The complete sequence and comparative analysis of ape sex chromosomes

• 成果类型: Article
• 署名作者: 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.; Sweeten, Alex; Tassia, Michael G.; Thibaud-Nissen, Francoise; 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.
• 署名单位: Pennsylvania Commonwealth System of Higher Education (PCSHE); Pennsylvania State University; Pennsylvania State University - University Park; National Institutes of Health (NIH) - USA; NIH National Human Genome Research Institute (NHGRI); University of Connecticut; University of California System; University of California Santa Cruz; University of Washington; University of Washington Seattle; Johns Hopkins University; Universita degli Studi di Bari Aldo Moro; University of Munster; Stowers Institute for Medical Research; Oregon Health & Science University; Oregon Health & Science University; Oregon National Primate Research Center; Pennsylvania Commonwealth System of Higher Education (PCSHE); Pennsylvania State University; Penn State Health; Alphabet Inc.; Google Incorporated; National Institutes of Health (NIH) - USA; NIH National Library of Medicine (NLM); Jackson Laboratory; University of California System; University of California Santa Barbara; Pennsylvania Commonwealth System of Higher Education (PCSHE); Temple University; Arizona State University; Arizona State University-Tempe; University of California System; University of California Berkeley; HSE University (National Research University Higher School of Economics); Zoological Society of San Diego; Tel Aviv University; Howard Hughes Medical Institute; University of Washington; University of Washington Seattle
• 刊物名称: Nature
• ISSN/ISSBN: 0028-5052
• DOI: 10.1038/s41586-024-07473-2
• 发表日期: 2024-06-01
• 页码: 70-+
• 关键词: mammalian y-chromosomes; genetic-variation; dna methylation; copy number; rna genes; EVOLUTION; palindromes; diversity; heterochromatin; degeneration

摘要

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.