Draft sequencing and assembly of the genome of the world’s largest fish, the whale shark: Rhincodon typus Smith 1828

The whale shark (Rhincodon typus) has by far the largest body size of any elasmobranch (shark or ray) species and is therefore also the largest extant species of the paraphyletic assemblage commonly referred to as “fishes”. As both a phenotypic extreme and a member of the group basal to the remaining gnathostomes, which includes all tetrapods and therefore also humans, its genome is of substantial comparative interest. Whale sharks are also listed as a “vulnerable” species on the International Union for Conservation of Nature (IUCN)'s Red List of threatened species and are of growing popularity as both a target of ecotourism and as a charismatic conservation ambassador for the pelagic ecosystem. A genome map for this species would aid in defining effective conservation units and understanding global population structure. We characterised the nuclear genome of the whale shark using next generation sequencing (454, Illumina) and de novo assembly and annotation methods, based on material collected from the Georgia Aquarium. The data set consisted of 878,654,233 reads, which assembled into 11,347,816 contigs and 3,606,038 scaffolds. The estimated genome size was 3.44Gb. As expected, the proteome of the whale shark was most closely related to the only other complete genome of a cartilaginous fish, the Holocephali Elephant shark. The whale shark contained a novel Toll-like-receptor protein with sequence conservation to both the TLR4 and TLR13 proteins of mammals. The data are publicly available on a Galaxy bioinformatic server (http://whaleshark.georgiaaquarium.org). This represents the first shotgun elasmobranch genome and will aid studies of molecular systematics, biogeography, genetic differentiation, and conservation genetics in this and other shark species, as well as providing comparative data for studies of evolutionary biology and immunology across the jawed vertebrate lineages.