Download Hanada_et_all_cover_ml_shs - Shiu Lab

Nov. 26, 2007
Dear Editors,
Enclosed please find the manuscript entitled “Influence of Gene Function and Duplication
Mechanism on the Retention of Duplicate Genes During Vascular Plant Evolution”. From the
gene content perspective, plants are distinct from most other eukaryotes in that they contain
a higher proportion of recent duplicate genes. This is due to more frequent genome doubling
and tandem duplication. Given that gene duplication provides much of the raw material for
functional evolution of genes, we are particularly interested in determining, over the course
of land plant evolution, if there is functional bias in the genes that are retained and if the
mechanism of gene duplication affects such bias.
We have conducted a global analysis of gene families from four plant species (moss, rice,
poplar, and Arabidopsis thaliana) and found that duplication mechanisms have a significant
effect on expansion patterns. In addition, genes that have expanded via tandem duplication
are enriched in categories related to responses to environmental stimuli while those that
have expanded via non-tandem mechanisms tend to have intracellular regulatory roles.
Furthermore, we found that tandem duplicates are more likely to be up-regulated under
stress conditions than non-tandem duplicates. Our findings suggest that genes expanded via
tandem duplication are enriched in stress responsive genes which may be important for
adaptive evolution to rapidly changing environments.
To our knowledge, this is the first comparative analysis of lineage-specific expansion,
functional bias of expanded genes, and influence of duplication mechanism in eukaryotes.
We believe that these results will be of general and immediate interest to the readers of
PNAS.
Recommended Editorial Board Members:
Doebley, John F.
Li, Wen-Hsiung
Clegg, Michael T.
Suggested Referees:
Yves Van de Peer, Ghent University
Liqing Zhang, Virginia Tech
Brandon Gaut, University of California, Irvine
Todd Vision, University of North Carolina
Jim Leebens-Mack, University of Georgia
Sincerely,
Shin-Han Shiu
Michigan State University
Dept. Plant Biology
[email protected]