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Isolation and characterization of new repetitive sequences from the mollusk Donax trunculus

Genome of the clam Donax trunculus harbors a number of low-abundant (up to 2%) satellite DNA (satDNA) sequences (Cytogenet. Genome Res. 2009 ; 124:63, and references therein). In order to amend our knowledge about repetitive DNAs in this organism, genomic libraries were constructed. Screening of colonies was preformed with labeled complete genomic DNA as a probe. In the first round, six sequences of interest, ranging in size from 306 to 1456 bp, were selected. Four of them comprise tandem repeats that could be identified as a BIV160 satDNA family, a large group of sequences widely spread in bivalve species and related to the MITE-like mobile element Pearl of oysters. Interestingly, detected sequence variants are intermediary, being distantly related to the known representatives of BIV160 family, while they are in the same time related to one of the previously characterized D. trunculus satDNAs. Another genomic clone comprises two repeats (128 and 130 bp), found in an interspersed pattern. BLAST search with these two stretches did not reveal any sequence similarity. The last fragment analyzed in this set contains four 145 bp long tandem repeats of already described D. trunculus DTHS3 satDNA family, and includes a junction between this satDNA and an uncharacterized sequence. Surprisingly, all repetitive sequences detected by this approach are AT-rich, although D. trunculus chromosomes show a dominance of GC-rich heterochromatin, and thus the presence of GC-rich repetitive DNA.

satellite DNA; genome library; Bivalvia

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