The study presents a comprehensive analysis of the sex chromosomes in great apes, focusing on the X and Y chromosomes. The Y chromosome, crucial for male reproduction, has undergone rapid evolution with high levels of structural rearrangements, repetitive elements, and gene expansions. In contrast, the X chromosome, essential for both reproduction and cognition, has maintained a more stable structure. The researchers used telomere-to-telomere (T2T) assembly methods to produce gapless assemblies of the X and Y chromosomes for five great apes and one lesser ape, revealing detailed insights into their evolution. They found that the Y chromosome exhibits dynamic evolution, with lineage-specific expansions and contractions of ampliconic regions and palindromes, while the X chromosome remains relatively stable. The study also highlights the importance of palindromes in counteracting the degradation of the Y chromosome and the role of segmental duplications and repetitive elements in maintaining genetic content. Additionally, the analysis of intraspecific diversity and selection patterns on the Y chromosome suggests that purifying selection acts on ancestral genes, and that the Y chromosome may be under selection due to differences in sperm competition among species. The complete assemblies provide valuable resources for understanding human evolution and conservation genetics of non-human apes.The study presents a comprehensive analysis of the sex chromosomes in great apes, focusing on the X and Y chromosomes. The Y chromosome, crucial for male reproduction, has undergone rapid evolution with high levels of structural rearrangements, repetitive elements, and gene expansions. In contrast, the X chromosome, essential for both reproduction and cognition, has maintained a more stable structure. The researchers used telomere-to-telomere (T2T) assembly methods to produce gapless assemblies of the X and Y chromosomes for five great apes and one lesser ape, revealing detailed insights into their evolution. They found that the Y chromosome exhibits dynamic evolution, with lineage-specific expansions and contractions of ampliconic regions and palindromes, while the X chromosome remains relatively stable. The study also highlights the importance of palindromes in counteracting the degradation of the Y chromosome and the role of segmental duplications and repetitive elements in maintaining genetic content. Additionally, the analysis of intraspecific diversity and selection patterns on the Y chromosome suggests that purifying selection acts on ancestral genes, and that the Y chromosome may be under selection due to differences in sperm competition among species. The complete assemblies provide valuable resources for understanding human evolution and conservation genetics of non-human apes.