Satellite DNAs represent the most abundant fraction of repetitive sequences in genomes of almost all eukaryotic species. Long arrays of satellite DNA monomers form densely packed heterochromatic genome compartments and also span over the functionally important centromere locus. Many specific features can be ascribed to the evolution of tandemly repeated genomic components. This chapter focuses on the structural and evolutionary dynamics of satellite DNAs and the potential molecular mechanisms responsible for rapid changes of the genomic areas they constitute. Monomer sequences of a satellite DNA evolve concertedly through a process of molecular drive in which mutations are homogenized in a genome and fixed in a population. This process results in divergence of satellite sequences in reproductively isolated groups of organisms. However, some satellite DNA sequences are conserved over long evolutionary periods. Since many satellite DNAs exist in a genome, the evolution of species-specific satellite DNA composition can be directed by copy number changes within a library of satellite sequences common for a group of species. There are 2 important features of these satellite DNAs: long time sequence conservation and, at the same time, proneness to rapid changes through copy number alterations. Sequence conservation may be enhanced by constraints such as those imposed on functional motifs and/or architectural features of a satellite DNA molecule. Such features can limit the selection of sequences able to persist in a genome, and can direct the evolutionary course of satellite DNAs spanning the functional centromeres.

The centromere is a chromosomal locus responsible for the faithful segregation of genetic material during cell division. It has become evident that centromeres can be established literally on any DNA sequence, and the possible synergy between DNA sequences and the most prominent centromere identifiers, protein components, and epigenetic marks remains uncertain. However, some evolutionary preferences seem to exist, and long-term established centromeres are frequently formed on long arrays of satellite DNAs and/or transposable elements. Recent progress in understanding functional centromere sequences is based largely on the high-resolution DNA mapping of sequences that interact with the centromere-specific histone H3 variant, the most reliable marker of active centromeres. In addition, sequence assembly and mapping of large repetitive centromeric regions, as well as comparative genome analyses offer insight into their complex organization and evolution. The rapidly advancing field of transcription in centromere regions highlights the functional importance of centromeric transcripts. Here, we comprehensively review the current state of knowledge on the composition and functionality of DNA sequences underlying active centromeres and discuss their contribution to the functioning of different centromere types in higher eukaryotes.

According to the established classical view, satellite DNAs are defined as abundant non-coding DNA sequences repeated in tandem that build long arrays located in heterochromatin. Advances in sequencing methodologies and development of specialized bioinformatics tools enabled defining a collection of all repetitive DNAs and satellite DNAs in a genome, the repeatome and the satellitome, respectively, as well as their reliable annotation on sequenced genomes. Supported by various non-model species included in recent studies, the patterns of satellite DNAs and satellitomes as a whole showed much more diversity and complexity than initially thought. Differences are not only in number and abundance of satellite DNAs but also in their distribution across the genome, array length, interspersion patterns, association with transposable elements, localization in heterochromatin and/or in euchromatin. In this review, we compare characteristic organizational features of satellite DNAs and satellitomes across different animal and plant species in order to summarize organizational forms and evolutionary processes that may lead to satellitomes’ diversity and revisit some basic notions regarding repetitive DNA landscapes in genomes.