Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures

Area of Science:

• Genomics
• Human Genetics
• Evolutionary Biology

Background:

• The human Y chromosome exhibits significant structural dynamism, with diversity obscured by repetitive elements like palindromes and large duplications.
• Understanding the interplay of these variations, their recurrence across lineages, and conserved organizational aspects remains a challenge.

Purpose of the Study:

• To generate a population-scale resource of human Y chromosome assemblies for studying its biology and diversity.
• To investigate how structural variations are organized across the entire Y chromosome and their evolutionary patterns.

Main Methods:

• Analysis of 142 near-complete human Y chromosome assemblies from 17 major haplogroups.
• Examination of structural variation in specific regions like the azoospermia factor c (AZFc) region and ampliconic gene families.
• Assessment of centromere and Yq12 heterochromatin organization and methylation patterns.

Main Results:

• Structural changes on the Y chromosome are recurrent but constrained, even in repetitive regions.
• The AZFc region exhibits a limited set of structural haplotypes generated by recurrent rearrangements.
• Ampliconic gene families (DAZ, RBMY, TSPY) show distinct evolutionary trajectories and copy number variations.
• Centromeric and Yq12 heterochromatin regions maintain stable higher-order organization despite size variation.
• Methylation patterns are structured by repeat class, copy order, and local architecture.

Conclusions:

• The study provides a valuable population-scale resource for human Y chromosome research.
• Rapid structural evolution of the Y chromosome is consistently channeled into a restricted set of architectural outcomes.