The DOI matches its Crossref record; 98 of the 98 references it cites were found in a registry or an index.
The structure, function and evolution of a complete human chromosome 8
Open accessAbstract
The complete assembly of each human chromosome is essential for understanding human biology and evolution 1,2 . Here we use complementary long-read sequencing technologies to complete the linear assembly of human chromosome 8. Our assembly resolves the sequence of five previously long-standing gaps, including a 2.08-Mb centromeric α-satellite array, a 644-kb copy number polymorphism in the β-defensin gene cluster that is important for disease risk, and an 863-kb variable number tandem repeat at chromosome 8q21.2 that can function as a neocentromere. We show that the centromeric α-satellite array is generally methylated except for a 73-kb hypomethylated region of diverse higher-order α-satellites enriched with CENP-A nucleosomes, consistent with the location of the kinetochore. In addition, we confirm the overall organization and methylation pattern of the centromere in a diploid human genome. Using a dual long-read sequencing approach, we complete high-quality draft assemblies of the orthologous centromere from chromosome 8 in chimpanzee, orangutan and macaque to reconstruct its evolutionary history. Comparative and phylogenetic analyses show that the higher-order α-satellite structure evolved in the great ape ancestor with a layered symmetry, in which more ancient higher-order repeats locate peripherally to monomeric α-satellites. We estimate that the mutation rate of centromeric satellite DNA is accelerated by more than 2.2-fold compared to the unique portions of the genome, and this acceleration extends into the flanking sequence.
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Cites
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Initial sequencing and analysis of the human genome
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Cited by
The complete sequence of a human genome
Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L., Gershman, A., et al. (2022) · Science · doi:10.1126/science.abj6987 · Cited by 3,136
Self-citationTowards complete and error-free genome assemblies of all vertebrate species
Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Kim, J., et al. (2021) · Nature · doi:10.1038/s41586-021-03451-0 · Cited by 3,097
Self-citationTowards complete and error-free genome assemblies of all vertebrate species
Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Gedman, G. L., et al. (2020) · doi:10.1101/2020.05.22.110833 · Cited by 3,097
Self-citationA draft human pangenome reference.
Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05896-x · Cited by 1,129
“…parts of the pangenome, our initial population-genetic analysis of these regions (Methods) leaves open questions about assembly accuracy and alignment especially in areas of the genome where mutation rates are thought to be an order of magnitude greater (Logsdon et al., 2021).”
BackgroundSelf-citationHaplotype-resolved diverse human genomes and integrated analysis of structural variation
Ebert, P., Audano, P. A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M. J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R., et al. (2021) · Science · doi:10.1126/science.abf7117 · Cited by 702
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Metadata
- Authors
- Logsdon, G. A., Vollger, M. R., Hsieh, P., Mao, Y., Liskovykh, M. A., Koren, S., Nurk, S., Mercuri, L., Dishuck, P. C., Rhie, A., de Lima, L. G., Dvorkina, T., Porubsky, D., Harvey, W. T., Mikheenko, A., Bzikadze, A. V., Kremitzki, M., Graves-Lindsay, T. A., Jain, C., Hoekzema, K., Murali, S. C., Munson, K. M., Baker, C., Sorensen, M., Lewis, A. M., Surti, U., Gerton, J. L., Larionov, V., Ventura, M., Miga, K. H., Phillippy, A. M., & Eichler, E. E.
- Venue
- Nature
- Published
- 2021-04-07
- Volume
- 593
- Issue
- 7857
- Pages
- 101-107
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W3148425969
- Cited by
- 341
- References
- 98
- FWCI
- 37.24
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Logsdon, G. A., Vollger, M. R., Hsieh, P., Mao, Y., Liskovykh, M. A., Koren, S., Nurk, S., Mercuri, L., Dishuck, P. C., Rhie, A., de Lima, L. G., Dvorkina, T., Porubsky, D., Harvey, W. T., Mikheenko, A., Bzikadze, A. V., Kremitzki, M., Graves-Lindsay, T. A., Jain, C., . . . Eichler, E. E. (2021). The structure, function and evolution of a complete human chromosome 8. Nature. https://doi.org/10.1038/s41586-021-03420-7
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