Tandem repeat-containing MITEs in the clam Donax trunculus

Šatović, Eva; Plohl, Miroslav (2013) Tandem repeat-containing MITEs in the clam Donax trunculus. Genome Biology and Evolution, 5 (12). pp. 2549-2559. ISSN 1759-6653

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Abstract

Two distinct classes of repetitive sequences, interspersed mobile elements and satellite DNAs, shape eukaryotic genomes and drive their evolution. Short arrays of tandem repeats can also be present within non autonomous miniature inverted repeat transposable elements (MITEs). In the clam Donax trunculus, we characterized a composite, high copy number MITE,named DTC84. It is omposed of a central region built of upto five core repeats linked to a microsatellite segment at one array end and flanked by sequences holding short inverted repeats. The modular composition and the conserved putative target site duplication sequence AA at the element termini are equivalent to the composition of several elements found in the cupped oyster Crassostrea virginica and in some insects. A unique featureof D. trunculus element is ordered array of core repeat variants,distinctive by diagnostic changes. Position of variants in the array is fixed, regardless of alterations in the core repeat copy number. Each repeat harbors a palindrome near the junction with the following unit, being a potential hotspot responsible for array length variations. As a consequence, variations in number of tandem repeats and variations in flanking sequences make every sequenced element unique. Core repeats may be thus considered as individual units within the MITE, with flanking sequences representing a “cassette” for internal repeats. Our results demonstrate that onset and spread of tandem repeats can be more intimately linked to processes of transposition than previously thought and suggest that genomes are shaped by interplays within a complex network of repetitive sequences.

Item Type:	Article
Uncontrolled Keywords:	mobile element; MITE; satellite DNA; tandem repeats; sequence rearrangements; evolution
Subjects:	NATURAL SCIENCES > Biology > Genetics, Evolution and Phylogenetics
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:	Eva Šatović Vukšić
Date Deposited:	25 Jan 2016 16:03
URI:	http://fulir.irb.hr/id/eprint/2414
DOI:	10.1093/gbe/evt202

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