Biology Faculty Articles

Document Type

Article

Publication Date

3-5-2019

Publication Title

Proceedings of the National Academy of Sciences of the United States of America

Keywords

Comparative genomics, Genome stability, Elasmobranch evolution

ISSN

0027-8424

Volume

116

Issue/No.

10

First Page

4446

Last Page

4455

Abstract

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.

Comments

©2019 National Academy of Sciences

Additional Comments

GenBank accession #s: QUOW00000000, QUOW01000000; Foundation for Science and Technology project #s: PTDC/AAG-GLO/6887/2014 (POCl-01-0124-FEDER-016845), NORTE-01-0145-FEDER-031774; Genome Russia grant #: 1.52.1647.2016; Russian Foundation for Basic Research grant #s: 17-00-00144 as part of 17-00-00148

ORCID ID

0000-0001-7353-8301

ResearcherID

G-4080-2013, N-1726-2015

DOI

10.1073/pnas.1819778116

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