Evaluation of intra- and interspecific divergence of satellite DNA sequences by nucleotide frequency calculation and pairwise sequence comparison

Abstract

Satellite DNA sequences are known to be highly variable and to have been subjected to concerted evolution that homogenizes member sequences within species. We have analyzed the mode of evolution of satellite DNA sequences in four fishes from the genus Diplodus by calculating the nucleotide frequency of the sequence array and the phylogenetic distances between member sequences. Calculation of nucleotide frequency and pairwise sequence comparison enabled us to characterize the divergence among member sequences in this satellite DNA family. The results suggest that the evolutionary rate of satellite DNA in D. bellottii is about two-fold greater than the average of the other three fishes, and that the sequence homogenization event occurred in D. puntazzo more recently than in the others. The procedures described here are effective to characterize mode of evolution of satellite DNA.

Fig. 1

Alignment of nucleotide sequences of Sparidae satellite DNA monomeric units. Dashes (-) indicate the sites of gaps. Nucleotide position 1 is located at the C residue of the HindIII restriction site. Sequence origins and accession numbers are given at the left.

Fig. 2

Subrepeat alignment of Percoidei satellite monomeric units. A satellite DNA member from Diplodus annularis (Z48694) exemplifies the subrepeat organization. The satellite DNA monomers are each divided into two subregions, and the potential subrepeats are aligned. The hot spot for insertion/deletion is underlined and highly variable sites (SI(k)<0.8; see Fig. 3) are double-underlined. The monomeric unit of current Sparidae satellite DNA consists of the eight subrepeats in the order EFFFFEEF as noted previously (14).

Fig. 3

Distribution of SI(k) scores in satellite DNA. The geometric means of six Sparidae fishes are calculated for each position and plotted against the nucleotide sequence.

Fig. 4

Comparison of 2lt scores obtained using two different protocols. The 2λt scores calculated for six Sparidae fishes by pairwise sequence comparison (J-Cd, vertical axis) are plotted against those obtained by nucleotide frequency calculation (SIGM, horizontal axis).

Fig. 5

Unrooted Fitch-Margoliash tree for six Sparidae fishes. The branch lengths and tree topology were computed using the program "Fitch" (18) according to the method of Fitch and Margoliash (22). Distance matrix of average J-Cd scores (Table 2) is used to reconstruct the tree. The tree was drawn using the program "TreeView PPC" (23). Formulas yielding the branch lengths and the calculated branch length scores are shown for the respective branches.