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The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes.
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; Bomberg, 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; Kosakovsky Pond, Sergei L; LaPolice, Troy M; Lee, Charles; Lewis, Alexandra P; Loh, Yong-Hwee E; Masterson, Patrick; McCoy, Rajiv C; Medvedev, Paul; Miga, Karen H; Munson, Katherine M; Pak, Evgenia.
Afiliación
  • Makova KD; Penn State University, University Park, PA, USA.
  • Pickett BD; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
  • Harris RS; Penn State University, University Park, PA, USA.
  • Hartley GA; University of Connecticut, Storrs, CT, USA.
  • Cechova M; University of California Santa Cruz, Santa Cruz, CA, USA.
  • Pal K; Penn State University, University Park, PA, USA.
  • Nurk S; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
  • Yoo D; University of Washington School of Medicine, Seattle, WA, USA.
  • Li Q; Johns Hopkins University, Baltimore, MD, USA.
  • Hebbar P; University of California Santa Cruz, Santa Cruz, CA, USA.
  • McGrath BC; Penn State University, University Park, PA, USA.
  • Antonacci F; Università degli Studi di Bari Aldo Moro, Italy.
  • Aubel M; University of Münster, Münster, Germany.
  • Biddanda A; Johns Hopkins University, Baltimore, MD, USA.
  • Borchers M; Stowers Institute, Kansas City, MO, USA.
  • Bomberg E; University of Münster, Münster, Germany.
  • Bouffard GG; MPI for Developmental Biology, Tübingen, Germany.
  • Brooks SY; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
  • Carbone L; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
  • Carrel L; Oregon Health & Science University, Portland, OR, USA.
  • Carroll A; Oregon National Primate Research Center, Hillsboro, OR, USA.
  • Chang PC; Penn State University School of Medicine, Hershey, PA, USA.
  • Chin CS; Google, Mountain View, CA, USA.
  • Cook DE; Google, Mountain View, CA, USA.
  • Craig SJC; Foundation of Biological Data Sciences, Belmont, CA, USA.
  • de Gennaro L; Google, Mountain View, CA, USA.
  • Diekhans M; Penn State University, University Park, PA, USA.
  • Dutra A; Università degli Studi di Bari Aldo Moro, Italy.
  • Garcia GH; University of California Santa Cruz, Santa Cruz, CA, USA.
  • Grady PGS; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
  • Green RE; University of Washington School of Medicine, Seattle, WA, USA.
  • Haddad D; University of Connecticut, Storrs, CT, USA.
  • Hallast P; University of California Santa Cruz, Santa Cruz, CA, USA.
  • Harvey WT; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
  • Hickey G; The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
  • Hillis DA; University of Washington School of Medicine, Seattle, WA, USA.
  • Hoyt SJ; University of California Santa Cruz, Santa Cruz, CA, USA.
  • Jeong H; University of California Santa Barbara, Santa Barbara, CA, USA.
  • Kamali K; University of Connecticut, Storrs, CT, USA.
  • Kosakovsky Pond SL; University of Washington School of Medicine, Seattle, WA, USA.
  • LaPolice TM; Penn State University, University Park, PA, USA.
  • Lee C; Temple University, Philadelphia, PA, USA.
  • Lewis AP; Penn State University, University Park, PA, USA.
  • Loh YE; The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
  • Masterson P; University of Washington School of Medicine, Seattle, WA, USA.
  • McCoy RC; University of California Santa Barbara, Santa Barbara, CA, USA.
  • Medvedev P; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
  • Miga KH; Johns Hopkins University, Baltimore, MD, USA.
  • Munson KM; Penn State University, University Park, PA, USA.
  • Pak E; University of California Santa Cruz, Santa Cruz, CA, USA.
bioRxiv ; 2023 Dec 01.
Article en En | MEDLINE | ID: mdl-38077089
ABSTRACT
Apes possess two sex chromosomes-the male-specific Y and the X shared by males and females. The Y chromosome is crucial for male reproduction, with deletions linked to infertility. The X chromosome carries genes vital for reproduction and cognition. Variation in mating patterns and brain function among great apes suggests corresponding differences in their sex chromosome structure and evolution. However, due to their highly repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the state-of-the-art experimental and computational methods developed for the telomere-to-telomere (T2T) human genome, we produced gapless, complete assemblies of the X and Y chromosomes for five great apes (chimpanzee, bonobo, gorilla, Bornean and Sumatran orangutans) and a lesser ape, the siamang gibbon. These assemblies completely resolved ampliconic, palindromic, and satellite sequences, including the entire centromeres, allowing us to untangle the intricacies of ape sex chromosome evolution. We found that, compared to the X, ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements. This divergence on the Y arises from the accumulation of lineage-specific ampliconic regions and palindromes (which are shared more broadly among species on the X) and from the abundance of transposable elements and satellites (which have a lower representation on the X). Our analysis of Y chromosome genes revealed lineage-specific expansions of multi-copy gene families and signatures of purifying selection. In summary, the Y exhibits dynamic evolution, while the X is more stable. Finally, mapping short-read sequencing data from >100 great ape individuals revealed the patterns of diversity and selection on their sex chromosomes, demonstrating the utility of these reference assemblies for studies of great ape evolution. These complete sex chromosome assemblies are expected to further inform conservation genetics of nonhuman apes, all of which are endangered species.
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Texto completo: 1 Banco de datos: MEDLINE Idioma: En Revista: BioRxiv Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
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XML
PubMed Links
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Texto completo: 1 Banco de datos: MEDLINE Idioma: En Revista: BioRxiv Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos