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 nonredundant 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. The random sequences of the elephant fish contain 6.4% repetitive elements (Supplemental data). This value is comparable to that found in the fugu [4] and chicken [5] genomes, but much lower than in mammalian genomes (46% in human, 38% in mouse) [6]. The most abundant elements are non-LTR retrotransposons of the L2/CR1/Rex family (2.1%) (Supplemental data), which are also the most common retroelements in non-mammalian vertebrates such as fugu [4] and chicken [5]. We also identified 134 complete introns in the elephant fish sequences, which range in size from 71 bp to 613 bp, with a mean value of 240 bp ( ± 11 SE). Their homologs in the fugu and human genomes vary from 60 bp to 1,390 bp (180 ± 21 bp) and 77 bp to 22,301 bp (2,246 ± 290 bp), respectively. These data show that the small size of the elephant fish genome is largely due to relatively small introns and a paucity of repetitive sequences. Interestingly, coding sequences of 149 non-redundant elephant fish sequences showed significantly higher similarity (>105-fold lower Evalue) to human than to pufferfish (fugu and Tetraodon) and zebrafish sequences (Supplemental data). When the human proteins matching these sequences were searched against the pufferfish and zebrafish protein databases, and the non-redundant protein database of all known proteins, five of them had no significant match (E-value >10−5) in any rayfinned fish (Table 1). However, one of these human proteins, Tigger transposable element derived 4, has homologs in all the sequenced invertebrate genomes (E-value ≥ Figure 1. Phylogenetic tree showing the relationships of cartilaginous fishes to tetrapods and ray-finned fishes. The approximate time of divergence of major lineages is indicated. Cyclostomes are jawless vertebrates. Tetrapods