BACKGROUND: We recently reported the existence of large numbers of regions up to 
80 kb long that lack transposon insertions in the human, mouse and opossum 
genomes. These regions are significantly associated with loci involved in 
developmental and transcriptional regulation.
RESULTS: Here we report that transposon-free regions (TFRs) are prominent 
genomic features of amphibian and fish lineages, and that many have been 
maintained throughout vertebrate evolution, although most transposon-derived 
sequences have entered these lineages after their divergence. The zebrafish 
genome contains 470 TFRs over 10 kb and a further 3,951 TFRs over 5 kb, which is 
comparable to the number identified in mammals. Two thirds of zebrafish TFRs 
over 10 kb are orthologous to TFRs in at least one mammal, and many have 
orthologous TFRs in all three mammalian genomes as well as in the genome of 
Xenopus tropicalis. This indicates that the mechanism responsible for the 
maintenance of TFRs has been active at these loci for over 450 million years. 
However, the majority of TFR bases cannot be aligned between distantly related 
species, demonstrating that TFRs are not the by-product of strong primary 
sequence conservation. Syntenically conserved TFRs are also more enriched for 
regulatory genes compared to lineage-specific TFRs.
CONCLUSION: We suggest that TFRs contain extended regulatory sequences that 
contribute to the precise expression of genes central to early vertebrate 
development, and can be used as predictors of important regulatory regions.