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MBE Advance Access originally published online on April 6, 2006
Molecular Biology and Evolution 2006 23(6):1318-1323; doi:10.1093/molbev/msk017
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© The Author 2006. 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@oxfordjournals.org

Research Article

CpG + CpNpG Analysis of Protein-Coding Sequences from Tomato

Asger Hobolth*, Rasmus Nielsen{dagger}, Ying Wang{ddagger}, Feinan Wu{ddagger} and Steven D. Tanksley{ddagger}

* Bioinformatics Research Center, North Carolina State University; {dagger} Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark; and {ddagger} Department of Plant Biology, Cornell University

E-mail: asger{at}daimi.au.dk.

We develop codon-based models for simultaneously inferring the mutational effects of CpG and CpNpG methylation in coding regions. In a data set of 369 tomato genes, we show that there is very little effect of CpNpG methylation but a strong effect of CpG methylation affecting almost all genes. We further show that the CpNpG and CpG effects are largely uncorrelated. Our results suggest different roles of CpG and CpNpG methylation, with CpNpG methylation possibly playing a specialized role in defense against transposons and RNA viruses.

Key Words: codon model • context dependency • CpG + CpNpG methylation


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