtelomeric repeats in Xenopus tropicalis. Pericentromeric (red) and subtelomeric (purple) regions were used to obtain enriched repeats, excluding chromosomes with short p-arms (chromosomes 3, 8, and 10). Pericentromeric repeats (yellow) correspond to selected subsets of non-LTR retrotransposons (CR1, L1, and Penelope), LTR retrotransposons (Ty3), and DNA transposons (PiggyBac and Harbinger). Subtelomere-enriched repeats (blue) correspond mainly to satellite repeats and LTR retrotransposons (Ty3, Ngaro). Densities of each repeat type plotted as kb/Mb. Chromosomes are centered by the position of centromeric tandem repeats (black dots). Rates of recombination (Rec. rate) in cM/Mb are shown as solid black lines. Tick marks indicate 10 Mb blocks (Supplementary Fig. 5). kb kilobases, Mb megabases, cM centiMorgans. Source data are provided as a Source Data file.
	Fig. 3: Subtelomeric repeats highlight regions of chromosome fusion. Examples of (a) conserved structure and pericentromere maintenance of H. boettgeri (Hbo), X. tropicalis (Xtr), and X. laevis (Xla) chromosomes; b a Robertsonian translocation in the lineage leading to E. coqui (Eco), shown compared with E. pustulosus (Epu) and X. tropicalis; and c an end-to-end fusion that occurred in the lineage giving rise to X. tropicalis and subsequent pericentromere loss, shown compared with L. ailaonicum (Lai) and P. adspersus (Pad). The analyzed species were visualized with a custom script, alignment_plots.py (v1.0, https://github.com/abmudd/Assembly). For each plot, the Hi-C inference-based centromeric regions are depicted with black stars, the X. tropicalis centromeric satellite repeat from tandem repeat analysis with a red star (on X. tropicalis chromosomes 7 and 1 (a, b), the stars overlap), the density of L1 repeats per chromosome with gold densities, and the runs of collinearity containing at least one kilobase of aligned sequence between the species with connecting black lines. kb kilobases, Mb megabases. Source data are provided as a Source Data file.
	Fig. 4: Organization of X. tropicalis chromosomes into Rabl-like configuration and distinct nuclear territories. a Hi-C contact matrices for chromosomes 1 and 2 (lower-left and upper-right gold boxes, respectively) showing features of the three-dimensional chromatin architecture within X. tropicalis blood cell nuclei. Blue pixels represent chromatin contacts between X–Y pairs of 500 kb genomic loci, with intensity proportional to contact frequency. Hi-C read pairs are mapped stringently (MQ ≥ 30) above the diagonal and permissively (MQ ≥ 0) below the diagonal. The characteristic A/B-compartment (“checkerboard”) and Rabl-like (“angel wing”) interarm contact patterns within each chromosome are evident. Above the diagonal, an increased frequency of interchromosomal chromatin contacts is observed between pericentromeres (connected by dotted lines) and between chromosome arms (Supplementary Tables 18, 19, and 21), suggesting a centromere-clustered organization of chromosomes in a Rabl-like configuration. Below the diagonal, high-intensity pixels near the ends of chromosomes not present above the diagonal suggest a telomere-proximal spatial bias in the distributions of similar genomic repeats. See Supplementary Fig. 1e for a plot showing all chromosomes. b Chromosome territories within the nucleus. Yellow, white, and blue colors indicate the normalized relative enrichment, parity, and depletion of chromatin contacts between non-homologous chromosomes (Supplementary Tables 21 and 22). For example, chromosome 1 exhibits higher relative contact frequencies with all chromosomes except chromosomes 7, 9, and 10, which are generally depleted of contacts except among themselves (MQ ≥ 30; χ2 (81, n = 24,987,749) = 3,049,787; Hochberg-corrected P < 4.46 × 10−308; Relative range: 0.82774–1.16834). Note, due to the inbred nature of the Nigerian strain, contacts could not be partitioned by haplotype, and so the results reported here represent chromosomal averages. c Schematic representation of chromosome territories from (b). The size of each chromosome number is approximately proportional to the number of enriched interactions. Darker and lighter colors indicate chromosomes nearer and more distant to the reader, respectively. Mb megabases, MQ mapping quality. Source data are provided as a Source Data file.
	Fig. 5: A/B-compartment structure and gene/repeat densities. a Correlation matrix of intra-chromosomal Hi-C contact densities between all pairs of nonoverlapping 250 kb loci on chromosome 1. Yellow and blue pixels indicate correlation and anti-correlation, respectively, and reveal which genomic loci occupy the same or different chromatin compartment. Black pixels indicate weak/no correlation. b The first principal component (PC) vector revealing the compartment structure along chromosome 1, obtained by singular value decomposition of the correlation matrix in panel a. Yellow (positive) and blue (negative) loadings indicate regions of chromosome 1 partitioned into A and B compartments, respectively. c Gene density (genes per megabase) distributions in A (yellow) vs. B (blue) compartments genome-wide and per chromosome. Sample sizes and significance statistics provided in Supplementary Table 20. d Repeat classes significantly enriched by density (repeats per megabase) in A (yellow) vs. B (blue) compartments. Sample sizes and significance statistics provided in Supplementary Table 20. Each boxplot summarizes the combined (A + B) density distribution (Y-axis) per class (X axis); lower and upper bounds of each box (black) delimit the first and third quartiles, respectively, and whiskers extend to 1.5 times the interquartile range, while the median per class is represented as a filled white circle. e The PC3 loadings (purple line) from the repeat density matrix inversely correlate with alternating A/B-compartment loadings (green) for chromosome 1. See Supplementary Fig. 5b for all chromosomes. Purple rectangles plotted on the X axis denote subtelomeric regions, the red rectangle spans the pericentromere, and the black point marks the median centromere-associated tandem repeat position. Mb megabases. Source data are provided as a Source Data file.
	Supplementary Fig. 1 Xenopus tropicalis genome assembly process and Hi-C contact map. (a) Round 1 of metassembly with quickmerge: de novo (D) and hybrid (H) contigs are used as both “donor” and “acceptor” sequences in a reciprocal merging strategy to produce two metassemblies, MHD and MDH, which are then corrected for misassemblies using Juicer and Juicebox Assembly Tools (JBAT) with manual curation. This results in two sets of corrected contigs, M’HD and M’DH. Round 2: the process is repeated with M’HD and M’DH to produce a final second-order metassembly, M’HD,DH. (b) The median depth of coverage (Y-axis) was calculated for each contig (blue dots) and plotted against its log10-transformed length (X-axis) to identify redundant sequences. The plot shows that contig sequences can be stratified into longer full-depth (y = 58×) and shorter half-depth (y = 29×) categories. (c) Black horizontal bars are regions of the genome well-supported by spanning PacBio read alignments (thin grey horizontal bars). The light grey region labeled “BREAK” lacks support by read data and represents a DBG2OLC assembly error likely introduced by incorporating a single PacBio polymerase read that was not successfully broken into individual subreads. Dark blue horizontal bars represent the aligned Sanger-based v9 assembly, while gold and light blue horizontal bars represent the raw Canu and Supernova contigs underlying the hybrid assembly. Note that both these sequences flank the BREAK region, meaning these contigs span the artefact and can be used to patch it. (d) GenomeScope model fit and genome-size estimate for X. tropicalis Nigerian F17 female. Observed k-mer frequency per depth-of-coverage bin as blue vertical lines; error model curve fit to k-mer frequencies resulting from sequencing errors in brown; model fit curve to k-mer frequencies generated from unique genomic sequence in yellow; combined unique and error model fit curve in solid black; vertical dashed lines represent one-, two-, three-, and four-copy sequence depth peaks, respectively. (e) Hi-C contact matrix from red blood nuclei at 500 kb resolution, balanced using the Knight-Ruiz algorithm, showing reads with a minimum mapping quality (MQ) ≥ 0 below the diagonal and reads with MQ ≥ 30 above the diagonal. Chromosomes (gold boxes) are shown in ascending numeric order along the X-axis, with p-arms oriented toward the lower left of the figure and q-arms toward the upper right. The intensity of blue pixels is proportional to chromatin contact frequencies between X-Y pairs of 500 kb genomic loci. Intra-chromosomal contacts exhibit the highest frequency of contacts between adjacent loci along the linear chromosome (along the diagonal). Above the diagonal, inter-chromosomal contacts are the strongest between centromeres (puncta), while below the diagonal the strongest contacts are observed between subtelomeric sequences. This contact density map was visualized with Juicebox1,2. kb, kilobases; Mb, megabases. Source data are provided as a Source Data file.
	Supplementary Fig. 2 Xenopus tropicalis GC landscape, tandem repeats, and recovered genes. (a) Long arrays of tandem repeats localize to subtelomeric portions of the genome. A total of 68.27 Mb (4.71%) of the X. tropicalis (Xtr) genome assembly was not covered by Sanger shotgun sequences. Of the regions lacking Sanger read alignments, 48.6% overlapped with tandem repeats and 34.77% with other types of repetitive elements. Of the 4,718 CDS not supported by Sanger reads, 3,511 (74.41%) of them are localized in close proximity (< 2 kb) to tandem repeats. GC% content in distal subtelomeric regions is elevated, and regions lacking Sanger read coverage are more prevalent in the subtelomeres (48.6% of these regions overlap with tandem repeats). Telomere-associated tandem repeats, (TTAGGG)n, are indicated with plus ("+") symbols. Gaps in the current v10 reference genome assembly tend to co-localize with long tandem arrays. The locations of clusters of 5S (green), 18S (blue), and 28S (green) rRNAs, tRNAs, and snRNAs are indicated. Red vertical lines indicate the position of centromeres. (b) An example of subtelomere boundary inference for chromosome 1 (vs. chromosome 2) using feature selection with k-means clustering on a matrix selecting for repetitive Hi-C read placements in the subtelomeres (yellow, high-density corners), depletion of subtelomere-specific signal with the rest of the chromosome (blue edges), and background/aspecific repetitive signal (center). Dashed horizontal and vertical lines demarcate the inferred subtelomere boundaries. (c) Principal component analysis of the chromosome 1 matrix in panel b, decomposing variances into subtelomere-specific (positive Y values) and subtelomere-depleted repeat signals (negative Y values). Dashed vertical lines demarcate the inferred subtelomere boundaries. (d–f) IGV3 (v2.7.2) views from two fully-assembled loci in the current X. tropicalis (v10) assembly previously fragmented in the v9 assembly due to lack of Sanger read coverage. (d) atp4a (Xetrov107051369m; Chr7:129,430,384–129,450,182) was partially assembled in v9. Note that most regions not covered by Sanger (yellow) overlap repeats (blue). (e) dnai1 (Xetrov107008718m; Chr1:216,212,747– 216,291,747) was completely missing from v9 and is now captured in the v10 assembly. (f) Due to the highly repetitive nature of the sequence surrounding the myod1 locus (Xetrov107027728m; Chr4:719,782–1,128,311) this gene remains fragmented in the v10 assembly. The number below the “Lack Sanger coverage” track corresponds to the size of the fragment not covered by reads. (g) GC% distribution of genomic regions greater than 100 bp that were covered (n = 140,598) or not-covered (n = 95,475) by Sanger reads. kb, kilobases; Mb, megabases. Source data are provided as a Source Data file.
	Supplementary Fig. 3 Assembly of five additional frog species. (a) A representative Hymenochirus boettgeri metaphase chromosome spread selected from among n = 75 independent cell spreads prepared from ten individual H. boettgeri tadpoles. Nine chromosome pairs can be observed for a karyotype of 2n = 18 (mode = 18, mean ± SEM = 18.09 ± 0.22). The scale bar represents 10 µm. Panels b–f present whole-genome Juicebox1,2 visualizations of Hi-C contact maps from (b) H. boettgeri, (c) Eleutherodactylus coqui, (d) Engystomops pustulosus, (e) Pyxicephalus adspersus, and (f) Leptobrachium (Vibrissaphora) ailaonicum chromosomes. Hi-C contact matrices balanced using the Knight-Ruiz algorithm, showing reads with a minimum mapping quality (MQ) ≥ 0 below the diagonal and reads with MQ ≥ 30 above the diagonal. Chromosomes (gold boxes) are shown in ascending numeric order along the X-axis and the intensity of blue pixels is proportional to chromatin contact frequencies between X-Y pairs of non-overlapping genomic loci. Source data are provided as a Source Data file.
	Supplementary Fig. 4 Comparison of gene content among assemblies. In the above occurrence tables, green and grey represent the presence or absence, respectively, of a species in a gene family cluster. The cluster count column summarizes the number of such gene family clusters with that occurrence pattern, while the protein count column lists the number of genes included in those gene clusters. Tables (a) containing three or more species with the v10 annotation primary transcripts, (b) containing three or more species with the v9 annotation longest transcripts4 (NCBI Annotation Release 103 of RefSeq assembly accession GCF_000004195.3 [https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000004195.3]), and (c) containing four or more species with both v9 and v10 against the longest transcripts of Danio rerio (NCBI Annotation Release 106 of RefSeq assembly accession GCF_000002035.6 [https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000002035.6]), Gallus gallus (NCBI Annotation Release 104 of RefSeq assembly accession GCF_000002315.6 [https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000002315.6]) Homo sapiens (NCBI Annotation Release 109 of RefSeq assembly accession GCF_000001405.39 [https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001405.39]), and Mus musculus (NCBI Annotation Release 108 of RefSeq assembly accession GCF_000001635.26 [https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001635.26]). Occurrence tables of gene homology clusters containing (d) three or more species among the five frog annotations newly generated for this study and (e) six or more members among the full set of seven frogs and—with both X. laevis L and S homoeolog sets represented—eight (sub)genomes analyzed here. All OrthoVenn25 clustering analyses were completed with the longest transcript amino acid sequences extracted using gff3ToGenePred and genePredToProt (UCSC Genomics Institute6 KentTools binaries downloaded March 5, 2019) as well as custom script largestgenePred.py (v1.0, https://github.com/abmudd/Assembly). Source data are provided as a Source Data file.
	Supplementary Fig. 5 Xenopus tropicalis repeat density principal components projected on genomic coordinates. (a) The first two principal components (PCs) of the repeat density matrix describe subtelomeric and pericentromeric regions of the chromosomes. The first component (PC1, blue lines) strongly correlates with GC content (Pearson’s r = +0.796). The grey horizontal line is the value for which the smoothed PC2 (red lines) was thresholded to discriminate between distal-subtelomeric (purple boxes), pericentromeric (red boxes), and arm regions (grey) of each chromosome. Chromosomes are centered by the median position of centromere-associated tandem repeats (black dots). Tick lines correspond to distances of 10 Mb. (b) Plot as in panel a showing the third principal component (PC3, purple lines) of the repeat matrix plotted with the eigenvector that defines A/B compartment structure (green; A and B compartments above and below the X-axis, respectively) obtained from the Hi-C contact matrix. PC3 and the Hi-C-derived eigenvector show a moderately negative correlation (Pearson’s r = −0.64) when analyzed in 500 kb windows along the genome. This negative correlation with PC3 is maintained, although weaker, when the analysis is repeated with consecutive Hi-C windows with equivalent signs collapsed into larger A/B compartment domain block intervals (Pearson’s r = −0.44). Harbinger-N9_XT is positively associated with PC3 (Pearson’s r = +0.50), whereas DNA/hAT-Ac appears strongly negatively correlated with PC3 (Pearson’s r = −0.80). (c) Repeat landscape of L1 (red) and CR1 (green) Non-LTR retrotransposons, satellite repeats (blue), and DNA transposons (orange). Recombination rate plotted along the X-axis as a density gradient track (black = high, white = low). Centromere positions are represented with red stars. (d) Jukes-Cantor (JC) distance (X-axis) from the consensus sequence for the repeats shown in panel a. Only the most abundant L1 repeat families are shown from panel b. kb, kilobases; Mb, megabases. Source data are provided as a Source Data file.
	Supplementary Fig. 6 Xenopus tropicalis Nigerian strain residual heterozygosity. Heterozygosity rates for the N17 genome frog (an F17 inbred line; blue) and two pooled F13 inbred Nigerian strain datasets: N13_f, eight Nigerian females (orange); and N13_m, twelve Nigerian males (yellow). Rates are measured as heterozygous SNP positions per kilobase. kb, kilobases; Mb, megabases; SNP, single-nucleotide polymorphism. Source data are provided as a Source Data file
	Supplementary Fig. 7 Xenopus tropicalis gene collinearity with the genomes of six frogs and axolotl. Circos plots with runs of collinearity containing at least 5 kb of aligned sequence between Xenopus tropicalis (left, Xtr) and (a) Eleutherodactylus coqui (right, Eco), (b) Engystomops pustulosus (right, Epu), (c) Hymenochirus boettgeri (right, Hbo), (d) Leptobrachium (Vibrissaphora) ailaonicum (right, Lai), (e) Pyxicephalus adspersus (right, Pad), (f) X. laevis L subgenome (right, Xla L), and (g) X. laevis S subgenome (right, Xla S). Chromosomes are represented by light grey bars, Hi-C-based and tandem repeat centromere positions are marked with black and red intersecting lines, respectively. Minor and major ticks delimit 5 Mb and 25 Mb intervals, respectively. (h) Percent of total chromosome sequence size for each ancestral unit, gene density in genes per 100 kb for each ancestral unit, and repeat density in repeats per 1 kb for each ancestral unit. Boundaries of the ancestral units were extracted from runs of collinearity containing at least 1 kb of sequence aligned against L. ailaonicum. Circos plots with runs of collinearity, as in panels a–g, for (i) Ambystoma mexicanum (right, Ame); X. tropicalis and A. mexicanum chromosomes are scaled evenly. Runs of collinearity are colored with respect to the 13 ancestral chromosomes (A: black, B: grey, C: red, D: orange, E: yellow, F: bright green, G: dark green, H: cyan, I: blue, J: purple, K: magenta, L: dark brown, and M: tan). kb, kilobases; Mb, megabases. Source data are provided as a Source Data file.
	Supplementary Fig. 8 Chromosome fusions in Xenopus laevis and Hymenochirus boettgeri. (a) Heatmap of repeat density in X. laevis showing repeats enriched in subtelomeric (blue tracks), pericentromeric (orange tracks), and arm regions (grey tracks) for chromosome 7L and the fused chromosome 9_10S. Three bands of subtelomeric signal can be detected on chromosome 9_10S, the signal between 30 and 50 Mb corresponds to the fusion of the subtelomeres from ancestral pipid chromosomes 9 and 10. (b) Scatterplots of two subtelomeric repeats showing, for each X. laevis chromosome (X-axis), the length (Y-axis) and Jukes-Cantor (JC) distance of the repeats colored as indicated by the histogram on the bottom right. The dotted vertical line on the histogram indicates the 95th percentile. The median JC distances from subtelomeres from all chromosomes (JC = 0.054) is lower than the median JC distances from the region of the chromosome 9_10 fusion (JC = 0.157), and for the relatively recent p-arm inversion on chromosomes 8S (JC = 0.099) and 2S (JC = 0.076), suggesting that the p-arm inversions from chromosomes 8S and 2S7 occurred after the divergence from the pipid ancestor but after the fusion of chromosome 9_10S. Kolobok-N8_XL, a more recent repeat that expanded post-chromosome fusion and inversion of the p-arm of chromosomes 9S and 2S. (c) Hi-C contacts from chromosome 8_10 of H. boettgeri shows conserved intra-chromosomal contact boundaries compared to ancestral chromosomes 8 and 10. (d) Heatmap showing the density of subtelomeric repeats in H. boettgeri chromosome 8_10, between 85 and 120 Mb, from the fusion of ancestral chromosomes 8 and 10. (e) Enriched centromere-centromere contacts between H. boettgeri chromosome 1 (Y-axis) and chromosome 8_10 (X-axis), with the strongest centromeric interactions at x, y = 55 Mb, 170 Mb; suggesting that the active centromere of chromosome 8_10 was inherited from ancestral chromosome 10. A schematic of each chromosome, with pericentromeres colored black, are drawn along the axes. Enriched contacts shown in red, depletion in blue, and parity in white. Contacts enriched in the upper- and lower-right corners represent subtelomere-subtelomere contacts between the two chromosomes. Matrix of observed counts divided by expected counts, at 2.5 Mb matrix resolution (mapping quality ≥ 30, Knight-Ruiz balanced). bp, basepairs; Mb, megabases. Source data are provided as a Source Data file.
	Supplementary Fig. 9 Estimating the positions of Xenopus tropicalis centromeres. (a) Genome-wide Hi-C contact map of X. tropicalis. Intersecting horizontal and vertical dashed black lines mark the Centurionestimated centromeres. Yellow puncta reflect centromere-centromere contact enrichment between chromosomes, suggesting centromere clustering on the inner nuclear periphery. Yellow, white, and blue colors indicate the normalized relative enrichment, parity, and depletion (respectively) between a pair of 1 Mb genomic loci. Intra-chromosomal contacts have been masked (solid white boxes). Axis coordinates in Mb. (b) Box plots comparing the variation in differences between manual and Centurion centromere estimates by mapping quality (MQ) for thresholds MQ ≥ 0 (MQ0) and MQ ≥ 30 (MQ30), where each blue point represents an estimate for a single chromosome. For each boxplot, n = the haploid number of chromosomes for the species-MQ combination indicated (X-axis). Lower and upper box edges denote the first and third quartiles, respectively, and whiskers extend to 1.5 times the interquartile range, while thick center lines represent medians. (c) ChIP-seq signal for Cenp-a, Histones H4 and H3. Samples are normalized by the read depth of the DNA associated with free-mononucleosomes (input). The presence of 205 bp tandem monomer sequences associated with Centromeric Tandem Repeats is indicated in red. (d) Zoomed-in view showing the organization of tandem centromeric repeat sequences (monomer = 205 bp) for each chromosome. A 300 kb window surrounding the presumptive centromeric repeats. Monomers found in the forward and reverse strands are shown in blue and yellow, respectively. Monomers sharing above 95% identity to the repeat consensus are shown in black. (e) The percentage of the major base per position of the multiple alignment of 3,693 genomic BLASTN hits from the initial 205 bp monomer sequence. To generate the 205 bp consensus we considered the most represented base per site (positions where alignments were over 50% gaps were omitted). bp, basepairs; kb, kilobases; Mb, megabases. Source data are provided as a Source Data file.
	Supplementary Fig. 10 Xenopus tropicalis recombination landscape. (a) Scatterplot of physical (X-axis) vs. genetic (Y-axis) position of the genetic map based on the X. tropicalis v10 genome assembly. Genetic map distances (blue dots) smoothened by cubic spline linear interpolation (blue line). Recombination rates (cM/Mb, red line) were obtained from the smoothened genetic distances. (b) Cumulative distribution of recombination rates. The distribution of recombination rates (lower histogram) was used to determine genetic positions with high and low recombination (75th percentile, red dotted line). Boxplot whiskers represent 1.5 times the interquartile range, the left and right boundaries of the box bound the first and third quartiles, respectively, and the center line marks the median. (c) Recombination rate (cM/Mb) distribution per chromosomal segment: 5 Mb surrounding centromere (pericentromeres), 30 Mb from the end of chromosme arms (p- and qsubtelomeres, excluding pericentromeres of acrocentric chromosomes), and the remaining chromosome arms. Significant differences are observed between distributions of the arms vs. subtelomeres (Hochberg-corrected p = 5.2×10−321) and the arms vs. pericentromeres (Hochberg-corrected p = 3.2×10−42 ) using two-sample Kolmogorov–Smirnov two-sided tests. Mb, megabases; cM, centiMorgans. Source data are provided as a Source Data file.
	Supplementary Fig. 11 Distributions of satellite repeats in Xenopus tropicalis. (a) Distribution of tandem repeats enriched in pericentromeric and subtelomeric regions. Tandem repeat monomers are overrepresented in pericentromeric (tracks a–e; red and oranges) and subtelomeric (tracks f–q; yellow–purple) regions. Each tick on the graph represents the alignment of a consensus monomer sequence sharing >90% of sequence identity. Sequence track a (red), 205-bp monomer, is the only monomer exclusive to the pericentromeric regions and is referred to as the Centromeric Tandem Repeat (CTR). The median position of CTRs per chromosome is indicated by the vertical dotted line and the black circle. The dashed vertical line indicates the estimated centromeric position from Hi-C using stringent mapping parameters. The purple horizontal lines correspond to 30 Mb spanning the subtelomeric domains. Monomer sequences best hit aligned against the repeat database can be found in Supplementary Table 16. (b) Scatter plot representing repeat length (Y-axis) and sequence divergence (Jukes-Cantor distance, color scheme) from satellite families: Xtr-5_family-21 (track q in panel a), Xtr-5_family-1304, and a SINEV/tRNA: Xla-4_family-206 (track p in panel a). Long satellite repeats with low sequence divergence localize at subtelomeric portions overlapping areas of high recombination rates (red line). The bottom ticks indicate the presence of the monomer unit of the satellite repeats. The complete sequence of SINE-V/tRNA is relatively uniformly distributed in chromosome arms, except near the pericentromeres and subtelomeres. A minisatellite originated from a portion of the SINE-V/tRNA. Red curves plot the recombination rate profile in cM/Mb. The histogram of JC distances from SINE/tRNA-V sequences is subdivided by sequence length. Note how centromere-associated repeats preclude subtelomeric repeats in acrocentric chromosomes 3, 8, and 10. bp, basepairs; kb, kilobases; Mb, megabases; cM, centiMorgans. Source data are provided as a Source Data file.
	Supplementary Fig. 12 Correlates of recombination rate in Xenopus tropicalis. (a) Scatterplots comparing the genome-wide recombination rates (X-axis) against the 12 highest correlated genomic features. PC1 corresponds to the first principal component (PC) obtained from repeat densities. Y-axis is the number of bases per 1-Mb size bins for regions with available genetic markers. A table of all genomic features correlated with recombination rate can be found in Supplementary Table 14. Each red line is the linear regression model for the plotted data points, while each semi-transparent red band highlights the 95% confidence interval of the linear model. (b) Enriched tetramers in subtelomeric sequences. The distribution of tetramers in genomic regions (> 300 bp) overlapping tandem repeats and other non-tandem repeats (grey) in the distal subtelomeric portions of (sub)metacentric chromosomes. The two most enriched monomers (AGGG/CCCT and TGGG/CCCA) are similar to the 7-nucleotide oligomer CCTCCCT and CCCACCCC that have been associated with recombination hotspots in human8 and in mouse9 . bp, basepairs; Mb, megabases. Source data are provided as a Source Data file.
	Supplementary Fig. 13 Zebra finch subtelomeric tandem repeats. Genomic distributions of tandem repeats enriched in the subtelomeric portions of chromosomes (larger than 20 Mb in size). Grey vertical lines demarcate the first and last 5 Mb, where recombination rates are highest10. The tandem repeat sequences appear in at least four of the larger chromosomes and in most microchromosomes. Mb, megabases. Source data are provided as a Source Data file.
	Supplementary Fig. 14 Microsatellite origin SINE/tRNA evolved into a microsatellite sequence. (a) A schematic of the structure of Xenopus SINE/tRNA (top), as described by Ogiwara et al.11. The nucleotide sequence alignment of consensus SINE/tRNA obtained from different frog species (bottom) and the 52-mer sequence where the minisatellite sequence was derived. The multiple sequence alignment (MSA) of the consensus SINE/tRNA identified for the frogs in this study (except E. coqui) shows high levels of sequence similarity. MSA regions colored as in the schematic. The alignment includes the 52-bp monomer sequence that conforms to the minisatellite. The 52-mer consensus sequence shows perfect alignment with X. tropicalis (Xtr) and X. laevis (Xla). The last base of the monomer is a “G” substitution of a “T.” Notice that E. pustulosus (Epu), X. borealis (Xbo), and H. boettgeri (Hbo) lack the first “AGGA” box from the consensus sequence. (b) Representation of an unequal crossingover event between a pair of unequally-aligned 3'UTR SINE/tRNA sequences. The unequal crossing over produces a duplication of the 51-mer + “G” (top) and a deletion of the sequence (bottom). (c) An example of the alignment of an intact SINE/tRNA in X. tropicalis genome. MSA regions colored as in the schematic in panel a. (d) Example of an ancestral SINE/tRNA (Chr2:10,640,159– 10,647,735) that contains 78 copies of the 52-mer sequence and has extended over 7.5 kb in length. Sequence regions colored as in the schematic in panel a. (e) The GC% of the consensus SINE/tRNA oscillates between 46 and 48%, while the sequence of the monomer is slightly higher at 51% (51.9% with the addition to the T>G substitution), thus it would be expected that the extension of the tandem would cause a gradual increase in local GC content (see graph on the right). (f) Example of the deletion of the 52-mer that possibly resulted from unequal crossing over. MSA regions colored as in the schematic in panel a. Hsa, Homo sapiens; bp, basepairs; kb, kilobases. Source data are provided as a Source Data file.
	Supplementary Fig. 15 Enrichments of Rabl-like chromosome contacts. Select inter-chromosomal Hi-C contact matrices exemplifying different chromosome-structure combinations observed. Contact enrichment, parity, and depletion between 1 Mb non-overlapping loci colored gold, white, and blue, respectively. Regions of each matrix sampled to measure median centromere-centromere (cc, black outlined box), centromere-telomere (ct, grey dotted boundary lines), and centromere-to-telomere polarity arm-arm (aa, black dotted boundary lines) contact densities are labeled. (a) submetacentric X. tropicalis (Xtr) chromosomes 1 and 4; (b) submetacentric and acrocentric E. pustulosus (Epu) chromosomes 1 and 4, respectively; (c) metacentric and telocentric/acrocentric P. adspersus (Pad) chromosomes 1 and 7, respectively; and (d) telocentric/acrocentric P. adspersus (Pad) chromosomes 7 and 8. Mb, megabases. Source data are provided as a Source Data file.
	Supplementary Fig. 16 Xenopus tropicalis 3D chromatin structure and nuclear organization. (a) Genome-wide, a non-random association of chromosomal arm-arm contacts is observed (c2 (361, n = 28,366,570) = 58,25,879.96, Hochberg-corrected p < 4.46×10−308; inter-arm relative range: 0.654–3.829). Chromosome arms are 2.60× enriched for intra-chromosomal contacts over inter-chromosomal contacts (c2 (1, n = 4,957,102) = 979,083.44, Hochberg-corrected p < 4.46×10−308). Between chromosomes, p-p and q-q arms contacts are, respectively, 1.077× and 1.0412× enriched over p-q arm contacts (c2 (1, n = 24,786,496) = 17,037, Hochberg-corrected p < 4.46×10−308). Note: 4.46×10−308 is the post-correction value for 2.23×10−308, the lower numerical limit of a signed, double-precision floating-point value computed in the R statistical language on a 64-bit computer. See Supplementary Table 21 for association statistics for all species. (b) In panels c–j, PC1 or PC2 vector points are colored tan, black, and brown to differentiate 1-Mb windows along the p-arm, near the centromere, and the q-arm, respectively; a schematic of this coloring scheme is shown for clarity. Visualizing example Rabl-like chromatin configurations for (c) chromosome 1, blood cell nuclei; (d) chromosome 4, blood cell nuclei; (e) chromosome 8, blood cell nuclei; (f) chromosome 9, blood cell nuclei; (g) chromosome 10, blood cell nuclei; (h) chromosome 1, sperm; (i) chromosome 1, NF stage 8; (j) chromosome 1, adult brain. All contact maps generated using contacts with mapping quality ≥ 30. For visualization, the contrast level for each Hi-C contact density map has been adjusted to accommodate each dataset. The target chromosome is plotted on the Y-axis of each heatmap, with the comparator chromosome on the X-axis. Contact enrichment, parity, and depletion between 1 Mb non-overlapping loci colored gold, white, and blue, respectively. PC, principal component; Mb, megabases. Source data are provided as a Source Data file.
	Supplementary Fig. 17 Xenopus tropicalis A/B compartment domain size distributions. The size distributions for A (gold) and B (blue) compartment domains from X. tropicalis blood cell nuclei. Mb, megabases. Source data are provided as a Source Data file.

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