Pufferfish and new paradigm for comparative genome analysis

Because of their special genetic and biological features, species such as bacteria, yeast, mouse ear cress (Arabidopsis), rice, nematodes, fruit flies, and the laboratory mouse have provided an important comparative perspective to the Human Genome Project. Some of these species are models for human genetic diseases, and all greatly facilitate fundamental biological and genetic studies. This combination of species is not ideal for many comparative studies, however. For example, most of the model species are too divergent evolutionarily for human gene probes to recognize their homologs directly in DNA-DNA hybridization experiments. Mice are appropriately close for reliable cross-hybridization, but many genome mapping and sequencing problems are as hard in mice as they are in humans because their genomes have comparable complexity. It now appears that a new member of the genome club of model species, pufferfish (Fugu rubripes), will solve some of these problems. Pufferfish is an excellent vertebrate for comparative genome analysis because its genome is small but complex. Its genome is about 7.5-fold smaller than the human genome ( 400 Mb vs. 3000 Mb; ref. 1). Reassociation kinetics and sequence analysis of randomly selected genomic clones suggest that only -7.6% of the genome is repetitive DNA or ribosomal genes and that the remaining -92.4% is unique (2). By comparison, '40% of the human genome is unique. Because repetitive DNA tends to be clustered, the reduced genome size results from less "junk" DNA. In addition, intron sizes are smaller. For the pufferfish homolog of the Huntington disease gene, intron sizes range from 47 bp to 1476 bp as compared to 131 bp to 12,286 bp for their human homologs (3). Although its genome size is reduced, gene structures have been preserved. For example, boundaries for all 67 exons of the Huntington disease gene are identical in pufferfish, mice, and humans (3). Despite its small size, the pufferfish genome retains considerable complexity. As vertebrates, they share with mammals