Diversity in coding tandem repeats in related Neisseria spp.

A total of 28 genes were identified. Of these, 22 contain coding tandem repeats that vary in copy number between the three sequenced strains, three strain specific genes were included for investigation on the basis of having >90% identity between repeated units, and three genes with repeated elements of >250 bp were included although no length variations were seen in the genomes. Amplification, and sequencing of repeats showing altered copy number, of these 28 coding tandem repeat containing regions, from a set of largely unrelated strains, revealed further repeat length variation in several cases.Eighteen genes were identified which have variation in repeat copy number between strains of the same species, twelve of which show greater diversity in repeat copy number than is present in the sequenced genomes. In some cases, this may reflect a mechanism for the generation of antigenic variation, as previously described in other species. However, some of the genes identified encode proteins with cytoplasmic functions, including sugar metabolism, DNA repair, and protein production, in which repeat length variation may have other functions. Coding tandem repeats appear to represent a largely unexplored mechanism of generating diversity in the Neisseria spp.Variable copy number tandem repeats have been observed in a number of prokaryotic genomes [1,2]. These are adjacent sequences that are directly repeated, the repeated units of which may be identical or partially degenerate. Coding tandem repeats are those tandem repeats that are completely contained within a coding sequence and are composed of repeated units in which copy number will not disrupt the reading frame. Therefore, all coding tandem repeats have repeated units composed of 3 bp or multiples of 3 bp. These are distinct from intergenic repeats and from repeats such as those that mediate phase variation. There are many examples in which variation in copy number within coding tandem repeats has been shown to affect