Analyses of highly repetitive DNAs in the genome of the red crab Geyron quinquedens

Previous studies on the genome organization of brachyurans (true crabs) have demonstrated the presence of large amounts of highly repetitive DNA either by density separations or reassociation techniques. Demonstration of highly repetitive DNA interspersed with single copy DNA distinguishes the genome of the red crab, Geryon quinquedens, from other eukaryotes which have been examined in this way. This interspersion feature has not been investigated for other brachyurans. The general organization of the genome of the red crab is the short period interspersion pattern typical of organisms in a wide range of taxonomic groups. The experiments in Part I define this general pattern and also show that fraction of both repetitive components, present at 4x10⁶ and 8x10⁵ copies per genome, are interspersed with single copy DNA. After isolation of these kinetic fractions and digestion with HindIII restriction endonuclease, several fragments of discrete size are produced. In Part II these fragments are shown to be elements of a multimeric series based on an 8l nucleotide (nt) fragment. The relative amounts of each of the multimers suggest that random mutation alone cannot explain a distribution of restriction sites featuring enhanced amounts of dimer, tetramer and octamer. Restriction endonuclease analyses of the octamer indicate the presence of large amounts of a divergent octamer. The pathway of evolutionary change which emerges is amplification of DNA with an 8l nt repeat unit followed by divergence followed by a second amplification of only a fraction of the original repetitive sequences.

In Part III the sequences of the basic repeating unit in the HindIII multimeric series are presented. Their characteristics are discussed relative to those of highly repetitive DNAs in other organisms. Indications of nonrandom sequence alterations in the multimers support the idea that divergent sequences have been amplified. Also present are examples of random evolutionary changes. In addition, divergence estimates based on HhaI digestion have been performed for individual multimers as a comparison to the one obtained from HindIII digestion of total DNA (Part II). The low level of divergence (4%) due to random mutation indicated from quantitation of the products of Hhal digestion is incompatible with the large amounts of dimer, tetramer and octamer produced by HindIlI digestion being formed by random mutation alone. Either selective mutation or selective amplification must be invoked to explain these results. The large number of constraints required for selective mutation to have produced the observed distribution of HindIII multimers makes a model of selective amplification more plausible.