Recombination between heterologous human acrocentric chromosomes
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Abstract
The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share large homologous regions, including ribosomal DNA repeats and extended segmental duplications 1,2 . Although the resolution of these regions in the first complete assembly of a human genome—the Telomere-to-Telomere Consortium’s CHM13 assembly (T2T-CHM13)—provided a model of their homology 3 , it remained unclear whether these patterns were ancestral or maintained by ongoing recombination exchange. Here we show that acrocentric chromosomes contain pseudo-homologous regions (PHRs) indicative of recombination between non-homologous sequences. Utilizing an all-to-all comparison of the human pangenome from the Human Pangenome Reference Consortium 4 (HPRC), we find that contigs from all of the SAACs form a community. A variation graph 5 constructed from centromere-spanning acrocentric contigs indicates the presence of regions in which most contigs appear nearly identical between heterologous acrocentric chromosomes in T2T-CHM13. Except on chromosome 15, we observe faster decay of linkage disequilibrium in the pseudo-homologous regions than in the corresponding short and long arms, indicating higher rates of recombination 6,7 . The pseudo-homologous regions include sequences that have previously been shown to lie at the breakpoint of Robertsonian translocations 8 , and their arrangement is compatible with crossover in inverted duplications on chromosomes 13, 14 and 21. The ubiquity of signals of recombination between heterologous acrocentric chromosomes seen in the HPRC draft pangenome suggests that these shared sequences form the basis for recurrent Robertsonian translocations, providing sequence and population-based confirmation of hypotheses first developed from cytogenetic studies 50 years ago 9 .
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The remaining interchromosomal joins may be the result of misalignment, nonallelic gene conversion or other biological mechanisms that maintain large-scale homology between the short arms of the acrocentrics.
“This may be the result of misalignment, nonallelic gene conversion or other biological mechanisms that maintain large-scale homology between the short arms of the acrocentrics—a phenomenon that we have studied in an associated paper22.”
From A draft human pangenome reference. (2023) · cites this paper as [22]
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Self-citationAnalysis of a Novel Human Protein, ORF3, Encoded by Spacer rDNA
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Self-citationThe paradox of extremely fast evolution driven by genetic drift in multi-copy gene systemsPreprint
Wang, X., Ruan, Y., Zhang, L., Chen, X., Shi, Z., Wang, H., Chen, B., Tracy, M. E., Wu, C.-I., & Wen, H. (2024) · eLife · doi:10.7554/elife.99992.2 · Cited by 1 · see citing works
The paradox of extremely fast evolution driven by genetic drift in multi-copy gene systemsPreprint
Wang, X., Ruan, Y., Zhang, L., Chen, X., Shi, Z., Wang, H., Chen, B., Tracy, M. E., Huang, L.-Y., Wu, C.-I., et al. (2025) · eLife · doi:10.7554/elife.99992.3 · Cited by 1 · see citing works
KaryoScope: rapid, alignment-free sequence annotation for the pangenome eraPreprint
Ranallo-Benavidez, T. R., Chen, Y., Potapova, T., Alanko, J., Loucks, H., Lucas, J., Guarracino, A., Puglisi, S. J., Marchet, C., Miga, K. H., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.15.725544 · Cited by 1 · see citing works
Self-citationThe paradox of extremely fast evolution driven by genetic drift in multi-copy gene systemsPreprint
Wang, X., Ruan, Y., Zhang, L., Chen, X., Chen, B., Tracy, M. E., Huang, L.-Y., Liufu, Z., Wu, C.-I., & Wen, H. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.06.14.545040
- Authors
- Guarracino, A., Buonaiuto, S., de Lima, L. G., Potapova, T., Rhie, A., Koren, S., Rubinstein, B., Fischer, C., Human Pangenome Reference Consortium, Abel, H. J., Antonacci-Fulton, L. L., Asri, M., Baid, G., Baker, C. A., Belyaeva, A., Billis, K., Bourque, G., Carroll, A., Chaisson, M. J. P., Chang, P.-C., Chang, X. H., Cheng, H., Chu, J., Cody, S., Cook, D. E., Cook-Deegan, R. M., Cornejo, O. E., Diekhans, M., Doerr, D., Ebert, P., Ebler, J., Eichler, E. E., Eizenga, J. M., Fairley, S., Fedrigo, O., Felsenfeld, A. L., Feng, X., Flicek, P., Formenti, G., Frankish, A., Fulton, R. S., Gao, Y., Garg, S., Garrison, N. A., Giron, C. G., Green, R. E., Groza, C., Haggerty, L., Hall, I., Harvey, W. T., Haukness, M., Haussler, D., Heumos, S., Hickey, G., Hoekzema, K., Hourlier, T., Howe, K., Jain, M., Jarvis, E. D., Ji, H. P., Kenny, E. E., Koenig, B. A., Kolesnikov, A., Korbel, J. O., Kordosky, J., Lee, H., Lewis, A. P., Li, H., Liao, W.-W., Lu, S., Lu, T.-Y., Lucas, J. K., Magalhães, H., Marco-Sola, S., Marijon, P., Markello, C., Marschall, T., Martin, F. J., McCartney, A., McDaniel, J., Miga, K. H., Mitchell, M. W., Monlong, J., Mountcastle, J., Munson, K. M., Mwaniki, M. N., Nattestad, M., Novak, A. M., Nurk, S., Olsen, H. E., Olson, N. D., Paten, B., Pesout, T., Popejoy, A. B., Porubsky, D., Prins, P., Puiu, D., Rautiainen, M., Regier, A. A., Sacco, S., Sanders, A. D., Schneider, V. A., Schultz, B. I., Shafin, K., Sibbesen, J. A., Sirén, J., Smith, M. W., Sofia, H. J., Tayoun, A. N. A., Thibaud-Nissen, F., Tomlinson, C., Tricomi, F. F., Villani, F., Vollger, M. R., Wagner, J., Walenz, B., Wang, T., Wood, J. M. D., Zimin, A. V., Zook, J. M., Gerton, J. L., Phillippy, A. M., Colonna, V., & Garrison, E.
- Affiliations
- University of Tennessee Health Science Center (US)
- Institute of Genetics and Biophysics (IT)
- Stowers Institute for Medical Research (US)
- National Institutes of Health (US)
- Washington University in St. Louis (US)
- University of California, Santa Cruz (US)
- Google (United States) (US)
- University of Washington (US)
- European Bioinformatics Institute (GB)
- Kyoto University (JP)
- University of Southern California (US)
- Harvard University (US)
- Dana-Farber Cancer Institute (US)
- Washington Center (US)
- Washington State University (US)
- Heinrich Heine University Düsseldorf (DE)
- Howard Hughes Medical Institute (US)
- Rockefeller University (US)
- Children's Hospital of Philadelphia (US)
- Technical University of Denmark (DK)
- University of California, Los Angeles (US)
- McGill University (CA)
- Yale University (US)
- Quantitative Biology Center (DE)
- Wellcome Sanger Institute (GB)
- Northeastern University (US)
- Stanford Medicine (US)
- Icahn School of Medicine at Mount Sinai (US)
- University of California, San Francisco (US)
- European Molecular Biology Laboratory (DE)
- National Institute of Standards and Technology (US)
- Coriell Institute For Medical Research (US)
- University of Pisa (IT)
- University of California, Davis (US)
- Johns Hopkins University (US)
- Max Delbrück Center (DE)
- University of Copenhagen (DK)
- Al Jalila Foundation (AE)
- Corresponding author
- Garrison, Erik
- ORCID
- Guarracino, Andrea
- Buonaiuto, Silvia
- de Lima, Leonardo Gomes
- Potapova, Tamara
- Rhie, Arang
- Koren, Sergey
- Rubinstein, Boris
- Abel, Haley J.
- Asri, Mobin
- Baid, Gunjan
- Belyaeva, Anastasiya
- Billis, Konstantinos
- Bourque, Guillaume
- Carroll, Andrew
- Chaisson, Mark J. P.
- Chang, Pi-Chuan
- Chang, Xian H.
- Cheng, Haoyu
- Chu, Justin
- Cook, Daniel E.
- Cook-Deegan, Robert M.
- Cornejo, Omar E.
- Diekhans, Mark
- Doerr, Daniel
- Ebert, Peter
- Ebler, Jana
- Eichler, Evan E.
- Eizenga, Jordan M.
- Fairley, Susan
- Fedrigo, Olivier
- Feng, Xiaowen
- Flicek, Paul
- Formenti, Giulio
- Frankish, Adam
- Fulton, Robert S.
- Gao, Yan
- Garg, Shilpa
- Garrison, Nanibaa’ A.
- Green, Richard E.
- Groza, Cristian
- Haggerty, Leanne
- Hall, Ira
- Harvey, William T.
- Haukness, Marina
- Haussler, David
- Heumos, Simon
- Hickey, Glenn
- Hoekzema, Kendra
- Hourlier, Thibaut
- Howe, Kerstin
- Jain, Miten
- Jarvis, Erich D.
- Ji, Hanlee P.
- Kenny, Eimear E.
- Koenig, Barbara A.
- Kolesnikov, Alexey
- Korbel, Jan O.
- Lee, HoJoon
- Lewis, Alexandra P.
- Li, Heng
- Liao, Wen-Wei
- Lu, Shuangjia
- Lu, Tsung-Yu
- Lucas, Julian K.
- Magalhães, Hugo
- Marijon, Pierre
- Markello, Charles
- Marschall, Tobias
- Martin, Fergal J.
- McDaniel, Jennifer
- Miga, Karen H.
- Mitchell, Matthew W.
- Monlong, Jean
- Mountcastle, Jacquelyn
- Munson, Katherine M.
- Mwaniki, Moses Njagi
- Nattestad, Maria
- Novak, Adam M.
- Nurk, Sergey
- Olsen, Hugh E.
- Olson, Nathan D.
- Paten, Benedict
- Pesout, Trevor
- Popejoy, Alice B.
- Prins, Pjotr
- Puiu, Daniela
- Rautiainen, Mikko
- Regier, Allison A.
- Sacco, Samuel
- Sanders, Ashley D.
- Shafin, Kishwar
- Sibbesen, Jonas A.
- Sirén, Jouni
- Smith, Michael W.
- Sofia, Heidi J.
- Tayoun, Ahmad N. Abou
- Tomlinson, Chad
- Tricomi, Francesca Floriana
- Villani, Flavia
- Vollger, Mitchell R.
- Wagner, Justin
- Walenz, Brian
- Wang, Ting
- Wood, Jonathan M. D.
- Zimin, Aleksey V.
- Zook, Justin M.
- Gerton, Jennifer L.
- Phillippy, Adam M.
- Colonna, Vincenza
- Garrison, Erik
- Venue
- Nature
- Published
- 2023-05-10
- Volume
- 617
- Issue
- 7960
- Pages
- 335-343
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC10172130
- OpenAlex
- W4376132855
- Cited by
- 134
- References
- 67
- Citations by year
- 2026: 32 · 2025: 42 · 2024: 39 · 2023: 21
- FWCI
- 21.05
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Nature (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- UPCommons institutional repository (Universitat Politècnica de Catalunya) (submittedVersion, cc-by-nc-nd)
- Funders
- National Science Foundation (2118709)
- Stowers Institute for Medical Research
- Consiglio Nazionale delle Ricerche
- National Institutes of Health
- High Performance Research Computing, Texas A and M University
- National Institute on Drug Abuse (NIDA U01DA047638, U01DA047638)
- National Human Genome Research Institute (U01HG010963, U01HG010971, U24HG010262)
- National Cancer Institute (R01CA266339)
- National Institute of General Medical Sciences (R01GM123489)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Keywords
- acrocentric chromosomes, recombination, ribosomal DNA repeats, segmental duplication, Robertsonian translocation, linkage disequilibrium, inverted duplication, centromere, human pangenome, T2T-CHM13, Human Pangenome Reference Consortium, crossover
- MeSH terms
- Centromere, Chromosomes, Human, Cytogenetics, DNA, Ribosomal, Humans, Recombination, Genetic, Translocation, Genetic, Telomere
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