title: 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 tandem of primary repeat units. In beetle Tribolium castaneum, considered as a model case for genome studies, large tandem repeats have been identified, but no HORs have been reported. Here, using our novel robust repeat finding algorithm Global Repeat Map, we discover two regular and six complex HORs in T. castaneum. In organizational pattern, the integrity and homogeneity of regular HORs in T. castaneum resemble human regular HORs (with T. castaneum monomers 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. castaneum appear as most 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.
authors: Faculty of Science, University of Zagreb, Zagreb, Croatia.
authors: Ines
authors: I
authors: Vlahovic
authors: Faculty of Science, University of Zagreb, Zagreb, Croatia.
authors: Matko
authors: M
authors: Gluncic
authors: Croatian Academy of Sciences and Arts, Zagreb, Croatia.
authors: Marija
authors: M
authors: Rosandic
authors: Institute Ruder Boškovic, Zagreb, Croatia.
authors: Ðurdica
authors: Ð
authors: Ugarkovic
authors: Faculty of Science, University of Zagreb, Zagreb, Croatia.|Croatian Academy of Sciences and Arts, Zagreb, Croatia.
authors: Vladimir
authors: V
authors: Paar
mesh_terms: D000818:Animals; D017124:Conserved Sequence; D019143:Evolution, Molecular; D049750:Genome, Insect; D012091:Repetitive Sequences, Nucleic Acid; D014231:Tribolium / Q000235:genetics*
keywords: Global Repeat Map; Tribolium castaneum; higher order repeats; insect genome; regulatory elements