@article{1922753f5c024b96b2320d0841c42bfc,
title = "The whale shark genome reveals patterns of vertebrate gene family evolution",
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.",
keywords = "Cartilaginous Fishes, Chondrichthyes, Comparative genomics, Elasmobranchii, Fish, Gigantism, Gnathostomata, Innate immunity, Vertebrate evolution",
author = "Milton Tan and Redmond, {Anthony K.} and Helen Dooley and Ryo Nozu and Keiichi Sato and Shigehiro Kuraku and Sergey Koren and Phillippy, {Adam M.} and Dove, {Alistair D.M.} and Read, {Timothy D.}",
note = "Funding Information: The sequencing service was provided by the Norwegian Sequencing Centre (www.sequencing.uio.no), a national technology platform hosted by the University of Oslo and supported by the {"}Functional Genomics{"} and {"}Infrastructure{"} programs of the Research Council of Norway and the Southeastern Regional Health Authorities{"}. We thank F. Thibaud-Nissen for assistance with genome annotation through NCBI RefSeq. We thank B. Morgan and the High Performance Computing oversight committee for access and assistance with the Center for Advanced Science Innovation and Commerce (CASIC) supercomputer at Auburn University, R. A. Petit III for assistance with computing at Emory University, and High Performance Computing at George Washington University for assistance with Colonial One and Pegasus. We thank the staff of Laboratory of Phyloinformatics in RIKEN BDR for transcriptome sequencing. Inference of gigantism in the whale shark was made possible by body size data kindly provided by C. Mull. We are thankful for funding provided from the Georgia Aquarium and the Emory School of Medicine Development. S. Koren and A.M. Phillippy were supported by the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health. Silhouettes used throughout via PhyloPic: Callorhinchus, CC BY-SA by Milton Tan, originally by Tony Ayling; whale shark, CC BY-SA by Scarlet23 (vectorized by T. Michael Keesey); spotted gar, tilapia, stickleback, CC BY-NC-SA by Milton Tan; Asian arowana, coelacanth, CC BY-NC-SA by Maija Karala; clawed frog, anole, platypus, opossum, elephant, CC BY by Sarah Werning; alligator, CC BY-NC-SA by Scott Hartman; mouse, CC BY-SA by David Liao; dolphin, CC BY-SA by Chris Huh; catshark, brownbanded bamboo shark, white shark, zebrafish, pike, cod, ricefish, ocean sunfish, chicken, armadillo, hyrax, human, dog, pig, cow, minke whale, bowhead whale, public domain. Publisher Copyright: {\textcopyright} 2021, eLife Sciences Publications Ltd. All rights reserved.",
year = "2021",
month = aug,
doi = "10.7554/eLife.65394",
language = "English (US)",
volume = "10",
journal = "eLife",
issn = "2050-084X",
publisher = "eLife Sciences Publications",
}