1 4 1 3 5 6 7 Until relatively recently, little was known about the biology of the largest shark in the world, the circum-tropical, filter-feeding whale shark, Rhincodon typus Smith 1828 [] (Fig.). Advances in tagging technology, combined with the discovery of several reliable, seasonal, near-coastal aggregations in different parts of the world [] have spurred a rapid expansion in whale shark science since 2000. These efforts have been further enhanced by the three International Whale Shark Conferences (the most recent collected at []), which have served to promote collaboration on what is otherwise a fairly intractable species to study, due to its size and oceanic habits. The maintenance of a collection of whale sharks at Georgia Aquarium has provided research opportunities not previously available in the natural setting of whale sharks, including the ability to collect samples suitable for genome sequencing. R. typus is an excellent model for comparative genomic study because cartilaginous fishes form the sister group to the remaining gnathostomes, because it represents a phenotypic extreme in body size among sharks and fishes generally, and because it is a charismatic subject of ecotourism, yet globally vulnerable to extinction.

The biology of the whale shark has been previously reviewed [1–4]. The whale shark was first described by Smith in 1828 based on a specimen from South Africa [8]. By far the largest species of fish, the largest confirmed size of a whale shark is 18.8 m in total length [9]. The whale shark is a pelagic filter-feeder and the only member of the family Rhincodontidae, whereas other members of the order Orectolobiformes – to which the species belongs – are benthic, bottom-feeding sharks. The whale shark also has the highest fecundity of any shark, with a single individual found bearing over three hundred developing embryos [10]. This species is primarily found in warm oceanic waters, though it is capable of diving to depths where waters approach freezing temperatures [11]. The whale shark is listed on the International Union for Conservation of Nature’s Red List of threatened species as endangered [12], and is a flagship species in marine conservation. Though the whale shark is targeted by fisheries in several countries and is occasionally taken as bycatch, much of the exploitation of whale sharks is for ecotourism around the world, rather than as a food source [3].

There are few publications on the genetics and genomics of whale sharks. Some of the first efforts at discriminating substructure in the global population were based on microsatellite [13] or mitochondrial control loop [14] sequences and failed to detect as much global population structure as might be expected. In a recent review incorporating natural history data, Sequeira et al. [15] concluded that whale sharks are part of a single global metapopulation. These studies have been contradicted by a more recent paper that found distinct genetic differences between Atlantic and Indo-Pacific whale sharks [16] based on additional microsatellite loci. Alam et al. [17] provided the first genomic exploration of the whale shark: the complete mitochondrial genome along with a phylogenomic comparison with representative members of the other major elasmobranch orders. The number of chromosomes in the whale shark genome has not yet been ascertained.

Rhincodon typus and other cartilaginous fishes are members of the Gnathostomata, or jawed vertebrates, a group which arose roughly halfway through the Palaeozoic era, and radiated to produce many of the groups of animals most familiar to the general public: sharks, bony fishes, amphibians, reptiles, birds and mammals, including humans. The transition from jawless to jawed vertebrates included several important adaptations that have defined the success of vertebrate life, including the adoption of antibody-based immune systems [18]. The closest relatives to the gnathostomes are jawless fishes, represented among extant taxa only by hagfish and lamprey [19]. Extant gnathostomes themselves are divided into two major clades: Chondrichthyes (cartilaginous fishes) and Osteichthyes (bony fishes and tetrapods). Cartilaginous fishes consist of holocephalans (ratfishes), and the elasmobranchs (sharks and rays). Comparative studies including cartilaginous fishes thus can provide insight into the origin and evolution of jawed vertebrates. Furthermore, cartilaginous fishes can be important model species for comparative studies of human evolution, including anatomy, physiology and immunology. Venkatesh and co-authors [18, 20–23] have explored the genomic basis of some of these adaptations in the elephant shark, Callorhinchus milii, a cartilaginous fish from the Holocephali; however, no elasmobranch species has had a complete nuclear genome published prior to this study. Mitochondrial phylogenetic analysis of the individual sequenced in this study was previously published [17]. Results recapitulated previously known relationships for the whale shark as a member of the order Orectolobiformes, with all five orectolobiform shark species forming a clade. This was congruent with a prior study with higher taxon sampling and fewer mitochondrial genes that placed the whale shark among orectolobiform sharks as the sister group to a clade formed by two species that represented the families Ginglystomatidae and Stegostomatidae [24].

In this short report we present the preliminary whole genome shotgun sequencing analysis of a R. typus male. The current data set has already been of use to researchers studying shark biology and the evolution of Gnathostomata. In future work, we will present a more complete genome assembly, which is currently in progress.