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dc.contributor.authorTan, Milton
dc.contributor.authorRedmond, Anthony K
dc.contributor.authorDooley, Helen
dc.contributor.authorNozu, Ryo
dc.contributor.authorSato, Keiichi
dc.contributor.authorKuraku, Shigehiro
dc.contributor.authorKoren, Sergey
dc.contributor.authorPhillippy, Adam M
dc.contributor.authorDove, Alistair Dmen_US
dc.contributor.authorRead, Timothyen_US
dc.date.accessioned2021-08-25T18:27:35Z
dc.date.available2021-08-25T18:27:35Z
dc.date.issued2021-08-19
dc.identifier.urihttp://hdl.handle.net/10713/16467
dc.description.abstractChondrichthyes (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.en_US
dc.description.urihttps://doi.org/10.7554/eLife.65394en_US
dc.language.isoenen_US
dc.publishereLife Sciences Publicationsen_US
dc.relation.ispartofeLifeen_US
dc.subjectevolutionary biologyen_US
dc.subjectgeneticsen_US
dc.subjectgenomicsen_US
dc.titleThe whale shark genome reveals patterns of vertebrate gene family evolutionen_US
dc.typeArticleen_US
dc.identifier.doi10.7554/eLife.65394
dc.identifier.pmid34409936
dc.source.journaltitleeLife
dc.source.countryEngland


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