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For: Greve G, Alechine E, Pasantes JJ, Hodler C, Rietschel W, Robinson TJ, Schempp W. Y-Chromosome variation in hominids: intraspecific variation is limited to the polygamous chimpanzee. PLoS One 2011;6:e29311. [PMID: 22216243 PMCID: PMC3246485 DOI: 10.1371/journal.pone.0029311] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 11/25/2011] [Indexed: 11/23/2022] Open

For:	Greve G, Alechine E, Pasantes JJ, Hodler C, Rietschel W, Robinson TJ, Schempp W. Y-Chromosome variation in hominids: intraspecific variation is limited to the polygamous chimpanzee. PLoS One 2011;6:e29311. [PMID: 22216243 PMCID: PMC3246485 DOI: 10.1371/journal.pone.0029311] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 11/25/2011] [Indexed: 11/23/2022] Open

Number

Cited by Other Article(s)

Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, Bornberg-Bauer E, Bouffard GG, Brooks SY, Carbone L, Carrel L, Carroll A, Chang PC, Chin CS, Cook DE, Craig SJC, de Gennaro L, Diekhans M, Dutra A, Garcia GH, Grady PGS, Green RE, Haddad D, Hallast P, Harvey WT, Hickey G, Hillis DA, Hoyt SJ, Jeong H, Kamali K, Pond SLK, LaPolice TM, Lee C, Lewis AP, Loh YHE, Masterson P, McGarvey KM, McCoy RC, Medvedev P, Miga KH, Munson KM, Pak E, Paten B, Pinto BJ, Potapova T, Rhie A, Rocha JL, Ryabov F, Ryder OA, Sacco S, Shafin K, Shepelev VA, Slon V, Solar SJ, Storer JM, Sudmant PH, Sweetalana, Sweeten A, Tassia MG, Thibaud-Nissen F, Ventura M, Wilson MA, Young AC, Zeng H, Zhang X, Szpiech ZA, Huber CD, Gerton JL, Yi SV, Schatz MC, Alexandrov IA, Koren S, O'Neill RJ, Eichler EE, Phillippy AM. The complete sequence and comparative analysis of ape sex chromosomes. Nature 2024;630:401-411. [PMID: 38811727 PMCID: PMC11168930 DOI: 10.1038/s41586-024-07473-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/26/2024] [Indexed: 05/31/2024]

Affiliation(s)

Kateryna D Makova Penn State University, University Park, PA, USA.
Brandon D Pickett National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Robert S Harris Penn State University, University Park, PA, USA
Gabrielle A Hartley University of Connecticut, Storrs, CT, USA
Monika Cechova University of California Santa Cruz, Santa Cruz, CA, USA
Karol Pal Penn State University, University Park, PA, USA
Sergey Nurk National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
DongAhn Yoo University of Washington School of Medicine, Seattle, WA, USA
Qiuhui Li Johns Hopkins University, Baltimore, MD, USA
Prajna Hebbar University of California Santa Cruz, Santa Cruz, CA, USA
Barbara C McGrath Penn State University, University Park, PA, USA
Francesca Antonacci Università degli Studi di Bari Aldo Moro, Bari, Italy
Margaux Aubel University of Münster, Münster, Germany
Arjun Biddanda Johns Hopkins University, Baltimore, MD, USA
Matthew Borchers Stowers Institute, Kansas City, MO, USA
Erich Bornberg-Bauer University of Münster, Münster, Germany MPI for Developmental Biology, Tübingen, Germany
Gerard G Bouffard National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Shelise Y Brooks National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Lucia Carbone Oregon Health and Science University, Portland, OR, USA Oregon National Primate Research Center, Hillsboro, OR, USA
Laura Carrel Penn State University School of Medicine, Hershey, PA, USA
Andrew Carroll Google, Mountain View, CA, USA
Pi-Chuan Chang Google, Mountain View, CA, USA
Chen-Shan Chin Foundation of Biological Data Sciences, Belmont, CA, USA
Daniel E Cook Google, Mountain View, CA, USA
Sarah J C Craig Penn State University, University Park, PA, USA
Luciana de Gennaro Università degli Studi di Bari Aldo Moro, Bari, Italy
Mark Diekhans University of California Santa Cruz, Santa Cruz, CA, USA
Amalia Dutra National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Gage H Garcia University of Washington School of Medicine, Seattle, WA, USA
Patrick G S Grady University of Connecticut, Storrs, CT, USA
Richard E Green University of California Santa Cruz, Santa Cruz, CA, USA
Diana Haddad National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
Pille Hallast The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
William T Harvey University of Washington School of Medicine, Seattle, WA, USA
Glenn Hickey University of California Santa Cruz, Santa Cruz, CA, USA
David A Hillis University of California Santa Barbara, Santa Barbara, CA, USA
Savannah J Hoyt University of Connecticut, Storrs, CT, USA
Hyeonsoo Jeong University of Washington School of Medicine, Seattle, WA, USA
Kaivan Kamali Penn State University, University Park, PA, USA
Sergei L Kosakovsky Pond Temple University, Philadelphia, PA, USA
Troy M LaPolice Penn State University, University Park, PA, USA
Charles Lee The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
Alexandra P Lewis University of Washington School of Medicine, Seattle, WA, USA
Yong-Hwee E Loh University of California Santa Barbara, Santa Barbara, CA, USA
Patrick Masterson National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
Kelly M McGarvey National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
Rajiv C McCoy Johns Hopkins University, Baltimore, MD, USA
Paul Medvedev Penn State University, University Park, PA, USA
Karen H Miga University of California Santa Cruz, Santa Cruz, CA, USA
Katherine M Munson University of Washington School of Medicine, Seattle, WA, USA
Evgenia Pak National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Benedict Paten University of California Santa Cruz, Santa Cruz, CA, USA
Brendan J Pinto Arizona State University, Tempe, AZ, USA
Tamara Potapova Stowers Institute, Kansas City, MO, USA
Arang Rhie National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Joana L Rocha University of California Berkeley, Berkeley, CA, USA
Fedor Ryabov Masters Program in National Research, University Higher School of Economics, Moscow, Russia
Oliver A Ryder San Diego Zoological Society, San Diego, CA, USA
Samuel Sacco University of California Santa Cruz, Santa Cruz, CA, USA
Kishwar Shafin Google, Mountain View, CA, USA
Valery A Shepelev Institute of Molecular Genetics, Moscow, Russia
Viviane Slon Tel Aviv University, Tel Aviv, Israel
Steven J Solar National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Jessica M Storer University of Connecticut, Storrs, CT, USA
Peter H Sudmant University of California Berkeley, Berkeley, CA, USA
Sweetalana Penn State University, University Park, PA, USA
Alex Sweeten National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA Johns Hopkins University, Baltimore, MD, USA
Michael G Tassia Johns Hopkins University, Baltimore, MD, USA
Françoise Thibaud-Nissen National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
Mario Ventura Università degli Studi di Bari Aldo Moro, Bari, Italy
Melissa A Wilson Arizona State University, Tempe, AZ, USA
Alice C Young National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Huiqing Zeng Penn State University, University Park, PA, USA
Xinru Zhang Penn State University, University Park, PA, USA
Zachary A Szpiech Penn State University, University Park, PA, USA
Christian D Huber Penn State University, University Park, PA, USA
Jennifer L Gerton Stowers Institute, Kansas City, MO, USA
Soojin V Yi University of California Santa Barbara, Santa Barbara, CA, USA
Michael C Schatz Johns Hopkins University, Baltimore, MD, USA
Ivan A Alexandrov Tel Aviv University, Tel Aviv, Israel
Sergey Koren National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Rachel J O'Neill University of Connecticut, Storrs, CT, USA
Evan E Eichler University of Washington School of Medicine, Seattle, WA, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
Adam M Phillippy National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.

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Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, Bomberg E, Bouffard GG, Brooks SY, Carbone L, Carrel L, Carroll A, Chang PC, Chin CS, Cook DE, Craig SJ, de Gennaro L, Diekhans M, Dutra A, Garcia GH, Grady PG, Green RE, Haddad D, Hallast P, Harvey WT, Hickey G, Hillis DA, Hoyt SJ, Jeong H, Kamali K, Kosakovsky Pond SL, LaPolice TM, Lee C, Lewis AP, Loh YHE, Masterson P, McCoy RC, Medvedev P, Miga KH, Munson KM, Pak E, Paten B, Pinto BJ, Potapova T, Rhie A, Rocha JL, Ryabov F, Ryder OA, Sacco S, Shafin K, Shepelev VA, Slon V, Solar SJ, Storer JM, Sudmant PH, Sweetalana, Sweeten A, Tassia MG, Thibaud-Nissen F, Ventura M, Wilson MA, Young AC, Zeng H, Zhang X, Szpiech ZA, Huber CD, Gerton JL, Yi SV, Schatz MC, Alexandrov IA, Koren S, O’Neill RJ, Eichler E, Phillippy AM. The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569198. [PMID: 38077089 PMCID: PMC10705393 DOI: 10.1101/2023.11.30.569198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]

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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Affiliation(s)

Kateryna D. Makova Penn State University, University Park, PA, USA
Brandon D. Pickett National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Robert S. Harris Penn State University, University Park, PA, USA
Gabrielle A. Hartley University of Connecticut, Storrs, CT, USA
Monika Cechova University of California Santa Cruz, Santa Cruz, CA, USA
Karol Pal Penn State University, University Park, PA, USA
Sergey Nurk National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
DongAhn Yoo University of Washington School of Medicine, Seattle, WA, USA
Qiuhui Li Johns Hopkins University, Baltimore, MD, USA
Prajna Hebbar University of California Santa Cruz, Santa Cruz, CA, USA
Barbara C. McGrath Penn State University, University Park, PA, USA
Francesca Antonacci Università degli Studi di Bari Aldo Moro, Italy
Margaux Aubel University of Münster, Münster, Germany
Arjun Biddanda Johns Hopkins University, Baltimore, MD, USA
Matthew Borchers Stowers Institute, Kansas City, MO, USA
Erich Bomberg University of Münster, Münster, Germany MPI for Developmental Biology, Tübingen, Germany
Gerard G. Bouffard National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Shelise Y. Brooks National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Lucia Carbone Oregon Health & Science University, Portland, OR, USA Oregon National Primate Research Center, Hillsboro, OR, USA
Laura Carrel Penn State University School of Medicine, Hershey, PA, USA
Andrew Carroll Google, Mountain View, CA, USA
Pi-Chuan Chang Google, Mountain View, CA, USA
Chen-Shan Chin Foundation of Biological Data Sciences, Belmont, CA, USA
Daniel E. Cook Google, Mountain View, CA, USA
Sarah J.C. Craig Penn State University, University Park, PA, USA
Luciana de Gennaro Università degli Studi di Bari Aldo Moro, Italy
Mark Diekhans University of California Santa Cruz, Santa Cruz, CA, USA
Amalia Dutra National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Gage H. Garcia University of Washington School of Medicine, Seattle, WA, USA
Patrick G.S. Grady University of Connecticut, Storrs, CT, USA
Richard E. Green University of California Santa Cruz, Santa Cruz, CA, USA
Diana Haddad National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
Pille Hallast The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
William T. Harvey University of Washington School of Medicine, Seattle, WA, USA
Glenn Hickey University of California Santa Cruz, Santa Cruz, CA, USA
David A. Hillis University of California Santa Barbara, Santa Barbara, CA, USA
Savannah J. Hoyt University of Connecticut, Storrs, CT, USA
Hyeonsoo Jeong University of Washington School of Medicine, Seattle, WA, USA
Kaivan Kamali Penn State University, University Park, PA, USA
Sergei L. Kosakovsky Pond Temple University, Philadelphia, PA, USA
Troy M. LaPolice Penn State University, University Park, PA, USA
Charles Lee The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
Alexandra P. Lewis University of Washington School of Medicine, Seattle, WA, USA
Yong-Hwee E. Loh University of California Santa Barbara, Santa Barbara, CA, USA
Patrick Masterson National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
Rajiv C. McCoy Johns Hopkins University, Baltimore, MD, USA
Paul Medvedev Penn State University, University Park, PA, USA
Karen H. Miga University of California Santa Cruz, Santa Cruz, CA, USA
Katherine M. Munson University of Washington School of Medicine, Seattle, WA, USA
Evgenia Pak National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Benedict Paten University of California Santa Cruz, Santa Cruz, CA, USA
Brendan J. Pinto Arizona State University, Tempe, AZ, USA
Tamara Potapova Stowers Institute, Kansas City, MO, USA
Arang Rhie National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Joana L. Rocha University of California Berkeley, Berkeley, CA, USA
Fedor Ryabov Masters Program in National Research University Higher School of Economics, Moscow, Russia
Oliver A. Ryder San Diego Zoological Society, San Diego, CA, USA
Samuel Sacco University of California Santa Cruz, Santa Cruz, CA, USA
Kishwar Shafin Google, Mountain View, CA, USA
Valery A. Shepelev Institute of Molecular Genetics, Moscow, Russia
Viviane Slon Tel Aviv University, Israel
Steven J. Solar National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Jessica M. Storer University of Connecticut, Storrs, CT, USA
Peter H. Sudmant University of California Berkeley, Berkeley, CA, USA
Sweetalana Penn State University, University Park, PA, USA
Alex Sweeten National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA Johns Hopkins University, Baltimore, MD, USA
Michael G. Tassia Johns Hopkins University, Baltimore, MD, USA
Françoise Thibaud-Nissen National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
Mario Ventura Università degli Studi di Bari Aldo Moro, Italy
Melissa A. Wilson Arizona State University, Tempe, AZ, USA
Alice C. Young National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Huiqing Zeng Penn State University, University Park, PA, USA
Xinru Zhang Penn State University, University Park, PA, USA
Zachary A. Szpiech Penn State University, University Park, PA, USA
Christian D. Huber Penn State University, University Park, PA, USA
Jennifer L. Gerton Stowers Institute, Kansas City, MO, USA
Soojin V. Yi University of California Santa Barbara, Santa Barbara, CA, USA
Michael C. Schatz Johns Hopkins University, Baltimore, MD, USA
Ivan A. Alexandrov Tel Aviv University, Israel
Sergey Koren National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Rachel J. O’Neill University of Connecticut, Storrs, CT, USA
Evan Eichler University of Washington School of Medicine, Seattle, WA, USA Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
Adam M. Phillippy National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA

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Vegesna R, Tomaszkiewicz M, Ryder OA, Campos-Sánchez R, Medvedev P, DeGiorgio M, Makova KD. Ampliconic Genes on the Great Ape Y Chromosomes: Rapid Evolution of Copy Number but Conservation of Expression Levels. Genome Biol Evol 2021;12:842-859. [PMID: 32374870 PMCID: PMC7313670 DOI: 10.1093/gbe/evaa088] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2020] [Indexed: 12/16/2022] Open

The Y chromosomes of the great apes. Hum Genet 2017;136:511-528. [PMID: 28265767 DOI: 10.1007/s00439-017-1769-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 02/19/2017] [Indexed: 12/22/2022]

Ghenu AH, Bolker BM, Melnick DJ, Evans BJ. Multicopy gene family evolution on primate Y chromosomes. BMC Genomics 2016;17:157. [PMID: 26925773 PMCID: PMC4772468 DOI: 10.1186/s12864-015-2187-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 11/02/2015] [Indexed: 12/12/2022] Open

Abstract

Background

The primate Y chromosome is distinguished by a lack of inter-chromosomal recombination along most of its length, extensive gene loss, and a prevalence of repetitive elements. A group of genes on the male-specific portion of the Y chromosome known as the “ampliconic genes” are present in multiple copies that are sometimes part of palindromes, and that undergo a form of intra-chromosomal recombination called gene conversion, wherein the nucleotides of one copy are homogenized by those of another. With the aim of further understanding gene family evolution of these genes, we collected nucleotide sequence and gene copy number information for several species of papionin monkey. We then tested for evidence of gene conversion, and developed a novel statistical framework to evaluate alternative models of gene family evolution using our data combined with other information from a human, a chimpanzee, and a rhesus macaque.

Results

Our results (i) recovered evidence for several novel examples of gene conversion in papionin monkeys and indicate that (ii) ampliconic gene families evolve faster than autosomal gene families and than single-copy genes on the Y chromosome and that (iii) Y-linked singleton and autosomal gene families evolved faster in humans and chimps than they do in the other Old World Monkey lineages we studied.

Conclusions

Rapid evolution of ampliconic genes cannot be attributed solely to residence on the Y chromosome, nor to variation between primate lineages in the rate of gene family evolution. Instead other factors, such as natural selection and gene conversion, appear to play a role in driving temporal and genomic evolutionary heterogeneity in primate gene families.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2187-8) contains supplementary material, which is available to authorized users.

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Pratas D, Silva RM, Pinho AJ, Ferreira PJ. An alignment-free method to find and visualise rearrangements between pairs of DNA sequences. Sci Rep 2015;5:10203. [PMID: 25984837 PMCID: PMC4434998 DOI: 10.1038/srep10203] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 04/07/2015] [Indexed: 12/19/2022] Open