Data from: White shark genome reveals ancient elasmobranch adaptations associated with wound healing and the maintenance of genome stability
Fasta file of predicted transcripts mRNA sequence above 10 KbpThe following is a fasta file of the predicted transcripts from the Maker Genome annotation for all scaffolds greater than 10 kilobase in lengthtranscripts_above_10_kb.fastaproteins_from_10kbp_scaffoldsThese are the predicted protein sequences from maker for scaffolds greater than 10 kbp in lengthGFF annotation file from maker annotation of genome including all scaffoldsThis is the maker generated annotation file containing all repeat, gene, and protein annotations for the maker assembly that is uploaded on NCBI associated with the genome sequence for the manuscript "White shark genome: ancient elasmobranch adaptations associated with wound healing and the maintenance of genome stability."genome_annotation_from_maker.tar.gzblast2go_blastx_results_proteinsThis file is a file containing the blast descriptions for all of the predicted proteins (regardless of scaffold size) for the genome.blast2go_results_prot.txt,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.
Komissarov, Aleksey; Wang, Minghui; Bitar, Paulina Pavinski; Stanhope, Bryce J.; O’Brien, Stephen J.; Shivji, Mahmood S.; Richards, Vincent P.; Kliver, Sergey; Sun, Qi; Winkler, Chuck; Rayko, Mike; Jue, Nathaniel K.; Antunes, Agostinho; Marra, Nicholas J.; Stanhope, Michael J.; Jorgensen, Salvador (2019), "Data from: White shark genome reveals ancient elasmobranch adaptations associated with wound healing and the maintenance of genome stability", DRYAD, doi: 10.5061/dryad.9r2p3ks