The whale shark genome reveals patterns of vertebrate gene family evolution.
Animals
Biomarkers, Tumor
/ genetics
Cell Transformation, Neoplastic
/ genetics
Evolution, Molecular
Fish Proteins
/ genetics
Gene Duplication
Gene Expression Profiling
Gene Expression Regulation, Neoplastic
Genome
Humans
Immunity, Innate
/ genetics
Neoplasms
/ genetics
Phylogeny
Receptors, Immunologic
/ genetics
Sharks
/ genetics
Transcriptome
Whole Genome Sequencing
Rhincodon typus
chondrichthyes
evolutionary biology
fish
genetics
genomics
gnathostome
vertebrate
whale shark
Journal
eLife
ISSN: 2050-084X
Titre abrégé: Elife
Pays: England
ID NLM: 101579614
Informations de publication
Date de publication:
19 08 2021
19 08 2021
Historique:
received:
02
12
2020
accepted:
18
08
2021
pubmed:
20
8
2021
medline:
21
10
2021
entrez:
19
8
2021
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 34409936
doi: 10.7554/eLife.65394
pii: 65394
pmc: PMC8455134
doi:
pii:
Substances chimiques
Biomarkers, Tumor
0
Fish Proteins
0
Receptors, Immunologic
0
Banques de données
SRA
['SRX3471980']
Types de publication
Journal Article
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Déclaration de conflit d'intérêts
MT, AR, HD, RN, KS, SK, AP, AD, TR No competing interests declared, SK Reviewing editor, eLife
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