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

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28709399", "kind": "science-record", "revision": 4, "content_hash": "sha256:74813371b35cd327a4d24afb08471d01cc28a4dd26cae277fbe7f90e42524fe2", "created_at": "2026-11-01T15:40:27Z", "updated_at": "2026-11-01T21:21:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Draft sequencing and assembly of the genome of the world's largest fish, the whale shark: Rhincodon typus Smith 1828.", "doi": "10.1186/s12864-017-3926-9", "pmid": "28709399", "authors": ["Timothy D Read", "Robert A Petit", "Sandeep J Joseph", "Md Tauqeer Alam", "M Ryan Weil", "Maida Ahmad", "Ravila Bhimani", "Jocelyn S Vuong", "Chad P Haase", "D Harry Webb", "Milton Tan", "Alistair D M Dove"], "journal": "BMC genomics", "year": 2017, "abstract": "BACKGROUND: The whale shark (Rhincodon typus) has by far the largest body size of any elasmobranch (shark or ray) species. Therefore, it is 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 Chondrichthyes - the sister group 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 an endangered species on the International Union for Conservation of Nature'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.\nRESULTS: 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 yielded a draft assembly of 1,213,200 contigs and 997,976 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 holocephalan elephant shark. The whale shark contained a novel Toll-like-receptor (TLR) protein with sequence similarity to both the TLR4 and TLR13 proteins of mammals and TLR21 of teleosts. The data are publicly available on GenBank, FigShare, and from the NCBI Short Read Archive under accession number SRP044374.\nCONCLUSIONS: 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.", "claims": [{"id": "claim-method", "statement": "Maximum likelihood (ML) phylogenetic reconstruction was implemented using RAxML (v 7.2.8-ALPHA) [46]. The Jones-Taylor-Thornton (JTT) amino acid substitution model[47] of rate heterogeneity with 4 discrete rate categories was used. To evaluate statistical support, 100 bootstrap replicates were computed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28709399", "locator": "sections[6] \"Ortholog analysis\" paragraph 2", "quote": "Maximum likelihood (ML) phylogenetic reconstruction was implemented using RAxML (v 7.2.8-ALPHA) [46]. The Jones-Taylor-Thornton (JTT) amino acid substitution model[47] of rate heterogeneity with 4 discrete rate categories was used. To evaluate statistical support, 100 bootstrap replicates were computed."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and analyzed during the current study are publically available, including: the raw reads on the NCBI Short Read Archive (accession number SRP044374); genome assembly and proteome prior to exclusion of contigs below 200 bp on a Galaxy bioinformatic server; the genome assembly on GenBank (accession number LVEK00000000); the proteome on FigShare [53]; and additional scripts and supporting information have been placed on a public GitHub site [55].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28709399", "locator": "sections[15] \"Availability of data and materials\" paragraph 2", "quote": "The datasets generated and analyzed during the current study are publically available, including: the raw reads on the NCBI Short Read Archive (accession number SRP044374); genome assembly and proteome prior to exclusion of contigs below 200 bp on a Galaxy bioinformatic server; the genome assembly on GenBank (accession number LVEK00000000); the proteome on FigShare [53]; and additional scripts and supporting information have been placed on a public GitHub site [55]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used OrthoMCL-based ortholog clustering and maximum-likelihood phylogenetic reconstruction with 100 bootstrap replicates; its raw source data are publicly available through the NCBI Short Read Archive under accession SRP044374. The paper’s headline result was that it produced the first shotgun elasmobranch genome.", "kind": "quantitative", "target": {"value": 71.0, "unit": "per cent", "tolerance": null, "source": "In a discontiguous megablast alignment between the C. milii and whale shark scaffolds, the combined length of matches with an E value of <0.001 was only 42 Mb of the elephant shark genome (71% nucleotide identity). In addition, based on our phylogenetic analysis, the number of estimated substitutions is higher in whale shark than in elephant shark."}, "evidence": [{"asset": "source:pmid:28709399", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "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."}, {"asset": "source:pmid:28709399", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The data are publicly available on GenBank, FigShare, and from the NCBI Short Read Archive under accession number SRP044374."}, {"asset": "source:pmid:28709399", "locator": "sections[11] \"Preliminary comparisons\" paragraph 2", "quote": "In a discontiguous megablast alignment between the C. milii and whale shark scaffolds, the combined length of matches with an E value of <0.001 was only 42 Mb of the elephant shark genome (71% nucleotide identity). In addition, based on our phylogenetic analysis, the number of estimated substitutions is higher in whale shark than in elephant shark."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study used OrthoMCL-based ortholog clustering and maximum-likelihood phylogenetic reconstruction with 100 bootstrap replicates; its raw source data are publicly available through the NCBI Short Read Archive under accession SRP044374. 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