Regular higher order repeat structures in beetle tribolium castaneum genome

Abstract

Higher order repeats (HORs) containing tandems of primary and secondary repeat units (head-to-tail "tandem within tandem pattern"), referred to as regular HORs, are typical for primate alpha satellite DNAs and most pronounced in human genome. Regular HORs are known to be a result of recent evolutionary processes. In non-primate genomes mostly so called complex HORs have been found,without head to tail tandemof primary repeat units. In beetle Triboliumcastaneum, considered as amodel case for genome studies, large tandem repeats have been identified, but no HORs have been reported. Here, using our novel robust repeat finding algorithmGlobal RepeatMap, we discover two regular and six complex HORs in T. castaneum. In organizational pattern, the integrity and homogeneity of regular HORs in T. castaneumresemble human regular HORs (with T. castaneummonomers different from human alpha satellite monomers), involving a wider range of monomer lengths than in human HORs. Similar regular higher order repeat structures have previously not been found in insects. Some of these novel HORs in T. castaneumappear asmost regular among known HORs in non-primate genomes, although with substantial riddling. This is intriguing, in particular from the point of view of role of non-coding repeats in modulation of gene expression.