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

Pavlek, Martina; Gelfand, Yevgeniy; Plohl, Miroslav; Meštrović, Nevenka (2015) 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. DNA Research, 22 (6). pp. 1-15. ISSN 1340-2838

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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.

Item Type:

Article

Uncontrolled Keywords:

tandem repeats; euchromatic regions; evolutionary trends; transposition; Tribolium castaneum

Subjects:

NATURAL SCIENCES > Biology

Divisions:

Division of Molecular Biology

Projects:

Project title	Project leader	Project code	Project type
Evolution, properties and functional interactions of satellite DNA sequences (Evolucija, osobitosti i funkcionalne interakcije sekvenci satelitnih DNA)	Miroslav Plohl	098-0982913-2756	MZOS

Depositing User:

Martina Pavlek

Date Deposited:

03 May 2016 14:09

URI:

http://fulir.irb.hr/id/eprint/2789

DOI:

10.1093/dnares/dsv021