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White Shark Genome Reveals Ancient Elasmobranch Adaptations Associated with Wound Healing and the Maintenance of Genome Stability

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White Shark Genome Reveals Ancient Elasmobranch Adaptations Associated with Wound Healing and the Maintenance of Genome Stability White shark genome reveals ancient elasmobranch adaptations associated with wound healing and the maintenance of genome stability Nicholas J. Marraa,b,c,1,2, Michael J. Stanhopec,1,3,4, Nathaniel K. Jued, Minghui Wange, Qi Sune, Paulina Pavinski Bitarc, Vincent P. Richardsf, Aleksey Komissarovg, Mike Raykoh, Sergey Kliverg, Bryce J. Stanhopec, Chuck Winkleri, Stephen J. O’Brieng,j,4, Agostinho Antunesk,l, Salvador Jorgensenm, and Mahmood S. Shivjia,b,3,4 aSave Our Seas Shark Research Center, Nova Southeastern University, Dania Beach, FL 33004; bGuy Harvey Research Institute, Nova Southeastern University, Dania Beach, FL 33004; cPopulation Medicine and Diagnostic Sciences, Cornell College of Veterinary Medicine, Cornell University, Ithaca, NY 14853; dSchool of Natural Sciences, California State University, Seaside, CA 93955; eInstitute of Biotechnology, Bioinformatics Facility, Cornell University, Ithaca, NY 14853; fDepartment of Biological Sciences, Clemson University, Clemson, SC 29634; gTheodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004 St. Petersburg, Russia; hCenter for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, 199004 St. Petersburg, Russia; iAquatic Research Consultants, San Pedro, CA 90732; jGuy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Ft. Lauderdale, FL 33004; kInterdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450–208 Porto, Portugal; lDepartment of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal; and mConservation Research Department, Monterey Bay Aquarium, Monterey, CA 93940 Contributed by Stephen J. O’Brien, December 17, 2018 (sent for review November 19, 2018; reviewed by Brian W. Bowen, Christophe J. Douady, and Ben F. Koop) The white shark (Carcharodon carcharias; Chondrichthyes, Elasmo- branchii) is one of the most publicly recognized marine animals. Significance Here we report the genome sequence of the white shark and comparative evolutionary genomic analyses to the chondrichthyans, Sharks represent an ancient vertebrate lineage whose ge- whale shark (Elasmobranchii) and elephant shark (Holocephali), as nomes have been only minimally investigated. We here char- well as various vertebrates. The 4.63-Gbp white shark genome con- acterize the genome of the white shark, an apex marine tains 24,520 predicted genes, and has a repeat content of 58.5%. We predator. Its genome is 4.63 Gbp, over half of which is repre- provide evidence for a history of positive selection and gene-content sented by repeat sequences, including a large proportion of enrichments regarding important genome stability-related genes and transposable elements. Comparative analysis of white shark, functional categories, particularly so for the two elasmobranchs. We whale shark, chimaera, and several nonchondrichthyan verte- hypothesize that the molecular adaptive emphasis on genome stabil- brate genomes reveals positive selection and enrichment of ity in white and whale sharks may reflect the combined selective gene functional categories and pathways involved in wound pressure of large genome sizes, high repeat content, high long- healing, and in the maintenance of genome stability in sharks. interspersed element retrotransposon representation, large body size, Sharks show a limited repertoire of olfactory genes but an and long lifespans, represented across these two species. Molecular expanded vomeronasal (VR2) gene family, suggesting an al- adaptation for wound healing was also evident, with positive selec- ternative mechanism underlying their vaunted sense of smell. tion in key genes involved in the wound-healing process, as well as Gene Ontology enrichments in fundamental wound-healing path- Author contributions: M.J.S., S.J.O., and M.S.S. designed research; N.J.M. performed transcriptomics for the Atlantic individual and genome annotation; M.J.S. conducted comparative analyses and ways. Sharks, particularly apex predators such as the white shark, supervised sequencing of Atlantic individual; N.K.J. conducted Pacific individual/consensus transcrip- are believed to have an acute sense of smell. However, we found very tomics and analyses; M.W. and Q.S. performed genome assembly; P.P.B. performed laboratory work; few olfactory receptor genes, very few trace amine-associated recep- N.J.M., V.P.R., A.K., M.R., S.K., and B.J.S. performed bioinformatic analyses; C.W. conducted live tors, and extremely low numbers of G protein-coupled receptors. We capture and performed blood sampling; S.J.O. contributed bioinformatic resources; A.A. performed protein structural analyses and prepared figures; S.J. supervised sequencing of the Pacific individual; did however, identify 13 copies of vomeronasal type 2 (V2R) genes in M.J.S. and M.S.S. supervised the overall project; M.J.S., S.J., and M.S.S. acquired funding; and N.J.M., white shark and 10 in whale shark; this, combined with the over 30 M.J.S., and M.S.S. wrote the paper. V2Rs reported previously for elephant shark, suggests this gene family Reviewers: B.W.B., University of Hawaii; C.J.D., Université Claude Bernard Lyon 1; and may underlie the keen odorant reception of chondrichthyans. B.F.K., University of Victoria. The authors declare no conflict of interest. comparative genomics | genome stability | elasmobranch evolution Published under the PNAS license. Data deposition: The white shark whole-genome shotgun assembly discussed here has been hondrichthyan fishes (Elasmobranchii: sharks, rays, skates; deposited in DDBJ/ENA/GenBank (accession no. QUOW00000000; the version discussed in this CHolocephali: chimaeras) represent one of the oldest verte- paper is accession no. QUOW01000000). This genome-sequencing project is registered under bioproject PRJNA269969. The source for genomic DNA for that project comes from biosamples brate lineages, arising over 400 million y ago (Fig. 1). Sharks, SAMN01915239 and SAMN09832472. The genome sequencing reads are deposited in the specifically, comprise ∼45% of the known Elasmobranchii species NCBI Sequence Read Archive, https://www.ncbi.nlm.nih.gov/sra (accession no. SRP051049). (1) and include many of the meso- and apex-level oceanic pred- Transcriptome evidence comes from PRJNA313962, PRJNA177971,andPRJNA485795.Tran- ators. Perhaps the most recognized of all these predators is the scriptome biosamples for this latter project, involving the Pacific animals, come from Carcharodon carcharias SAMN09814228 and SAMN09832472 and are deposited in the NCBI Sequence Read Archive white shark ( ), capturing extraordinary (accession nos. SRR7771834, SRR7771833, SRR7771836,andSRR7771837). The Maker annota- attention from the public and media. The white shark has a largely tion of the white shark genome sequence is available on the Dryad Digital Repository at cosmopolitan distribution, but the species is thought to be of low https://doi.org/10.5061/dryad.9r2p3ks. abundance throughout this extensive range, and is classified as 1N.J.M. and M.J.S. contributed equally to this work. globally “vulnerable” (IUCN Red List category) (2). 2Present address: Department of Biology, Drury University, Springfield, MO 65802. Genomic resources for chondrichthyans are limited, with pub- 3M.J.S. and M.S.S. are joint PIs of this project. lished genome sequences confined until recently, to a single shark, 4To whom correspondence may be addressed. Email: [email protected], sobrien1@ the whale shark (Rhincodon typus; genome size, 3.44 Gbp) (3), and a nova.edu, or [email protected]. holocephalan, the elephant shark (Callorhinchus milii; genome size, This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. 975 Mb) (4); there is also an ongoing little skate (Leucoraja erinacea; 1073/pnas.1819778116/-/DCSupplemental. Superorder Batoidea, Order Rajiformes) genome project (5). Most Published online February 19, 2019. 4446–4455 | PNAS | March 5, 2019 | vol. 116 | no. 10 www.pnas.org/cgi/doi/10.1073/pnas.1819778116 Downloaded by guest on September 25, 2021 same for different lineages because of a history of specific and unique selective pressures for each lineage. Defects in the mecha- nisms regulating genome integrity result in genomic instability, which predisposes cells to malignant transformation (15), neurological disease (16), and premature aging (17). Little or nothing is known about the adaptive evolution of genome stability maintenance in sharks. Sharks are anecdotally reported to have superior wound- healing capabilities and there is recent empirical evidence from black tip sharks to support this (18). Wound healing, like genome stability, is a highly complex process involving several phases or in- terrelated steps. Although sharks appear to have exceptional wound- healing capabilities, little is known about why that might be the case. Comparative sequence data on a genomic scale provides the opportunity to explain major biological differences between or- ganisms at the molecular level. Three fundamental molecular characteristics responsible for biological differences between or- Fig. 1. Schematic, annotated, phylogenetic tree including the fish species ganisms are: (i) presence and absence of particular loci, (ii) positive used in our positive-selection analysis. Human is included only for compar- selection, and (iii) gene regulation. Our interest in the molecular ative and evolutionary reference. Lifespan, genome size, and percent
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