The complete sequence and comparative analysis of ape sex chromosomes

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 infertility 1 . The X chromosome is vital for reproduction and cognition 2 . Variation i...

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Published in:	Nature (London) Vol. 630; no. 8016; pp. 401 - 411
Main 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.
Format:	Journal Article
Language:	English
Published:	London Nature Publishing Group UK 13-06-2024 Nature Publishing Group
Subjects:	38/22 38/23 38/77 38/91 45 45/23 45/77 45/90 45/91 631/114/2785/2302 631/181/2474 631/181/735 631/208/212/2304 631/208/726/649/2157 Animals Apes Assemblies Chimpanzees Chromosomes Comparative analysis Conservation genetics Endangered species Evolution Evolutionary conservation Female Gene mapping Genes Genetics Genomes Gorilla gorilla - genetics Gorilla gorilla gorilla Hominidae - classification Hominidae - genetics Humanities and Social Sciences Humans Hylobates - classification Hylobates - genetics Male Males Monkeys & apes multidisciplinary Mutation Orangutans Palindromes Pan paniscus - genetics Pan troglodytes - genetics Phylogeny Pongo abelii - genetics Pongo pygmaeus - genetics Satellites Science Science (multidisciplinary) Sex Sex chromosomes Telomere - genetics Telomeres X Chromosome - genetics X chromosomes Y Chromosome - genetics Y chromosomes
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Summary:	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 infertility 1 . The X chromosome is vital for reproduction and cognition 2 . 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. Reference assemblies of great ape sex chromosomes show that Y chromosomes are more variable in size and sequence than X chromosomes and provide a resource for studies on human evolution and conservation genetics of non-human apes.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0028-0836 1476-4687 1476-4687
DOI:	10.1038/s41586-024-07473-2