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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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Fig. 3 — a, We focus on the first 25 Mb of chr. 13, shown here as a red box over T2T-CHM13 cytobands. PHRs are highlighted relative to T2T-CHM13 genome annotations for centromere and satellite repeats (CenSat annotation), GC percentage and genes (CAT/Liftoff genes). Top, regions of interest described in the main text: rDNA, the SST1 array, the centromere and q-arm. Bottom, relative homology mosaics based on the T2T-CHM13 assembly for each chr. 13-matched contig from HPRCy1-acro, with colours indicating the most similar reference chromosome (target). b,c,d, Aggregated untangle results in the SAACs. b, The count of HPRCy1 q-arm-anchored contigs mapping to each acrocentric chromosome (Contigs) aggregated by target chromosome and (c) the regional (50 kb) untangle entropy metric (Regional homology entropy) computed over the contigs’ untangling relative to T2T-CHM13. d, By considering the multiple untangling of each HPRCy1-acro contig, we develop a point-wise metric that captures diversity in homology patterns relative to T2T-CHM13 (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 and SST1 array units are enriched for PRDM9 binding motifs, and thus may host frequent double-stranded breaks during meiosis. In b–d, the grey background indicates regions with missing data due to the lack of non-T2T-CHM13 contigs.