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 (1.4× 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.
Highlights
Our understanding of the human genome has benefited greatly from comparative studies with other vertebrate genomes
We estimated the length of euchromatic DNA in the dog genome after survey-sequence coverage (2.43 Gb after 1.53 coverage [23]), and this value is very close to that estimated after more complete sequencing
Values (% sequenced genome) for each class of repeats were obtained for Takifugu rubripes, Tetraodon nigroviridis, Danio rerio, Xenopus tropicalis, Gallus gallus, and Homo sapiens from the University of California at Santa Cruz Genome Bioinformatics Site
Summary
Our understanding of the human genome has benefited greatly from comparative studies with other vertebrate genomes. Comparisons of the human and teleost fish genomes are complicated by the presence of many ‘‘fish-specific’’ duplicate gene loci in teleosts. These duplicate loci have been attributed to a ‘‘fish-specific’’ whole-genome duplication event that occurred in the ray-finned fish lineage approximately 350 My ago [9,10]. The extent and copies of ‘‘fish-specific’’ duplicated genes retained following the fish-specific genome duplication vary in different teleost lineages. Genome-wide comparison between zebrafish and Tetraodon has shown that different duplicated genes have been retained in these teleosts [11]. It is not always straightforward to define orthologous relationships between the genes of teleost fishes and human
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