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. 2023 May 10;617(7960):335–343. doi: 10.1038/s41586-023-05976-y

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 4 — (A) We focus on the first 25 Mbp of chromosome 13, shown here as a red box over T2T-CHM13 cytobands. Pseudo-homologous regions (PHRs), where diverse sets of acrocentric chromosomes recombine, are highlighted relative to T2T-CHM13 genome annotations for repeats, GC percentage, and genes. Above, we indicate regions of interest described in the main text: rDNA, SST1 array, centromere, and q-arm. Below, we show T2T-CHM13-relative homology mosaics for each chromosome 13 matched contig from HPRCy1-acro, with the most-similar reference chromosome at each region shown using the given colors (Target). (B) Aggregated untangle results in the SAACs. For each acrocentric chromosome, we show the count of its HPRCy1 q-arm-anchored contigs mapping itself and all other acrocentrics (Contigs), (C) as well as the regional (50kbp) untangle entropy metric (Regional homology entropy) computed over the contigs’ T2T-CHM13-relative untanglings. (D) By considering the multiple untangling of each HPRCy1-acro contig, we develop a point-wise metric that captures diversity in T2T-CHM13-relative homology patterns (Positional homology entropy), leading to our definition of the PHRs. (E) The patterns of homology mosaicism suggest ongoing recombination exchange in the SAACs. A scan over T2T-CHM13 reveals that the rDNA units are enriched for PRDM9 binding motifs, and thus may host frequent double stranded breaks during meiosis. In (B-D) a gray background indicates regions with missing data due to the lack of non-T2T-CHM13 contigs. We provide the Centromeric Satellite Annotation (CenSat Annotation) track legend in Extended Data Table 1.