TY - JOUR
T1 - White Shark Genome Reveals Ancient Elasmobranch Adaptations Associated with Wound Healing and the Maintenance of Genome Stability
AU - Marra, Nicholas J.
AU - Stanhope, Michael J
AU - Jue, Nathaniel K.
AU - Wang, Minghui
AU - Sun, Qi
AU - Pavinski Bitar, Paulina D.
AU - Richards, Vincent P.
AU - Komissarov, Aleksey S.
AU - Rayko, Mike
AU - Kliver, Sergey
AU - Stanhope, Bryce J.
AU - Winkler, Chuck
AU - O'Brien, Stephen James
AU - Antunes, Agostinho
AU - Jorgensen, Salvador
AU - Shivji, Mahmood S.
N1 - Publisher Copyright:
© 2019 National Academy of Sciences. All Rights Reserved.
PY - 2019/3/5
Y1 - 2019/3/5
N2 - The white shark ( Carcharodon carcharias ; Chondrichthyes, Elasmobranchii) is one of the most publicly recognized marine animals. Here we report the genome sequence of the white shark and comparative evolutionary genomic analyses to the chondrichthyans, whale shark (Elasmobranchii) and elephant shark (Holocephali), as well as various vertebrates. The 4.63-Gbp white shark genome contains 24,520 predicted genes, and has a repeat content of 58.5%. We provide evidence for a history of positive selection and gene-content enrichments regarding important genome stability-related genes and functional categories, particularly so for the two elasmobranchs. We hypothesize that the molecular adaptive emphasis on genome stability in white and whale sharks may reflect the combined selective pressure of large genome sizes, high repeat content, high long-interspersed element retrotransposon representation, large body size, and long lifespans, represented across these two species. Molecular adaptation for wound healing was also evident, with positive selection in key genes involved in the wound-healing process, as well as Gene Ontology enrichments in fundamental wound-healing pathways. Sharks, particularly apex predators such as the white shark, are believed to have an acute sense of smell. However, we found very few olfactory receptor genes, very few trace amine-associated receptors, and extremely low numbers of G protein-coupled receptors. We did however, identify 13 copies of vomeronasal type 2 (V2R) genes in white shark and 10 in whale shark; this, combined with the over 30 V2Rs reported previously for elephant shark, suggests this gene family may underlie the keen odorant reception of chondrichthyans.
AB - The white shark ( Carcharodon carcharias ; Chondrichthyes, Elasmobranchii) is one of the most publicly recognized marine animals. Here we report the genome sequence of the white shark and comparative evolutionary genomic analyses to the chondrichthyans, whale shark (Elasmobranchii) and elephant shark (Holocephali), as well as various vertebrates. The 4.63-Gbp white shark genome contains 24,520 predicted genes, and has a repeat content of 58.5%. We provide evidence for a history of positive selection and gene-content enrichments regarding important genome stability-related genes and functional categories, particularly so for the two elasmobranchs. We hypothesize that the molecular adaptive emphasis on genome stability in white and whale sharks may reflect the combined selective pressure of large genome sizes, high repeat content, high long-interspersed element retrotransposon representation, large body size, and long lifespans, represented across these two species. Molecular adaptation for wound healing was also evident, with positive selection in key genes involved in the wound-healing process, as well as Gene Ontology enrichments in fundamental wound-healing pathways. Sharks, particularly apex predators such as the white shark, are believed to have an acute sense of smell. However, we found very few olfactory receptor genes, very few trace amine-associated receptors, and extremely low numbers of G protein-coupled receptors. We did however, identify 13 copies of vomeronasal type 2 (V2R) genes in white shark and 10 in whale shark; this, combined with the over 30 V2Rs reported previously for elephant shark, suggests this gene family may underlie the keen odorant reception of chondrichthyans.
KW - Comparative genomics
KW - Genome stability
KW - Elasmobranch evolution
KW - Genomic Instability
KW - Proto-Oncogene Proteins/genetics
KW - Wound Healing/genetics
KW - Selection, Genetic
KW - Phylogeny
KW - DNA Transposable Elements
KW - Genes, p53
KW - Sharks/classification
KW - Adaptation, Physiological/physiology
KW - Animals
KW - Genome
UR - https://nsuworks.nova.edu/cnso_bio_facarticles/957
UR - http://www.scopus.com/inward/record.url?scp=85062658002&partnerID=8YFLogxK
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U2 - 10.1073/pnas.1819778116
DO - 10.1073/pnas.1819778116
M3 - Article
C2 - 30782839
SN - 0027-8424
VL - 116
SP - 4446
EP - 4455
JO - Proceedings of the National Academy of Sciences (PNAS)
JF - Proceedings of the National Academy of Sciences (PNAS)
IS - 10
ER -