Characterization of a complex satellite DNA in the mollusc Donax trunculus: analysis of sequence variations and divergence.

A highly repetitive sequence in the genomic DNA of the bivalve mollusc Donax trunculus (Dt) has been identified upon restriction with EcoRV. During the time-course of DNA digestion, genomic fragments resolved electrophoretically into a ladder-like banding pattern revealing a tandem arrangement of the repeated elements, thus representing satellite DNA sequences. Cloning and sequence analysis unraveled the presence of two groups of monomer units which can be considered distinctive satellite subfamilies. Each subclass is distinguishable by the presence of 17 evenly spread diagnostic nucleotides (nt). The respective consensus sequences are 155 bp in length and differ by 11%, while relevant internal substructures were not observed. The two satellite subfamilies constitute 0.23 and 0.09% of the Dt genome, corresponding to 20 000 and 7600 copies per haploid complement, respectively. Sequence mutations often appear to be shared between two or more monomer variants, indicating a high degree of homogenization as opposed to that of random mutational events. Shared mutations among variants appear either as single changes or in long stretches. This pattern may arise from gene conversion mechanisms acting at different levels, such as the spread of nt sequences of a similar length to the monomer repeat itself, and the diffusion of short tracts a few bp long. Subfamilies might have evolved from the occasional amplification and spreading of a monomer variant effected by gene conversion events.