Skip Navigation


MBE Advance Access originally published online on April 6, 2006
Molecular Biology and Evolution 2006 23(6):1318-1323; doi:10.1093/molbev/msk017
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (PDF) Freely available
Right arrow All Versions of this Article:
23/6/1318    most recent
msk017v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (4)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Hobolth, A.
Right arrow Articles by Tanksley, S. D.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Hobolth, A.
Right arrow Articles by Tanksley, S. D.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
M. Anisimova and C. Kosiol
Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models
Mol. Biol. Evol., February 1, 2009; 26(2): 255 - 271.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
B. R. Morton, V.-u.-N. Dar, and S. I. Wright
Analysis of Site Frequency Spectra from Arabidopsis with Context-Dependent Corrections for Ancestral Misinference
Plant Physiology, February 1, 2009; 149(2): 616 - 624.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
W. Delport, K. Scheffler, and C. Seoighe
Models of coding sequence evolution
Brief Bioinform, January 1, 2009; 10(1): 97 - 109.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
Y. Wang, A. Diehl, F. Wu, J. Vrebalov, J. Giovannoni, A. Siepel, and S. D. Tanksley
Sequencing and Comparative Analysis of a Conserved Syntenic Segment in the Solanaceae
Genetics, September 1, 2008; 180(1): 391 - 408.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
J. L. Thorne, S. C. Choi, J. Yu, P. G. Higgs, and H. Kishino
Population Genetics Without Intraspecific Data
Mol. Biol. Evol., August 1, 2007; 24(8): 1667 - 1677.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.