Data from: White shark genome reveals ancient elasmobranch adaptations associated with wound healing and the maintenance of genome stability

Agostinho Antunes, Interdisciplinary Centre of Marine and Environmental Research, University of Porto
Nicholas J. Marra, Guy Harvey Research Institute, Nova Southeastern University
Minghui Wang, Institute of Biotechnology, Bioinformatics Facility, Cornell University
Chuck Winkler, Aquatic Research Consultants
Michael J. Stanhope, Population Medicine and Diagnostic Sciences, Cornell College of Veterinary Medicine, Cornell University
Salvador Jorgensen, Conservation Research Department, Monterey Bay Aquarium
Stephen J. O’Brien, Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University
Paulina Pavinski Bitar, Population Medicine and Diagnostic Sciences, Cornell College of Veterinary Medicine, Cornell University
Bryce J. Stanhope, Population Medicine and Diagnostic Sciences, Cornell College of Veterinary Medicine, Cornell University
Qi Sun, Institute of Biotechnology, Bioinformatics Facility, Cornell University
Mike Rayko, Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University
Aleksey Komissarov, Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University
Sergey Kliver, Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University
Mahmood S. Shivji, Save Our Seas Shark Research Center, Nova Southeastern University
Vincent P. Richards, Department of Biological Sciences, Clemson University
Nathaniel K. Jue, School of Natural Sciences, California State University

Description

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.

Publication Date

2-19-2019

Publisher

Zenodo

DOI

10.5061/dryad.9r2p3ks

Document Type

Data Set

Identifier

4969981

Embargo Date

2-19-2019

Version

1

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