The complete sequence and comparative analysis of ape sex chromosomes

Abstract

Apes possess two sex chromosomes—the male-specific Y chromosome and the X chromosome, which is present in both males and females. The Y chromosome is crucial for male reproduction, with deletions being linked to infertility1. The X chromosome is vital for reproduction and cognition2. Variation in mating patterns and brain function among apes suggests corresponding differences in their sex chromosomes. However, owing to their repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the methodology developed for the telomere-to-telomere (T2T) human genome, we produced gapless assemblies of the X and Y chromosomes for five great apes (bonobo (Pan paniscus), chimpanzee (Pan troglodytes), western lowland gorilla (Gorilla gorilla gorilla), Bornean orangutan (Pongo pygmaeus) and Sumatran orangutan (Pongo abelii)) and a lesser ape (the siamang gibbon (Symphalangus syndactylus)), and untangled the intricacies of their evolution. Compared with the X chromosomes, the ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements—owing to the accumulation of lineage-specific ampliconic regions, palindromes, transposable elements and satellites. Many Y chromosome genes expand in multi-copy families and some evolve under purifying selection. Thus, the Y chromosome exhibits dynamic evolution, whereas the X chromosome is more stable. Mapping short-read sequencing data to these assemblies revealed diversity and selection patterns on sex chromosomes of more than 100 individual great apes. These reference assemblies are expected to inform human evolution and conservation genetics of non-human apes, all of which are endangered species.

Whole-genome DNA methylomes of Tree shrew brains reveal conserved and divergent roles of DNA methylation on sex chromosome regulation

“…5 ), indicating that we are observing reproducible patterns of DNA methylation from the tree shrew Y-chromosome. The observation that the putative Y-linked segments exhibit reduced methylation supports the idea that DNA methylation tends to be reduced in less transcriptionally active regions ( Makova et al, 2024 ) The comprehensive DNA methylome and gene expression data from tree shrews provide new insights into the evolution of genome, methylome and their interactions on the regulation of X chromosomes.…”

Ribosomal DNA arrays are the most H-DNA rich element in the human genome

“…We also downloaded T2T genomes for the following primates 35,36 , Gorilla gorilla, Pan paniscus, Pan troglodytes, Pongo abelii, Pongo pygmaeus and Symphalangus syndactylus from https://github.com/marbl/Primates. Associated files including genome annotations were downloaded from https://github.com/marbl/t2t-browser, from which we also derived annotations for centromere/satellite repeats and gene annotations.…”

“…Other recent efforts to assemble T2T organismal genomes are also ongoing. For instance, recent studies have completed the generation of T2T assemblies for multiple non-human primate species through which we can gain insights into the diversity, evolution and plasticity of different repeats in the primate lineage 35,36 .…”