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

BMC Genomics

Research Article

Ravila Bhimani¹  Timothy D. Read¹  Sandeep J. Joseph¹  Md. Tauqeer Alam¹  Chad P. Haase¹  M. Ryan Weil¹  Jocelyn S. Vuong¹  Robert A. Petit¹  Maida Ahmad¹  Milton Tan¹  D. Harry Webb²  Alistair D. M. Dove² 

[1] Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, 30322, Atlanta, GA, USA;Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, 30322, Atlanta, GA, USA;Georgia Aquarium, 225 Baker Street, 30313, Atlanta, GA, USA;

关键词: Fish;    Whole genome shotgun;    Whale shark;    Rhincodon typus;    Elasmobranch;    Gnathostomata;    Vertebrate;   

DOI  :  10.1186/s12864-017-3926-9

 received in 2017-01-10, accepted in 2017-07-06,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsWe 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.ConclusionsThis 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.

【 授权许可】

CC BY   
© The Author(s). 2017