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

Abstract

The prevalence of highly repetitive sequences within the human Y chromosome has led to its incomplete assembly and systematic omission from genomic analyses. Here, we present long-read de novo assemblies of 43 diverse Y-chromosomes, three contiguously assembled including two from deep-rooted African Y lineages. Examination of the full extent of genetic variation between Y chromosomes across 180,000 years of human evolution reveals its remarkable complexity and diversity in size and structure, in contrast with its low level of base substitution variation. The size of the Y chromosome assemblies vary extensively from 45.2 to 84.9 Mbp, with individual repeat arrays showing up to 6.7-fold difference in length across samples. Half of the male-specific euchromatic region is subject to large (up to 5.94 Mbp) inversions with a >2-fold higher recurrence rate compared to the rest of the human genome. The Y centromere, composed of 171 bp α-satellite monomer units, appears to have evolved from tandem arrays of a 36-mer ancestral higher order repeat (HOR), which has been predominantly replaced by a 34-mer HOR, and reveals a pattern of higher sequence variation towards the short-arm side. The Yq12 heterochromatic region is ubiquitously flanked by approximately 649 kbp and 472 kbp inversions that maintain the alternating arrays of DYZ1 and DYZ2 repeat units in between. While the sizes and the distribution of the DYZ1 and DYZ2 arrays vary considerably, primarily due to local expansions and contractions, the copy number ratio between the DYZ1 and DYZ2 monomer repeat units remains consistently close to 1:1. In addition, we have identified on average 65 kbp of novel sequence per Y chromosome. The availability of sequence-resolved Y chromosomes from multiple samples provides a basis for identifying new associations of specific traits with the Y chromosome and garnering novel evolutionary insights.

The complete sequence of a human Y chromosome

“…In contrast, our T2T-Y assembly resolved 46 protein-coding TSPY copies, including TSPY2, which was found in the distal part of the IR3, downstream of the TSPY array (at ~10 Mb). The distal positioning of TSPY2 in HG002 was confirmed among all other Y haplogroups except R and Q, which match the proximal positioning of GRCh38-Y 33 . All 45 protein-coding copies in the TSPY array were embedded in an array of composite repeat units, with one composite unit (~20.2 kb in size) per gene, such that an array of composite units includes multiple TSPY gene copies in tandem (Fig.…”

“…Because the validation signal at the three HSat positions was ambiguous, these regions were noted but left unchanged. The P5 inversion error was discovered only after the T2T-Y assembly had been fully annotated and released, and because this inversion appears as a true recurrent inversion in other individuals 33 , it was noted but left uncorrected in this release. The described T2T-Y assembly is 62,460,029 bases in length with no gaps or model sequences and an estimated error rate of less than 1 error per 10 Mb (Phred Q73.8), as measured by Merqury using a hybrid k-mer set from Illumina and HiFi reads 14,15 (Table 1, Supplementary Table 3).…”

“…Lessons learned from our assembly of T2T-Y informed the development of the Verkko assembler 93 , which automates the integration of HiFi and ONT data for diploid human genome assembly. The companion study of Hallast et al 33 successfully used Verkko to generate 43 near-T2T assemblies from a diverse panel of human Y chromosomes, revealing dynamic structural changes within this chromosome over the past 180,000 years of human evolution. Ultimately, as the complete, accurate, and gapless assembly of diploid human genomes becomes routine, we expect "reference genomes" will become known as simply "genomes".…”

The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes

“…On the Y chromosome, deletions within the ampliconic regions have been previously linked to infertility 109,110 . Additional intraspecific studies, comparing the complete sex chromosomes of multiple individuals within each species (as was recently done for humans 111 ), are now needed to reveal the full landscape of ape sex chromosome evolution and function.…”

eXclusionarY: Ten years later, where are the sex chromosomes in GWAS?

“…However, the Y chromosome has long been a thorn in the side of human geneticists: More than half of the Y chromosome is absent from GRCh38 76 . Two recent papers used combinations of multiple long-read next-generation sequencing technologies to generate much more complete sequence of the Y chromosome, and they also described a high degree of heterogeneity in chromosome length and content between individuals 76,77 .…”