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. 2024 May 29;630(8016):401–411. doi: 10.1038/s41586-024-07473-2

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© The Author(s) 2024

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. 5 — (a) Gallery view of Y chromosomes from species in this study. Chromosomes were FISH-labeled with rDNA- (BAC RP11-450E20, green) and SRY-containing (BAC RP11-400O10, red) BAC probes and counter-stained with DAPI. Siamang and both orangutans’ Y chromosomes have rDNA signal on the distal ends of the q-arms. (b) Siamang and Sumatran orangutan chrY rDNA copy number was quantified from the fraction of the total fluorescent intensity of rDNA signals on all chromosomes (from chromosome spreads as in panel a) and the Illumina sequencing estimate of the total copy number of rDNA repeats in the genome (339 copies in siamang, 814 in Sumatran orangutan). The mean and standard deviations from 20 chromosome spreads are shown near each box plot. The box plots show the median as the center line and the first and third quartiles as the bounds of the box; the whiskers extend to the minimum/maximum value, and all values are plotted as dots in front of the box plot.The rounded average of rDNA arrays on chrY were 16 copies for siamang and 3 copies for Sumatran orangutan. (c) A representative image of siamang chrY labeled by immuno-FISH with rDNA probe (green) and the antibody against rDNA transcription factor UBF (magenta). The chrY rDNA array is positive for the UBF signal. (d) Quantification of siamang chrY rDNA and UBF expressed as the fraction of the total fluorescent intensity of all rDNA-containing chromosomes in a chromosome spread. The box plots are plotted as in b from 20 chromosome spreads. ChrY rDNA arrays contain on average ~10% of the total chromosomal UBF signal. Siamang (e) and Sumatran (f) and Bornean (g) orangutan read-level plots showing ONT methylation patterns at the chrY rDNA locus and surrounding regions. The coverage track shows the depth of sequencing coverage across the rDNA array, and the methylation track displays the methylation status of individual cytosines. Hypomethylation of the 45 S units is evidence of active transcription in siamang and S. orangutan, but not B. orangutan. Only reads >100 kb that are anchored in unique sequence outside the rDNA array and (except for Bornean orangutan) span at least two 45 S units are shown.