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Interweaving of satellite DNAs and mobile elements in the Pacific oyster Crassostrea gigas (Thunberg, 1793)

Tandem and interspersed repetitive DNA sequences make up a large part of eukaryotic genomes, being present also in bivalves (class Bivalvia), a cosmopolitan group of organisms of large ecological and commercial importance. Bivalve genomes are populated by elements of a pearl family (Gaffney et al. J. Mol. Evol. 2003, 56:308), which are similar to MITEs (miniature inverted-repeat transposable elements) and bear short tandem repeats, thus linking satellite DNAs and transposable elements. These elements are characterized by a modular structure composed of a left flanking sequence followed by several tandem repeats of about 160 bp long repeat unit, an imperfect microsatellite repeat motif (ACRG)n and a right flanking sequence. Typically, imperfect inverted repeats (app. 10 - 20 bp) are located at terminal and subterminal positions and elements are flanked with a two-nucleotide target site duplication. Here we characterize a new MITE-like element, named Cragi 1, detected by bioinformatic analysis of the sequenced and assembled genome of the Pacific oyster, Crassostrea gigas. This element resembles pearl in its modular structure, while its internal tandem repeats show 80 - 82% sequence similarity with the highly abundant Cg170 satellite DNA already described in this species (Clabby et al. Gene 1996, 168:205). It was observed that internal tandem repeats found in Cragi 1 can be repeated up to 12 times, more than previously described for tandem repeat-containing MITEs. Stretches of the left and right flanking sequences show sequence similarity to the pearl element characterized in the oyster Crassostrea virginica. The highest sequence similarity is in the part that includes terminal and subterminal inverted repeats. Using primers for conserved left and right flanking regions, presence of Cragi 1 elements and their variability in terms of modular structure and DNA sequence were also explored experimentally. The described Cragi 1 MITE-like element and its sequence similarity with the species-specific satellite DNA reveal a close connection between the two groups of repetitive DNAs. We propose that such MITE-like elements could be critical in initial genesis of satellite repeats, a process which is still poorly understood.

repetitive DNA; satellite DNA; transposable elements

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