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Cited by 305Chromosomal and Genetic VariationsGenomics and Phylogenetic StudiesDevelopmental Biology and Gene Regulation

The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution

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Smith, Jeramiah J., Timoshevskaya, Nataliya, Ye, Chengxi, Holt, Carson, Keinath, Melissa C., Parker, Hugo J., Cook, Malcolm E., Hess, Jon E. +16 more·2018·Nature Genetics
DOI 10.1038/s41588-017-0036-1PMC PMC5805609
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Abstract

The sea lamprey ( Petromyzon marinus ) serves as a comparative model for reconstructing vertebrate evolution. To enable more informed analyses, we developed a new assembly of the lamprey germline genome that integrates several complementary data sets. Analysis of this highly contiguous (chromosome-scale) assembly shows that both chromosomal and whole-genome duplications have played significant roles in the evolution of ancestral vertebrate and lamprey genomes, including chromosomes that carry the six lamprey HOX clusters. The assembly also contains several hundred genes that are reproducibly eliminated from somatic cells during early development in lamprey. Comparative analyses show that gnathostome (mouse) homologs of these genes are frequently marked by polycomb repressive complexes (PRCs) in embryonic stem cells, suggesting overlaps in the regulatory logic of somatic DNA elimination and bivalent states that are regulated by early embryonic PRCs. This new assembly will enhance diverse studies that are informed by lampreys’ unique biology and evolutionary/comparative perspective.

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  • Comparison of chromosome-scale genomes across vertebrates has clarified the timing and consequences of ancient whole-genome duplications that led to extant vertebrate genomes, supporting Ohno's hypothesis.

    “Comparison of chromosome-scale genomes across vertebrates has clarified the timing and consequences of the ancient whole-genome duplications (WGDs) that led to extant vertebrate genomes (59–65), supporting Ohno's (66) hypothesis.”

    From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [60]

    The Results (Vertebrate Genome Evolution; page unavailable) use lamprey, chicken, and gar genome comparisons to infer the timing and pattern of ancestral vertebrate duplications. But the paper favors one whole-genome duplication preceded by three chromosome-scale duplications over an explanation involving two whole-genome duplications. It therefore does not fully support the citing sentence’s plural characterization of the ancient whole-genome duplications. (LLM, conf=0.87)

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Authors
Smith, J. J., Timoshevskaya, N., Ye, C., Holt, C., Keinath, M. C., Parker, H. J., Cook, M. E., Hess, J. E., Narum, S. R., Lamanna, F., Kaessmann, H., Timoshevskiy, V. A., Waterbury, C. K. M., Saraceno, C., Wiedemann, L. M., Robb, S. M. C., Baker, C., Eichler, E. E., Hockman, D., Sauka-Spengler, T., Yandell, M., Krumlauf, R., Elgar, G., & Amemiya, C. T.
Affiliations
  • University of Kentucky (US)
  • University of Maryland, College Park (US)
  • University of Utah (US)
  • Stowers Institute for Medical Research (US)
  • Columbia River Inter-Tribal Fish Commission (US)
  • Heidelberg University (DE)
  • University of Washington (US)
  • Howard Hughes Medical Institute (US)
  • University of Cape Town (ZA)
  • The Francis Crick Institute (GB)
  • University of California, Merced (US)
Corresponding author
Smith, Jeramiah J.
ORCID
Venue
Nature Genetics
Publisher
Springer Science and Business Media LLC
Published
2018-01-22
Volume
50
Issue
2
Pages
270-277
ISSN
  • 1061-4036 (ISSN-L)
  • 1546-1718
DOI
10.1038/s41588-017-0036-1
PMC
PMC5805609
OpenAlex
W2785695887
Cited by
305
References
6
Citations by year
2026: 25 · 2025: 30 · 2024: 21 · 2023: 29 · 2022: 40 · 2021: 48 · 2020: 47 · 2019: 41 · 2018: 21 · 2017: 1
FWCI
33.16
Type
journal article
Language
en
Update notices
Open access
Licence
Locations
  • Nature Genetics (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
  • Oxford University Research Archive (ORA) (University of Oxford) (submittedVersion, cc-by)
Funders
  • Howard Hughes Medical Institute
  • University of Kentucky
  • University of Utah
  • Stowers Institute for Medical Research
  • Francis Crick Institute (10075)
  • National Institutes of Health
  • Bonneville Power Administration
  • National Institute of General Medical Sciences (F32GM087919, R01GM104123)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
Keywords
sea lamprey, genome rearrangement, whole-genome duplication, chromosomal duplication, polycomb repressive complex, bivalent chromatin, embryonic stem cells, vertebrate evolution, comparative genomics
MeSH terms
Animals, Germ Cells, Vertebrates, Mutagenesis, Genome, Evolution, Molecular, Chromatin Assembly and Disassembly, Petromyzon, Cellular Reprogramming

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