Fish genomes flying

Introduction Fish models have become very popular during the past decade (see Fig. 1 for phylogenetic relationships). Recently established models for genomic studies (the Japanese and freshwater pufferfish, Fugu rubripes and Tetraodon nigroviridis, respectively) and for developmental biology (the zebrafish, Danio rerio) are now the focus of interest of many biologists, although ‘old’ models are still useful for the study of tumorigenesis (platyfish, Xiphophorus) and evolution, radiation and speciation (African cichlids), as well as for the evolution of sex determination and developmental genetics (the medaka, Oryzias latipes). Although the zebrafish and its features as an experimental system are well known among scientists within and outside the field, knowledge of the medaka has so far been restricted (with a few exceptions) to its home range, Japan, and some other countries in the Far East. In Japan, the breeding of medaka colour variants for ornamental purposes is a tradition that goes back several centuries. In the early twentieth century, the medaka was recruited as a model species for biological and genetic research. In fact, it was the study of the inheritance of body colour in the medaka by Toyama in 1916 that proved that Mendelian laws also apply to fish (Toyama, 1916). Another milestone achievement was the discovery of Y-chromosome-linked inheritance by Aida in 1921 (Aida, 1921). Within the past seven years, the number of publications on studies that involve the medaka have doubled each year, illustrating its increasing popularity as a model species. One of the scientific highlights of 2002 was the release of the draft version of the first whole-genome sequence of a teleost, that of the pufferfish Fugu rubripes. An advanced genome draft sequence is also now available for the related pufferfish species Tetraodon nigroviridis. However, neither species is used as an experimental system; the primary value of each is its exceptionally small genome size, which is an advantage in genome analysis. Phylogenetic studies place the medaka close to both pufferfish species, with an estimated divergence time of 60–80 million years (Myr) ago, which is less than the evolutionary distance between man and mouse. Medaka and zebrafish, now the most widely used fish model species, are relatively distant cousins that have evolved separately for at least 135 Myr. The key technologies that have made the zebrafish such a successful model species are fully applicable to the medaka. However, genomics in the medaka offers several advantages, such as the availability of divergent, perfectly inbred strains and a genome of only 800 million bases, half the size of the zebrafish genome. In addition, a practical aspect is that the sexes are easily distinguished in medaka, in contrast to zebrafish, facilitating breeding in general and genetic studies in particular. The recent symposium, Medaka Genomics 2002, was inaugurated with an introductory talk by A. Shima (Kashiwa City, Japan), who provided a historical overview of the Medaka Genome Initative. The inception of this project was a European-Union-sponsored practical