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Cited by 373Genomics and Phylogenetic StudiesChromosomal and Genetic VariationsGenetic diversity and population structure

A comparative genomics multitool for scientific discovery and conservation

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Zoonomia Consortium, Genereux, Diane P., Serres, Aitor, Armstrong, Joel, Johnson, Jeremy, Marinescu, Voichita D., Murén, Eva, Juan, David +41 more·2020·Nature
DOI 10.1038/s41586-020-2876-6PMC PMC7759459
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Abstract

The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.

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  • The amniote-wide alignment combines two smaller alignments: one for the Zoonomia project including 242 placental mammals representing most eutherian mammal families, and one for the Bird 10,000 genomes (B10K) project including 363 avians representing most bird families.

    “The amniote-wide alignment combines two smaller alignments: one created for the initial release of the Zoonomia project31, which includes 242 placental mammals representing most eutherian mammal families, and one for the Bird 10,000 genomes (B10K) project32, which includes 363 avians, also representing most bird families.”

    From Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020) · cites this paper as [31]

    Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

    Experimental — accuracy not yet measured

  • Comparative genomic analyses usually test for correlations between traits.

    “Comparative genomic analyses usually test for correlations between traits.”

    From A phylogenetic approach to comparative genomics (2025) · cites this paper as [76]

    The Genetic diversity and extinction risk section tests correlations between genomic diversity measures and species-level traits; Next steps also proposes genotype–phenotype correlations. Neither passage says comparative genomic analyses usually test correlations between traits themselves. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

  • TOGA provides a general strategy to cope with the annotation and orthology inference bottleneck.

    “With the tree of life becoming more densely populated with genomes, thanks to great efforts of large-scale projects and numerous laboratories (26–28, 39), TOGA provides a general strategy to cope with the annotation and orthology inference bottleneck.”

    From Integrating gene annotation with orthology inference at scale (2023) · cites this paper as [27]

  • The B10K and Zoonomia consortia are using this alignment for comparative analysis.

    “The B10K32 and Zoonomia31 consortia are using this alignment for comparative analysis, for example, analysing patterns of selection in unprecedented detail.”

    From Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020) · cites this paper as [31]

  • Comparing a highly-fragmented with a highly-contiguous assembly of two sperm whale species showed that orthologous genes located on a single scaffold in both species have a much higher sequence identity (mean 98.70%) than paralogous genes (mean 75.18%).

    “Indeed, comparing a highly-fragmented with a highly-contiguous assembly of two sperm whale species (27, 29) showed that orthologous genes located on a single scaffold in both species have a much higher sequence identity (mean 98.70%) than paralogous genes (mean 75.18%) (Fig. 4B).”

    From Integrating gene annotation with orthology inference at scale (2023) · cites this paper as [27]

    The Designing a comparative-genomics multitool section discusses assembly contiguity, and Whole-genome alignment describes a multispecies alignment, but neither reports this sperm-whale comparison. Searches for sperm whales, orthologous and paralogous genes, and the stated identity percentages found no passage addressing the result in our copy. (LLM, conf=0.76)

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Authors
Zoonomia Consortium, Genereux, D. P., Serres, A., Armstrong, J., Johnson, J., Marinescu, V. D., Murén, E., Juan, D., Bejerano, G., Casewell, N. R., Chemnick, L. G., Damas, J., Di Palma, F., Diekhans, M., Fiddes, I. T., Garber, M., Gladyshev, V. N., Goodman, L., Haerty, W., Houck, M. L., Hubley, R., Kivioja, T., Koepfli, K.-P., Kuderna, L. F. K., Lander, E. S., Meadows, J. R. S., Murphy, W. J., Nash, W., Noh, H. J., Nweeia, M., Pfenning, A. R., Pollard, K. S., Ray, D. A., Shapiro, B., Smit, A. F. A., Springer, M. S., Steiner, C. C., Swofford, R., Taipale, J., Teeling, E. C., Turner-Maier, J., Alfoldi, J., Birren, B., Ryder, O. A., Lewin, H. A., Paten, B., Marques-Bonet, T., Lindblad-Toh, K., & Karlsson, E. K.
Affiliations
  • Broad Institute (US)
  • Consejo Superior de Investigaciones Científicas (ES)
  • University of California, Santa Cruz (US)
  • Uppsala University (SE)
  • Stanford Medicine (US)
  • Liverpool School of Tropical Medicine (GB)
  • Zoological Society of San Diego (US)
  • University of California, Davis (US)
  • University of Massachusetts Chan Medical School (US)
  • Earlham Institute (GB)
  • Institute for Systems Biology (US)
  • University of Helsinki (FI)
  • Smithsonian Institution (US)
  • Texas A&M University (US)
  • Carnegie Mellon University (US)
  • Gladstone Institutes (US)
  • Texas Tech University (US)
  • Howard Hughes Medical Institute (US)
  • University of California, Riverside (US)
  • University College Dublin (IE)
  • University of East Anglia (GB)
Corresponding author
Karlsson, Elinor K.
ORCID
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2020-11-11
Volume
587
Issue
7833
Pages
240-245
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/s41586-020-2876-6
PMC
PMC7759459
OpenAlex
W3105951520
Cited by
373
References
4
Citations by year
2026: 68 · 2025: 81 · 2024: 62 · 2023: 62 · 2022: 59 · 2021: 37 · 2020: 4
FWCI
12.98
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, other-oa)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Repositori digital de la UPF (Universitat Pompeu Fabra) (publishedVersion, cc-by)
  • LSTM Online Archive (Liverpool School of Tropical Medicine) (acceptedVersion)
  • UEA Digital Repository (University of East Anglia) (acceptedVersion, cc-by-sa)
  • The Journal of the American Medical Association (JAMA) Network (American Medical Association) (submittedVersion, cc-by)
  • KTH Publication Database DiVA (KTH Royal Institute of Technology) (submittedVersion, other-oa)
  • DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, cc-by)
  • DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
  • eScholarship (California Digital Library) (submittedVersion)
  • eScholarship (California Digital Library) (submittedVersion, cc-by)
  • Työväentutkimus Vuosikirja (submittedVersion)
  • ThinkTech (Texas Tech University) (submittedVersion, cc-by)
  • Apollo (University of Cambridge) (submittedVersion, cc-by)
  • Apollo (cc-by)
Funders
  • National Science Foundation (1838283, 1753760, 2029774, 1457735)
  • Smithsonian Institution
  • Gladstone Institutes
  • Wellcome Trust (200517/Z/16/Z, 29558, 200517)
  • Broad Institute (Next10)
  • Centres de Recerca de Catalunya (GRC 2017 SGR 880)
  • Royal Society (200517/Z/16/Z)
  • Svenska Forskningsrådet Formas (2018‐05973, 864203, BFU2017-86471-P, GRC 2017 SGR 880, 221-2012-1531)
  • Irish Research Council
  • Generalitat de Catalunya (2017-SGR, BFU2017-86471-P, GRC 2017 SGR 880, 864203)
  • Knut och Alice Wallenbergs Stiftelse (2018-05973, 864203, GRC 2017 SGR 880, BFU2017-86471-P)
  • Vetenskapsrådet (BFU2017-86471-P, 05973, GRC 2017 SGR 880, 864203, 2018-, 201805973, grant 2018-05973)
  • Ministerio de Ciencia e Innovación (BFU2017-86471-P)
  • Uppsala Universitet (2018-05973)
  • Science for Life Laboratory (864203, BFU2017-86471-P, GRC 2017 SGR 880)
  • Prince Albert II of Monaco Foundation
  • National Institutes of Health
  • Medical Research Council (MR/P026028/1, P026028/1, 200517/Z/16/Z)
  • Biotechnology and Biological Sciences Research Council (BBS/E/T/000PR9783, BB/P016774/1, BBS/E/T/000PR9818, BBS/E/T/000PR9814)
  • National Institute on Aging (UH2AG064706, P01AG047200)
  • National Human Genome Research Institute (R01HG010485, R01HG008742, U41HG007234, U24HG007234, R01HG002939, U24HG010136)
  • FP7 Ideas: European Research Council (311000)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
Keywords
placental mammals, comparative genomics, genome assembly, whole-genome alignment, phylogenetic diversity, extinction risk, genetic diversity, evolutionary selection, reference genome, biodiversity conservation
MeSH terms
Eutheria, Animals, Conservation of Natural Resources, Humans, Infections, Neoplasms, Phylogeny, Selection, Genetic, Species Specificity, Genetic Variation, Venoms, Sequence Alignment, Risk Assessment, Evolution, Molecular, Loss of Heterozygosity, Genomics, Biomedical Research, Biodiversity, Genetic Speciation, Extinction, Biological, Knowledge Discovery

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