Hanada, Kousuke , Zou, Cheng , Shiu, Shin-Han .
Influence of Gene Functions and Duplication Mechanisms on the Retention of Duplicate Genes during Land Plant Evolution.
It is well known that plant genomes have gained many genes, mainly by tandem and whole-genome duplication, and that some duplicates are retained preferentially. However, the effects of the two different duplication mechanisms on duplicate retention have not been thoroughly investigated. By comparing Arabidopsis thaliana genes and genes from poplar, rice, or moss, we defined orthologous groups (OGs) to examine the retention patterns of genes duplicated via tandem and non-tandem mechanisms since most duplicated genes that are not tandem are mainly derived from whole genome duplications. Interestingly, tandem duplicated A. thaliana genes tend to be found in OGs that have expanded asymmetrically, particularly in OGs with inferred gene losses. On the other hand, duplicate genes that are not tandem tend to be enriched in OGs showing parallel lineage-specific expansion. To assess the functional bias of duplicate retention, we examined GeneOntology (GO) categories of A. thaliana genes experiencing significantly more than expected gene gains. We found that several stress related GO categories are over-represented due to the contribution of tandem duplicate genes. To determine the nature of stress conditions associated with lineage-specific expansion involving tandem duplication, we analyzed the A. thaliana stress expression dataset with 9 abiotic and 12 biotic stress conditions. We found that tandem duplicated genes are significantly up-regulated in biotic stress conditions only. Taken together, our findings indicate that tandem duplicates tend to experience asymmetric expansion, undergo more rapid turnover, and be significantly more responsive to biotic stress, reflecting strong selection pressure imposed by rapid changing environmental conditions, particularly biotic stress factors.
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1 - Michigan State University, Plant Biology
2 - Michigan State University, Plant Biology, S308 Plant Biology Building, Michigan State University, East Lansing, MI, 48824, USA
Presentation Type: Plant Biology Abstract
Location: Exhibit Hall (Northeast, Southwest & Southeast)/Hilton
Date: Sunday, July 8th, 2007
Time: 8:00 AM