The whale shark genome reveals patterns of vertebrate gene family evolution
Author
Tan, MiltonRedmond, Anthony K
Dooley, Helen
Nozu, Ryo
Sato, Keiichi
Kuraku, Shigehiro
Koren, Sergey
Phillippy, Adam M
Dove, Alistair Dm
Read, Timothy
Date
2021-08-19Journal
eLifePublisher
eLife Sciences PublicationsType
Article
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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.Identifier to cite or link to this item
http://hdl.handle.net/10713/16467ae974a485f413a2113503eed53cd6c53
10.7554/eLife.65394
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