Route 66: investigations into the organisation and distribution of the IS66 family of prokaryotic insertion sequences

We have analysed a large number of members of the IS66 family of prokaryotic insertion sequences which include three orfs (A, B and C) and we show that these are closely related to a second group (ISBst12) which includes only orfC, encoding the transposase TnpC. These two IS groups are also related by their terminal inverted repeats (IR) which show significant conservation. We propose that both groups be included in the same family, the IS66 family. We have also identified members of both IS groups which include passenger genes and which, together with those already identified in the IS1595 family, suggest that such structures are quite common.We observe that the classical elements are largely limited to the Proteobacteria, although one clade contains only Firmicutes and another is limited to the Bacteriodetes/Chlorobi. While also present in the Proteobacteria, ISBst12 group elements are much more widely spread among phyla. They are present in the Actinobacteria, Cyanobacteria, Deinococcus/Thermus, Firmicutes and Planctomycetes. Moreover, they are also found in the Euryarchaeota phylum of archaea (but not in the Crenarchaeota). All Euryarchaeota members are contained within a clade together with those from the Actinobacteria, Deinococcus/Thermus and Firmicutes.The specificity of both classical IS66 and ISBst12 clades may be useful in identifying specific bacterial and archaeal phyla in complex metagenomes.