Animal Cytogenetics and Comparative Mapping Cytogenet Cell Genet 94:173–179 (2001) Comparative mapping of the human 9q34 region in Fugu rubripes N. Bouchireb, a F. Grützner, b T. Haaf, b R.J. Stephens, a G. Elgar, a A.J. Green c and M.S. Clark a a MRC-HGMP Resource Centre, Wellcome Genome Campus, Hinxton, Cambridge (UK); b Max-Planck-Institute for Molecular Genetics, Berlin (Germany); c National Centre for Medical Genetics, Our Lady’s Hospital for Sick Children, Crumlin, Dublin (Ireland) Supported by grant Ha 1374/5-2 from the Deutsche Forschungsgemeinschaft (F.G. and T.H.), an MRC Programme Grant (M.S.C. and G.E.) and Action Research grant: S/P/2819 (N.B.). Received 10 June; manuscript accepted 17 September 2001. Request reprints from M.S. Clark, MRC-HGMP Resource Centre, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SB (UK); telephone: +44 1223 494562; fax: +44 1223 494512; email: mclark@hgmp.mrc.ac.uk ABC Fax + 41 61 306 12 34 E-mail karger@karger.ch www.karger.com © 2002 S. Karger AG, Basel 0301–0171/01/0944–0173$17.50/0 Accessible online at: www.karger.com/journals/ccg Abstract. Twenty-seven genes have been cloned and map- ped in Fugu which have orthologues within the human chromo- some 9q34 region. The genes are arranged into five cosmid and BAC contigs which physically map to two different Fugu chro- mosomes. Considering the gene content of these contigs, it is more probable that a translocation event took place early in the Fugu lineage to split the ancestral 9q34 region onto two chro- mosomes rather than the alternative hypothesis of a large-scale duplication of the region into two chromosomes with subse- quent rapid and dramatic gene loss. There are considerable dif- ferences in gene order between the two species, which would appear to be the result of a series of complex chromosome inversions; thus suggesting that there have been no positional constraints on this particular gene set. Copyright © 2002 S. Karger AG, Basel With the human sequence virtually complete there is in- creasing interest in the development of tools to help decipher this enormous amount of sequence information. One intriguing question to come out of all this data is how did the human or indeed the vertebrate genome evolve? Was it par hazard or carefully moulded by selectionary pressure on an extinct ances- tral vertebrate karyotype. Parallel with the vast increase in human genome data has been the development of high-resolu- tion radiation hybrid maps from a variety of different organ- isms, which are providing fascinating insights into the complex process of genome evolution and large-scale genomic rearrange- ments between species (O’Brien et al., 1999, Gellin et al., 2000, Graves and Shetty, 2000). However, in terms of species num- bers, this represents a considerable bias and taking a more glob- al overview, fish represent over half of all extant vertebrates. They diverged from the main tetrapod lineage approximately 450 Myr ago and therefore are ideally placed as an evolution- arily distant collection of organisms with which to study verte- brate evolution. Their diversity in terms of physiology, behav- iour and habitat and the genomic consequences of such is cur- rently underexploited. Comprehensive genetic maps exist for a number of fish species, particularly zebrafish (Woods et al., 2000; Postlethwait et al., 2000; Barbazuk et al., 2000), but also, trout (Young et al., 1998; Sakamoto et al., 2000), medaka (Na- ruse et al., 2000), tilapia (Kocher et al., 1998, Agresti et al., 2000; McConnell et al., 2000), salmon (Linder et al., 2000) and Xiphophorus (Kazianis et al., 1996). However integration and detailed comparison of these maps either within fish species or between fish and mammals is currently not yet possible due to the fact that relatively few genes (type I markers) have been used in these mapping studies. Fugu rubripes (Fugu) has been utilised over a number of years as a compact model genome (Brenner et al., 1993). It is one of our most distant vertebrate relatives, having diverged from the tetrapod lineage 450 Myr ago and with a genome size of 400 Mb, one-seventh the size of human. A considerable number of type I markers are available for this organism; either in full or as sequence scan fragments. Until now, these have remained as random contigs with no relative positional infor- mation (Elgar et al., 1999). Several investigations within our