Venkatesh, B., Kirkness, E.F., Loh, Y.H., Halpern, A.L., Lee, A.P., Johnson, J., Dandona, N., Viswanathan, L.D., Tay, A., Venter, J.C., Strausberg, R.L. and Brenner, S.
Cartilaginous fishes (sharks, rays, skates and chimaeras) are the phylogenetically oldest group of living jawed vertebrates. Owing to their phylogenetic position, cartilaginous fishes provide a critical reference for our understanding of the evolution of human and other vertebrate genomes. We previously proposed that the relatively small genome of the elephant shark, Callorhinchus milii, a chimaera, is an attractive ‘model’ cartilaginous fish genome for whole-genome sequencing and comparative analysis. Here, we describe survey sequencing (1.4× coverage) and comparative analysis of the elephant shark genome, the first cartilaginous fish genome to be sequenced to this depth. Repetitive sequences, represented mainly by a novel family of SINE-like and LINE-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 teleost fish and human 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 (fugu and zebrafish) genomes, even though humans are more closely related to teleost fishes than to the elephant shark. Furthermore, unlike teleost fish genomes, the elephant shark genome does not seem to have 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. Our study also demonstrates that a survey-sequencing approach can be applied productively for comparative analysis of distantly related vertebrate genomes.
The paper, published in PLoS Biol (5: e101. 2007), can be accessed at:
Click here for the Elephant Shark Genome Project webpage: