Genomic structure and comparative analysis of nine Fugu genes: Conservation of synteny with human chromosome Xp22.2-p22.1

The pufferfish Fugu rubripes has a compact 400-Mb genome that is similar to 7.5 times smaller than the human genome but contains a similar number of g enes. Focusing on the distal short arm of the human X chromosome, we have s tudied the evolutionary conservation of gene orders in Fugu and man. Sequen cing of 68 kb of Fugu genomic DNA identified nine genes in the following or der: (SCML2)-STK9, XLRS1, PPEF-1, KELCH2, KELCH1, PHKA2, AP19, and U2AF1-RS 2. Apart from an evolutionary inversion separating AP19 and U2AF1-RS2 from PHKA2, gene orders are identical in Fugu and man, and all nine human homolo gs map to the Xp22 band. All Fugu genes were found to be smaller than their human counterparts, but gene structures were mostly identical. These data suggest that genomic sequencing in Fugu is a powerful and economical strate gy to predict gene orders in the human genome and to elucidate the structur e of human genes.