Extended Data Fig. 1: Variation in structure and composition across Y-chromosomal subregions.
From: Assembly of 43 human Y chromosomes reveals extensive complexity and variation
a. Overview of the Y chromosome. A three-way comparison of sequence identity between GRCh38 Y, NA19317 (E1b1a1a1a1c1a1a3a1-CTS8030) and the T2T Y (excluding Yq12 and PAR2 subregions), highlighting substantial differences in the size and orientation of some subregions. b. Focus on Yq12. Sequence identity heatmaps of the Yq12 subregion for six contiguously assembled samples (HG01890, HG02666, HG01106, HG02011, HG00358 and HG01952), two samples (NA19705 and HG01928) with a single gap in the Yq12 subregion (gap ___location marked with asterisk) and the T2T Y using 5kb window size. c. Focus on TSPY repeat array. Sequence identity heatmaps of ~20.3-kbp TSPY repeat units for three males highlighting putative expansion events harbouring both single and multiple repeat units. Red shades from lighter to darker indicate sequence identity from 99–100%, respectively, while white fill indicates sequence identity <99%. The last copy on the right is the single separate repeat unit containing the TSPY2 gene. See Fig. S22 for heatmaps of all samples. d. Dotplots of the TSPY repeat array for HG02666 with 5 kbp of flanking regions showing identical matches of 2, 5, and 10 kbp in size indicating regions with high sequence identity. See Fig. S25 for additional examples.
