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MBE Advance Access originally published online on April 27, 2005
Molecular Biology and Evolution 2005 22(7):1621-1626; doi:10.1093/molbev/msi154
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oupjournals.org

Research Article

Evolution of Noncoding and Silent Coding Sites in the Plasmodium falciparum and Plasmodium reichenowi Genomes

Daniel E. Neafsey*,1, Daniel L. Hartl* and Matt Berriman{dagger}

* Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA; and {dagger} Wellcome Trust Sanger Institute, Hinxton, United Kingdom

E-mail: neafsey{at}broad.mit.edu.

We compared levels of sequence divergence between fourfold synonymous coding sites and noncoding sites from the intergenic and intronic regions of the Plasmodium falciparum and Plasmodium reichenowi genomes. We observed significant differences in the level of divergence between these classes of silent sites. Fourfold synonymous coding sites exhibited the highest level of sequence divergence, followed by introns, and then intergenic sequences. This pattern of relative divergence rates has been observed in primate genomes but was unexpected in Plasmodium due to a paucity of variation at silent sites in P. falciparum and the corollary hypothesis that silent sites in this genome may be subject to atypical selective constraints. Exclusion of hypermutable CpG dinucleotides reduces the divergence level of synonymous coding sites to that of intergenic sites but does not diminish the significantly higher divergence level of introns relative to intergenic sites. A greater than expected incidence of CpG dinucleotides in intergenic regions less than 500 bp from genes may indicate selective maintenance of regulatory motifs containing CpGs. Divergence rates of different classes of silent sites in these Plasmodium genomes are determined by a combination of mutational and selective pressures.

Key Words: malaria • plasmodium • reichenowi • noncoding • divergence • introns


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