ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2015
Genome-wide analysis of tandem repeats in Tribolium castaneum genome reveals abundant and highly dynamic tandem repeat families with satellite DNA features in euchromatic chromosomal arms.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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54 citing papers in PubMed, 92 citations in OpenAlex.
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- Satellite DNA Genomics: The Ongoing Story.International journal of molecular sciences · 2025Review
- Dynamic evolution of satellite DNAs drastically differentiates the genomes ofGenome research · 2025Article
- Repetitive DNAs and Karyotype Evolution in Phyllostomid Bats (Chiroptera: Phyllostomidae).Biomolecules · 2025Article
- Exploring the Satellitome of the Pest Aphid Acyrthosiphon pisum (Hemiptera, Aphididae): Insights Into Genome Organization and Intraspecies Evolution.Genome biology and evolution · 2025Article
- Large tandem repeats of grass frog (Rana temporaria) in silico and in situ.BMC genomics · 2025Article
- The highly dynamic satellitomes of cultivated wheat species.Annals of botany · 2024Article
- SatXplor-a comprehensive pipeline for satellite DNA analyses in complex genome assemblies.Briefings in bioinformatics · 2024Article
- Long-read genome assembly of the insect model organismGenome research · 2024Article
- Satellitome Analysis ofInternational journal of molecular sciences · 2024Article
- Comprehensive analysis of the Xya riparia genome uncovers the dominance of DNA transposons, LTR/Gypsy elements, and their evolutionary dynamics.BMC genomics · 2024Article
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- Evolution of ancient satellite DNAs in extant alligators and caimans (Crocodylia, Reptilia).BMC biology · 2024Article
- SINE-derived satellites in scaled reptiles.Mobile DNA · 2023Article
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- Reference-Guided De Novo Genome Assembly of the Flour BeetleInternational journal of molecular sciences · 2022Article
- Satellitome Analysis and Transposable Elements Comparison in Geographically Distant Populations ofLife (Basel, Switzerland) · 2022Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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