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Cited by 350Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalitiesChromosomal and Genetic Variations

High-resolution comparative analysis of great ape genomes

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Kronenberg, Zev N., Fiddes, Ian T., Gordon, David, Murali, Shwetha, Cantsilieris, Stuart, Meyerson, Olivia S., Underwood, Jason G., Nelson, Bradley J. +36 more·2018·Science
DOI 10.1126/science.aar6343PMC PMC6178954
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Abstract

A spotlight on great ape genomes: Most nonhuman primate genomes generated to date have been “humanized” owing to their many gaps and the reliance on guidance by the reference human genome. To remove this humanizing effect, Kronenberg et al. generated and assembled long-read genomes of a chimpanzee, an orangutan, and two humans and compared them with a previously generated gorilla genome. This analysis recognized genomic structural variation specific to humans and particular ape lineages. Comparisons between human and chimpanzee cerebral organoids showed down-regulation of the expression of specific genes in humans, relative to chimpanzees, related to noncoding variation identified in this analysis. Science , this issue p. eaar6343

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  • Progressive Cactus has been developed over several years and has already been successfully used as an integral component of high-profile comparative genomics projects.

    “Progressive Cactus has been developed over several years, and has already been successfully used as an integral component of high-profile comparative genomics projects16–20.”

    From Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020) · cites this paper as [20]

    The Results (Comparative sequence analyses; page unavailable) describe a five-way great ape genome alignment, but do not identify Progressive Cactus as a component. Searches for “Progressive Cactus” and “Cactus alignments” found only a reference to an earlier Cactus paper, not evidence that this project used Progressive Cactus or that it had been developed over several years. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

  • Progressive Cactus has already proved useful for comparison between assemblies of the same species.

    “Progressive Cactus has already proved useful for comparison between assemblies of the same species20.”

    From Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020) · cites this paper as [20]

    The Abstract and Results (Comparative sequence analyses; page unavailable) describe comparisons involving two human assemblies, but do not say Progressive Cactus was used. Searches for “Progressive Cactus,” “Cactus,” and same-species assembly alignment found only a Cactus citation in the References, not evidence of its usefulness for this comparison. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

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Authors
Kronenberg, Z. N., Fiddes, I. T., Gordon, D., Murali, S., Cantsilieris, S., Meyerson, O. S., Underwood, J. G., Nelson, B. J., Chaisson, M. J. P., Dougherty, M. L., Munson, K. M., Hastie, A. R., Diekhans, M., Hormozdiari, F., Lorusso, N., Hoekzema, K., Qiu, R., Clark, K., Raja, A., Welch, A. E., Sorensen, M., Baker, C., Fulton, R. S., Armstrong, J., Graves-Lindsay, T. A., Denli, A. M., Hoppe, E. R., Hsieh, P., Hill, C. M., Pang, A. W. C., Lee, J., Lam, E. T., Dutcher, S. K., Gage, F. H., Warren, W. C., Shendure, J., Haussler, D., Schneider, V. A., Cao, H., Ventura, M., Wilson, R. K., Paten, B., Pollen, A., & Eichler, E. E.
Affiliations
  • University of Washington (US)
  • University of California, Santa Cruz (US)
  • Howard Hughes Medical Institute (US)
  • University of California, San Francisco (US)
  • University of Southern California (US)
  • BioNano Genomics (United States) (US)
  • University of California, Davis (US)
  • University of Bari Aldo Moro (IT)
  • National Institutes of Health (US)
  • Washington University in St. Louis (US)
  • Salk Institute for Biological Studies (US)
  • National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Corresponding author
  • Fiddes, Ian T.
  • Gordon, David
  • Murali, Shwetha
  • Cantsilieris, Stuart
  • Meyerson, Olivia S.
  • Underwood, Jason G.
  • Nelson, Bradley J.
  • Eichler, Evan E.
ORCID
Venue
Science
Publisher
American Association for the Advancement of Science (AAAS)
Published
2018-06-08
Volume
360
Issue
6393
ISSN
  • 0036-8075 (ISSN-L)
  • 1095-9203
DOI
10.1126/science.aar6343
PMC
PMC6178954
OpenAlex
W2807521829
Cited by
350
References
14
Citations by year
2026: 25 · 2025: 28 · 2024: 35 · 2023: 46 · 2022: 37 · 2021: 53 · 2020: 61 · 2019: 51 · 2018: 13 · 2014: 1
FWCI
15.81
Type
journal article
Language
en
Open access
Locations
  • Science (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
  • CINECA IRIS Institutional Research Information System (University of Bari Aldo Moro) (submittedVersion, cc-by-nc-nd)
Funders
  • National Institutes of Health (HG002385, HG007635, HG003079, HG007990, HG006283, HG009478, HG009081, HG007234)
  • Ministero dell’Istruzione, dell’Università e della Ricerca (RBFR103CE3)
  • Howard Hughes Medical Institute (N/A)
  • National Health and Medical Research Council (1073726)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
Keywords
human evolution, structural variants, comparative genomics, long-read sequencing, full-length cDNA, brain organoids, radial glial progenitors, human-ape divergence
MeSH terms
Animals, Humans, Genetic Variation, Hominidae, Genome, Human, Sequence Analysis, DNA, Evolution, Molecular, Contig Mapping, Molecular Sequence Annotation

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