title: Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome.
abstract: Owing to their phylogenetic position, cartilaginous fishes (sharks, rays, skates, and chimaeras) provide a critical reference for our understanding of vertebrate genome evolution. The relatively small genome of the elephant shark, Callorhinchus milii, a chimaera, makes it an attractive model cartilaginous fish genome for whole-genome sequencing and comparative analysis. Here, the authors describe survey sequencing (1.4x coverage) and comparative analysis of the elephant shark genome, one of the first cartilaginous fish genomes to be sequenced to this depth. Repetitive sequences, represented mainly by a novel family of short interspersed element-like and long interspersed element-like sequences, account for about 28% of the elephant shark genome. Fragments of approximately 15,000 elephant shark genes reveal specific examples of genes that have been lost differentially during the evolution of tetrapod and teleost fish lineages. Interestingly, the degree of conserved synteny and conserved sequences between the human and elephant shark genomes are higher than that between human and teleost fish genomes. Elephant shark contains putative four Hox clusters indicating that, unlike teleost fish genomes, the elephant shark genome has not experienced an additional whole-genome duplication. These findings underscore the importance of the elephant shark as a critical reference vertebrate genome for comparative analysis of the human and other vertebrate genomes. This study also demonstrates that a survey-sequencing approach can be applied productively for comparative analysis of distantly related vertebrate genomes.
authors.affiliation: Institute of Molecular and Cell Biology, Singapore. mcbbv@imcb.a-star.edu.sg
authors.forename: Byrappa
authors.initials: B
authors.lastname: Venkatesh
authors.forename: Ewen F
authors.initials: EF
authors.lastname: Kirkness
authors.forename: Yong-Hwee
authors.initials: YH
authors.lastname: Loh
authors.forename: Aaron L
authors.initials: AL
authors.lastname: Halpern
authors.forename: Alison P
authors.initials: AP
authors.lastname: Lee
authors.forename: Justin
authors.initials: J
authors.lastname: Johnson
authors.forename: Nidhi
authors.initials: N
authors.lastname: Dandona
authors.forename: Lakshmi D
authors.initials: LD
authors.lastname: Viswanathan
authors.forename: Alice
authors.initials: A
authors.lastname: Tay
authors.forename: J Craig
authors.initials: JC
authors.lastname: Venter
authors.forename: Robert L
authors.initials: RL
authors.lastname: Strausberg
authors.forename: Sydney
authors.initials: S
authors.lastname: Brenner
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D004247:DNA; D016678:Genome; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D012091:Repetitive Sequences, Nucleic Acid; D012754:Sharks / Q000235:genetics*
chemical_list: D004247:DNA