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    The whale shark genome reveals patterns of vertebrate gene family evolution

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    Author
    Tan, Milton
    Redmond, Anthony K
    Dooley, Helen
    Nozu, Ryo
    Sato, Keiichi
    Kuraku, Shigehiro
    Koren, Sergey
    Phillippy, Adam M
    Dove, Alistair Dm
    Read, Timothy
    Date
    2021-08-19
    Journal
    eLife
    Publisher
    eLife Sciences Publications
    Type
    Article
    
    Metadata
    Show full item record
    See at
    https://doi.org/10.7554/eLife.65394
    Abstract
    Chondrichthyes (cartilaginous fishes) are fundamental for understanding vertebrate evolution, yet their genomes are understudied. We report long-read sequencing of the whale shark genome to generate the best gapless chondrichthyan genome assembly yet with higher contig contiguity than all other cartilaginous fish genomes, and studied vertebrate genomic evolution of ancestral gene families, immunity, and gigantism. We found a major increase in gene families at the origin of gnathostomes (jawed vertebrates) independent of their genome duplication. We studied vertebrate pathogen recognition receptors (PRRs), which are key in initiating innate immune defense, and found diverse patterns of gene family evolution, demonstrating that adaptive immunity in gnathostomes did not fully displace germline-encoded PRR innovation. We also discovered a new Toll-like receptor (TLR29) and three NOD1 copies in the whale shark. We found chondrichthyan and giant vertebrate genomes had decreased substitution rates compared to other vertebrates, but gene family expansion rates varied among vertebrate giants, suggesting substitution and expansion rates of gene families are decoupled in vertebrate genomes. Finally, we found gene families that shifted in expansion rate in vertebrate giants were enriched for human cancer-related genes, consistent with gigantism requiring adaptations to suppress cancer.
    Keyword
    evolutionary biology
    genetics
    genomics
    Identifier to cite or link to this item
    http://hdl.handle.net/10713/16467
    ae974a485f413a2113503eed53cd6c53
    10.7554/eLife.65394
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