Repeat arrays in protein-coding sequences were analyzed by a novel approach, based on analyzing the distribution of the pairwise proportion of nucleotide differences among units within a repeat array. The results showed that evidence of recent repeat array expansion was particularly characteristic of the repeat arrays of the malaria parasites (genus Plasmodium), supporting the hypothesis that Plasmodium is particularly prone to repeat array expansion by slipped-strand mispairing or a similar mechanism. Repeat arrays in Plasmodium asexual-stage antigens (which are exposed to the immune system of the vertebrate host) had unique characteristics with respect to the number of repeat units, as well as nucleotide and amino acid composition, suggesting that natural selection exerted by the host immune system has shaped features of these arrays.
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This research was supported by Grant GM043940 from the National Institutes of Health. I am grateful to Federica Verra for comments on the manuscript.
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