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Primate Research Institute, Kyoto University
Kato / Poster
Evaluation of the phylogenetic distances between alpha satellite DNA
Mikio KATO, Department of Life Sciences, Osaka Prefecture University
Background: The alpha-satellite DNA, tandem arrayed repetitive sequences in the primates, are known to be chromosome-specific, exist mainly in the centromeric region of the chromosomes, and participate in the centromere construction with centromere specific proteins (CENPs). Laursen et al. (1992) have compared the higher order repeat (HOR) units of alpha-satellite DNA from X chromosomes among five species of primates, and suggested the rapid alteration of the human satellite DNA. Organization of tandem arrayed repeating units has been analyzed by the pairwise comparison of monomers, and the molecular evolution of the HORs has been proposed (Greig et al., 1993). The pairwise base-to-base comparison is, however, not sufficient to explain the relationship among the alpha-satellite sequences in various chromosomes, since respective HORs have evolved differently due to the events of unequal crossing over and gene conversion which have occurred during evolutionary processes. Here we propose an alternative method of sequence comparison using nucleotide frequency, which allows us quantitative analysis of the distance between the tandem arrayed repetitive DNA sequences, and demonstrate the phylogenetic relationship of chromosome-specific satellite DNA. Method: Tandem arrayed repetitive DNA segments were aligned with unit length repeat, and the nucleotide frequency at each position was used to estimate the phylogenetic distance between repetitive DNA segments. Results: The calculation among human and chimpanzee X chromosome-specific satellites showed the results consistent with known relation of primates, indicating that the nucleotide frequency calculation worked effectively to estimate the distances between satellite arrays. Human chromosome-specific satellites had been grouped into three suprachromosomal families (I, II and III) by Alexandrov et al. (1988), and in the present work, the nucleotide frequency analysis has defined quantitative distances among these suprachromosomal families. The results suggest that the distances between human chromosomes 21 (family II)- and X (family III)-specific satellite DNA are about four-times larger than those between human and common chimpanzee X chromosome-specific satellite DNA.
Alexandrov, I A, Mitkevich, S P and Yurov, Y B (1988) Chromosoma 96: 443-453.