A compact cartilaginous fish model genome

The genomes of several vertebrates, including six mammals, the chicken, Xenopus and four ray-finned fishes have been sequenced or are currently being sequenced to provide a better understanding of the human genome through comparative analysis. However, this list does not include cartilaginous fishes, which are the most basal living jawed vertebrates [1]. The genomes of the current ‘popular’ cartilaginous fishes such as the nurse shark, dogfish, and horn shark are larger than the human genome (∼3800 Mb to 7000 Mb) [2], and are not attractive for whole-genome sequencing. Here, we report the characterization of the relatively small genome (1200 Mb) of a cartilaginous fish, the elephant fish (Callorhinchus milii), and propose it as a model for whole-genome sequencing. Cartilaginous fishes (Chondrichthyes) comprise two groups, the elasmobranchs (sharks, rays and skates) and the holocephalians (chimeras) (Figure 1). An earlier survey had shown that holocephalians have a smaller genome (1.6 pg/haploid cell) than the elasmobranchs (2.8–8.1 pg/haploid cell) [2]. This prompted us to measure the genome size of a holocephalian to look for a compact cartilaginous fish genome. We chose the elephant fish or elephant shark, which is found on the continental shelves off New Zealand and southern Australia. Adult elephant fish migrate into estuaries and shallower inshore bays in spring to lay eggs [3]. The haploid cellular DNA content of this fish was found to be 1.25 pg (∼1200 Mb), much smaller than the known cartilaginous fish genomes. To obtain an independent estimate of the genome size and to determine the composition of the genome, we generated 18 Mb of random sequence (Supplemental Data). These sequences constitute about 1.5% of the genome and should be representative of the whole genome. We searched these sequences against a non-redundant human protein database using the BLASTX program and found that 2.8% of the sequence represents coding sequence. As the human proteins in this database are encoded by 1.08% of the 2900 Mb human genome, we conclude that the elephant fish genome is (1.08/2.8) times smaller than the human genome, which amounts to a size of about 1130 Mb. Thus, two independent methods show that the genome of this fish is about 1200 Mb in size