Plant Physiol. PAM Fluorometers & Gas Exchange
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH
QUICK SEARCH:   [advanced]


     

Plant Physiology Preview
Published on September 15, 2006; 10.1104/pp.106.083642

This Article
Right arrow Full Text (Plant Physiology Preview (PDF))
Right arrow Supplemental Data
Right arrow All Versions of this Article:
142/3/820    most recent
pp.106.083642v1
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 PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Yang, X.
Right arrow Articles by Cheng, Z.-M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Yang, X.
Right arrow Articles by Cheng, Z.-M.
Agricola
Right arrow Articles by Yang, X.
Right arrow Articles by Cheng, Z.-M.

Received May 15, 2006
Accepted August 26, 2006

Divergence of the Dof Gene Families in Poplar, Arabidopsis and Rice Suggests Multiple Modes of Gene Evolution after Duplication

Xiaohan Yang , Gerald A. Tuskan , and (Max) Zong-Ming Cheng *

Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996; Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996

* Corresponding author; email: zcheng{at}utk.edu.

It is widely accepted that gene duplication is a primary source of genetic novelty. However, the evolutionary fate of duplicated genes remains largely unresolved. The classical Ohno's Duplication-Retention-Non/Neofunctionalization (DRNNF) theory, and the recently proposed alternatives such as subfunctionalization (SF) or duplication-degeneration-complementation (DDC), and subneofunctionalization (SNF), each can explain one or more aspects of gene fate after duplication. Duplicated genes are also affected by epigenetic changes. We constructed a phylogenetic tree using Dof (DNA-binding with one finger) protein sequences from poplar (Populus trichocarpa Torr. & Gray ex Brayshaw), Arabidopsis (Arabidopsis thaliana L.) and rice (Oryza sativa L.). From the phylogenetic tree, we identified 27 pairs of paralogous Dof genes in the terminal nodes. Analysis of protein motif structure of the Dof paralogs and their ancestors revealed six different gene fates after gene duplication. Differential protein methylation was revealed between a pair of duplicated poplar Dof genes, which have identical motif structure and similar expression pattern, indicating that epigenetics is involved in evolution. Analysis of RT-PCR, MPSS (massively parallel signature sequencing) and microarray data revealed that the paralogs differ in expression pattern. Furthermore, analysis of nonsynonymous and synonymous substitution rates indicated that divergence of the duplicated genes was driven by positive selection. About half of the motifs in Dof proteins were shared by non-Dof proteins in the three plants species, indicating that motif cooption may be one of the forces driving gene diversification. We provided evidence that the DRNNF, SF/DDC, and SNF hypotheses are complementary with, not alternative to, each other.




This article has been cited by other articles:


Home page
 Plant CellHome page
J. Nilsson, A. Karlberg, H. Antti, M. Lopez-Vernaza, E. Mellerowicz, C. Perrot-Rechenmann, G. Sandberg, and R. P. Bhalerao
Dissecting the Molecular Basis of the Regulation of Wood Formation by Auxin in Hybrid Aspen
PLANT CELL, April 1, 2008; 20(4): 843 - 855.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH
ASPB Publications PLANT PHYSIOLOGY THE PLANT CELL
Copyright © 2006 by the American Society of Plant Biologists