Estimation of synteny conservation and genome compaction between pufferfish (Fugu) and human

Background: Knowledge of the amount of gene order and synteny conservation between two species gives insights to the extent and mechanisms of divergen ce. The vertebrate Fugu rubripes (pufferfish) has a small genome with littl e repetitive sequence which makes it attractive as a model genome. Genome c ompaction and synteny conservation between human and Fugu were studied usin g data from public databases. Methods: Intron length and map positions of human and Fugu orthologues were compared to analyse relative genome compaction and synteny conservation re spectively. The divergence of these two genomes by genome rearrangement was simulated and the results were compared to the real data. Results: Analysis of 199 introns in 22 orthologous genes showed an eight-fo ld average size reduction in Fugu, consistent with the ratio of total genom e sizes, There was no consistent pattern relating the size reduction in ind ividual introns or genes to gene base composition in either species. For ge nes that are neighbours in Fugu (genes from the same cosmid or GenBank entr y), 40-50% have conserved synteny with a human chromosome. This figure may be underestimated by as much as two-fold, due to problems caused by incompl ete human genome sequence data and the existence of dispersed gene families , Some genes that are neighbours in Fugu have human orthologues that are se veral megabases and tens of genes apart. This is probably caused by small i nversions or other intrachromosomal rearrangements. Conclusions: Comparison of observed data to computer simulations suggests t hat 4000-16 000 chromosomal rearrangements have occurred since Fugu and hum an shared a common ancestor, implying a faster rate of rearrangement than s een in human/mouse comparisons. Copyright (C) 2000 John Wiley & Sons, Ltd.