Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate
Open accessAbstract
The hypothesis that the relatively large and complex vertebrate genome was created by two ancient, whole genome duplications has been hotly debated, but remains unresolved. We reconstructed the evolutionary relationships of all gene families from the complete gene sets of a tunicate, fish, mouse, and human, and then determined when each gene duplicated relative to the evolutionary tree of the organisms. We confirmed the results of earlier studies that there remains little signal of these events in numbers of duplicated genes, gene tree topology, or the number of genes per multigene family. However, when we plotted the genomic map positions of only the subset of paralogous genes that were duplicated prior to the fish-tetrapod split, their global physical organization provides unmistakable evidence of two distinct genome duplication events early in vertebrate evolution indicated by clear patterns of four-way paralogous regions covering a large part of the human genome. Our results highlight the potential for these large-scale genomic events to have driven the evolutionary success of the vertebrate lineage.
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The estimate of 23,300 genes in the sea urchin is similar to estimates for vertebrates, despite two whole-genome duplications believed to have occurred in the chordate lineage after divergence from echinoderms.
“Our estimate of 23,300 genes is similar to estimates for vertebrates, despite the fact that two whole-genome duplications are believed to have occurred in the chordate lineage after divergence from the lineage leading to the echinoderms (25)(26)(27).”
From The Genome of the Sea Urchin <i>Strongylocentrotus purpuratus</i> (2006) · cites this paper as [25]
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- Authors
- Dehal, P., & Boore, J. L.
- Affiliations
- Lawrence Berkeley National Laboratory (US)
- Venue
- PLoS Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2005-09-06
- Volume
- 3
- Issue
- 10
- Pages
- e314
- ISSN
- 1544-9173 (ISSN-L)
- 1545-7885
- PMC
- PMC1197285
- OpenAlex
- W2047405437
- Cited by
- 1,526
- References
- 54
- Citations by year
- 2026: 53 · 2025: 54 · 2024: 63 · 2023: 67 · 2022: 85 · 2021: 94 · 2020: 82 · 2019: 83 · 2018: 71 · 2017: 75 · 2016: 72 · 2015: 76 · 2014: 71 · 2013: 83 · 2012: 82
- FWCI
- 85.53
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- University of North Texas Digital Library (University of North Texas) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- U.S. Department of Energy (DE-AC03-?, AC03-76SF00098, DEAC03-76SF00098)
- Biological and Environmental Research
- Lawrence Berkeley National Laboratory (DE AC03 76SF00098)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- whole-genome duplication, vertebrate evolution, gene family evolution, paralogs, gene tree topology, tunicates, fish, mice, human, genome organization
- MeSH terms
- Animals, Ciona intestinalis, Drosophila, Multigene Family, Humans, Phylogeny, Vertebrates, Genome, Evolution, Molecular, Computational Biology, Genes, Duplicate, Takifugu, Mice
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