@article {329985,
	title = {The complete sequence and comparative analysis of ape sex chromosomes},
	journal = {Nature},
	year = {2024},
	month = {2024/05/29},
	abstract = {<p>Apes possess two sex chromosomes\&mdash;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\&nbsp;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\&mdash;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.</p>
},
	isbn = {1476-4687},
	doi = {https://doi.org/10.1038/s41586-024-07473-2},
	url = {https://www.nature.com/articles/s41586-024-07473-2},
	author = {Makova, Kateryna D. and Pickett, Brandon D. and Harris, Robert S. and Hartley, Gabrielle A. and Cechova, Monika and Pal, Karol and Nurk, Sergey and Yoo, DongAhn and Li, Qiuhui and Hebbar, Prajna and McGrath, Barbara C. and Antonacci, Francesca and Aubel, Margaux and Biddanda, Arjun and Borchers, Matthew and Bornberg-Bauer, Erich and Bouffard, Gerard G. and Brooks, Shelise Y. and Carbone, Lucia and Carrel, Laura and Carroll, Andrew and Chang, Pi-Chuan and Chin, Chen-Shan and Cook, Daniel E. and Craig, Sarah J. C. and de Gennaro, Luciana and Diekhans, Mark and Dutra, Amalia and Garcia, Gage H. and Grady, Patrick G. S. and Green, Richard E. and Haddad, Diana and Hallast, Pille and Harvey, William T. and Hickey, Glenn and Hillis, David A. and Hoyt, Savannah J. and Jeong, Hyeonsoo and Kamali, Kaivan and Pond, Sergei L. Kosakovsky and LaPolice, Troy M. and Lee, Charles and Lewis, Alexandra P. and Loh, Yong-Hwee E. and Masterson, Patrick and McGarvey, Kelly M. and McCoy, Rajiv C. and Medvedev, Paul and Miga, Karen H. and Munson, Katherine M. and Pak, Evgenia and Paten, Benedict and Pinto, Brendan J. and Potapova, Tamara and Rhie, Arang and Rocha, Joana L. and Ryabov, Fedor and Ryder, Oliver A. and Sacco, Samuel and Shafin, Kishwar and Shepelev, Valery A. and Slon, Viviane and Solar, Steven J. and Storer, Jessica M. and Sudmant, Peter H. and Sweetalana and Sweeten, Alex and Tassia, Michael G. and Thibaud-Nissen, Fran{\c c}oise and Ventura, Mario and Wilson, Melissa A. and Young, Alice C. and Zeng, Huiqing and Zhang, Xinru and Szpiech, Zachary A. and Huber, Christian D. and Gerton, Jennifer L. and Yi, Soojin V. and Schatz, Michael C. and Alexandrov, Ivan A. and Koren, Sergey and O{\textquoteright}Neill, Rachel J. and Eichler, Evan E. and Phillippy, Adam M.}
}
