Assembly of 43 diverse human Y chromosomes reveals extensive complexity and variation

Abstract

31 The prevalence of highly repetitive sequences within the human Y chromosome has led to its incomplete 32 assembly and systematic omission from genomic analyses. Here, we present long-read de novo 33 assemblies of 43 diverse Y-chromosomes, three contiguously assembled including two from deep- 34 rooted African Y lineages. Examination of the full extent of genetic variation between Y chromosomes 35 across 180,000 years of human evolution reveals its remarkable complexity and diversity in size and 36 structure, in contrast with its low level of base substitution variation. The size of the Y chromosome 37 assemblies vary extensively from 45.2 to 84.9 Mbp, with individual repeat arrays showing up to 6.7- 38 fold difference in length across samples. Half of the male-specific euchromatic region is subject to large 39 (up to 5.94 Mbp) inversions with a >2-fold higher recurrence rate compared to the rest of the human 40 genome. The Y centromere, composed of 171 bp α-satellite monomer units, appears to have evolved 41 from tandem arrays of a 36-mer ancestral higher order repeat (HOR), which has been predominantly 42 replaced by a 34-mer HOR, and reveals a pattern of higher sequence variation towards the short-arm 43 side. The Yq12 heterochromatic region is ubiquitously flanked by approximately 649 kbp and 472 kbp 44 inversions that maintain the alternating arrays of DYZ1 and DYZ2 repeat units in between. While the 45 sizes and the distribution of the DYZ1 and DYZ2 arrays vary considerably, primarily due to local 46 expansions and contractions, the copy number ratio between the DYZ1 and DYZ2 monomer repeat units 47 remains consistently close to 1:1. In addition, we have identified on average 65 kbp of novel sequence 48 per Y chromosome. The availability of sequence-resolved Y chromosomes from multiple samples 49 provides a basis for identifying new associations of specific traits with the Y chromosome and garnering 50 novel evolutionary insights. 51 2 bioRxiv preprint doi: https://doi.org/10.1101/2022.12.01.518658; this version posted December 1, 2022. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. 52