Satellite DNA as a Driver of Population Divergence in the Red Flour Beetle Tribolium castaneum

Abstract

Tandemly repeated satellite DNAs are among most rapidly evolving sequences in eukaryotic genome, usually differing significantly among closely related species. By inducing changes in heterochromatin and/or centromere, satellite DNAs are expected to drive population and species divergence. However, despite high evolutionary dynamics, divergence of satellite DNA profiles at the level of natural population which precedes and possibly triggers speciation process is not readily detected. Here, we characterize minor TCAST2 satellite DNA of the red flour beetle Tribolium castaneum and follow its dynamics among wild-type strains originating from diverse geographic locations. The investigation revealed presence of three distinct subfamilies of TCAST2 satellite DNA which differ in monomer size, genome organization, and subfamily specific mutations. Subfamilies Tcast2a and Tcast2b are tandemly arranged within pericentromeric heterochromatin whereas Tcast2c is preferentially dispersed within euchromatin of all chromosomes. Among strains, TCAST2 subfamilies are conserved in sequence but exhibit a significant content variability. This results in overrepresentation or almost complete absence of particular subfamily in some strains and enables discrimination between strains. It is proposed that homologous recombination, probably stimulated by environmental stress, is responsible for the emergence of TCAST2 satellite subfamilies, their copy number variation and dispersion within genome. The results represent the first evidence for the existence of population-specific satellite DNA profiles. Partial organization of TCAST2 satellite DNA in the form of single repeats dispersed within euchromatin additionally contributes to the genome divergence at the population level.

Great Abundance of Satellite DNA in <b><i>Proceratophrys</i></b> (Anura, Odontophrynidae) Revealed by Genome Sequencing

“…SatDNAs do not encode proteins; however, their transcription has been reported in many organisms, including vertebrates, invertebrates, and plants, where they participate in the formation of heterochromatin [Feliciello et al, 2015]. Moreover, Palacios-Gimenez et al [2018] have recently used Gryllus assimilis DNA and RNA sequences to address the content and transcriptional patterns of the satDNAs found in this cricket species.…”

Sex chromosome repeats tip the balance towards speciation

“…In these examples, the rapid evolution of satellite DNAs is implicated in speciation through incompatibilities observed in a hybrid state. A requisite for emerging incompatibilities at the population level is the rapid evolution of repeats concomitant with subpopulation level variation (Ugarkovic & Plohl, 2002), which has recently been detected employing genomics techniques (Feliciello, Akrap, Brajkovic, Zlatar, & Ugarkovic, 2014;Miga et al, 2014;White, Cheng, Simard, Costantini, & Besansky, 2010). Another facet of sex chromosome biology In mammals, dosage compensation, achieved by inactivation of a single X in females, is facilitated by a primary noncoding RNA, Xist (Monfort & Wutz, 2017).…”

Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata)

“…The stDNAs are considered to be involved in the organization of chromosomes during mitosis or meiosis; they are also genomic elements which differentiate rapidly within the genome [ 9 , 10 ]. Multiple stDNA families of independent origin coexist in the genome of a species, and they commonly differ in nucleotide sequences and copy number [ 9 , 11 – 15 ]. Within a species, monomers of a stDNA family may exhibit higher sequence similarity than the same stDNA family of related species [ 9 , 16 , 17 ].…”