The complete sequence and comparative analysis of ape sex chromosomes
Authors: Makova Kateryna D. , Pickett Brandon D. , Harris Robert S. , Hartley Gabrielle A. , Cechova Monika , Pal Karol , Nurk Sergey , Yoo DongAhn , Li Qiuhui , Hebbar Prajna , McGrath Barbara C. , Antonacci Francesca , Aubel Margaux , Biddanda Arjun , Borchers Matthew , Bornberg-Bauer Erich , Bouffard Gerard G. , Brooks Shelise Y. , Carbone Lucia , Carrel Laura , Carroll Andrew , Chang Pi-Chuan , Chin Chen-Shan , Cook Daniel E. , Craig Sarah J. C. , de Gennaro Luciana , Diekhans Mark , Dutra Amalia , Garcia Gage H. , Grady Patrick G. S. , Green Richard E. , Haddad Diana , Hallast Pille , Harvey William T. , Hickey Glenn , Hillis David A. , Hoyt Savannah J. , Jeong Hyeonsoo , Kamali Kaivan , Pond Sergei L. Kosakovsky , LaPolice Troy M. , Lee Charles , Lewis Alexandra P. , Loh Yong-Hwee E. , Masterson Patrick , McGarvey Kelly M. , McCoy Rajiv C. , Medvedev Paul , Miga Karen H. , Munson Katherine M. , Pak Evgenia , Paten Benedict , Pinto Brendan J. , Potapova Tamara , Rhie Arang , Rocha Joana L. , Ryabov Fedor , Ryder Oliver A. , Sacco Samuel , Shafin Kishwar , Shepelev Valery A. , Slon Viviane , Solar Steven J. , Storer Jessica M. , Sudmant Peter H. , Sweetalana  , Sweeten Alex , Tassia Michael G. , Thibaud-Nissen Françoise , Ventura Mario , Wilson Melissa A. , Young Alice C. , Zeng Huiqing , Zhang Xinru , Szpiech Zachary A. , Huber Christian D. , Gerton Jennifer L. , Yi Soojin V. , Schatz Michael C. , Alexandrov Ivan A. , Koren Sergey , O’Neill Rachel J. , Eichler Evan E. , Phillippy Adam M. 
Published: May 2024

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.