Inversions and inverted transpositions as generators of universal genome properties

Transpositions have been identified as built-in responses to genome shock [17] andas agents of genome variation. In addition, they seem to give rise to several universalgenome features that may be essential to distinguish functional genomes frommeaningless poly-nucleotide and, thus, may facilitate horizontal genome transfer.Examples of such universals appear to be the universal strand symmetry, sometimescalled "Chargaff's second parity rule", and the almost universal tri-nucleotide frequencydistribution, called "majority profile". Both could be explained as products of the actionsof countless inversions and inverted transpositions in the evolutionary past of thegenomes [1-3].As reported here, these particular products of inversions/transpositions give rise toyet another apparent universal in the following way. The genomes whose triplet profilesare almost identical with the majority profile define a large group of organisms called the'majority group'. In spite of the fact that the triplet profiles of their genomes are almostidentical with the majority profile, they may locally deviate from it, nevertheless. In thischapter I will introduce the graphs of these local deviations as "profile signatures" andshow their high degree of conservation during the evolution of orders. In addition, theyoffer rapid and comprehensive overviews over chromosome rearrangements and areas ofsynteny.The signatures themselves are obviously not genome universals. However, theunderlying process which causes their local deviations from the majority profile appearsto be yet another universal, which can be linked directly to the action of inversions/transpositions.