Genome-wide analysis of tandem repeats inTribolium castaneumgenome reveals abundant and highly dynamic tandem repeat families with satellite DNA features in euchromatic chromosomal arms

Abstract

Although satellite DNAs are well-explored components of heterochromatin and centromeres, little is known about emergence, dispersal and possible impact of comparably structured tandem repeats (TRs) on the genome-wide scale. Our bioinformatics analysis of assembled Tribolium castaneum genome disclosed significant contribution of TRs in euchromatic chromosomal arms and clear predominance of satellite DNA-typical 170 bp monomers in arrays of ≥5 repeats. By applying different experimental approaches, we revealed that the nine most prominent TR families Cast1–Cast9 extracted from the assembly comprise ∼4.3% of the entire genome and reside almost exclusively in euchromatic regions. Among them, seven families that build ∼3.9% of the genome are based on ∼170 and ∼340 bp long monomers. Results of phylogenetic analyses of 2500 monomers originating from these families show high-sequence dynamics, evident by extensive exchanges between arrays on non-homologous chromosomes. In addition, our analysis shows that concerted evolution acts more efficiently on longer than on shorter arrays. Efficient genome-wide distribution of nine TR families implies the role of transposition only in expansion of the most dispersed family, and involvement of other mechanisms is anticipated. Despite similarities in sequence features, FISH experiments indicate high-level compartmentalization of centromeric and euchromatic tandem repeats.

Comparative repeatome analysis on Triatoma infestans Andean and Non-Andean lineages, main vector of Chagas disease

“…infestans [36]. SatDNA characterization by genome sequencing suggests that their presence on the euchromatic regions is not uncommon, as has been reported in some insect species as Tribolium castaneum [37] and Locusta migratoria [16], as well as in plant species [38]. For these satDNA families it is probable that classical techniques for satDNA isolation fail due to their lower amount in comparison with the families located in the heterochromatin.…”

Adjacent sequences disclose potential for intra-genomic dispersal of satellite DNA repeats and suggest a complex network with transposable elements

“…The experimental approach has evident limitations, and can be easily biased, for example, due to the construction of genomic library and the library size. On the other hand, limitations in sequence assemblies regularly make large satDNA domains excluded from datasets, and, as a consequence, short arrays such as those of Cg170 satDNA may become apparently “enriched” in the assembled genome (for the discussion about this point, see [19]). Sets explored in this survey are of comparable size and represent a kind of genomic cross-section that can be indicative of at least some patterns of associations between satDNAs and other genomic sequences.…”

“…In addition to localized organization into long homogeneous arrays of heterochromatin, growing evidence suggests a much broader, genome-wide distribution of satDNAs [10, 18, 19]. Analysis of sequence variability performed on the 1.688 satDNA of Drosophila [20] and on satDNAs of the beetle Tribolium castaneum [19] showed that satDNA copies located in euchromatic chromosomal domains evolve under similar rules as their counterparts in heterochromatic compartments.…”

“…Analysis of sequence variability performed on the 1.688 satDNA of Drosophila [20] and on satDNAs of the beetle Tribolium castaneum [19] showed that satDNA copies located in euchromatic chromosomal domains evolve under similar rules as their counterparts in heterochromatic compartments. A heat-stress induced regulatory mechanism of transient genome-wide heterochromatinization has been recently proposed in T. castaneum as a possible functional role of isolated euchromatic satDNA copies [21].…”

“…SatDNA monomers at array ends often show enhanced level of decay, a phenomenon considered to be a consequence of the lack of sequence homogenization of terminal repeats by unequal crossover [22–25]. However, observed exceptions to this rule can be either because junctions were recently formed or because monomers are not homogenized by unequal crossover at all, for example, if arrays are too short and/or isolated from the rest [19, 26, 27], or are supposed to evolve under constraints [20, 21]. In any case, considering the available data, satDNA sequence ends mostly form well-defined junctions, irrespective of whether they are between different satDNAs [26–29], satDNAs and TEs [22, 30], or satDNAs and other sequences [20, 31].…”