Document Detail

Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus.
MedLine Citation:
PMID:  21974993     Owner:  NLM     Status:  MEDLINE    
Comparative analysis of multiple angiosperm genomes has implicated gene duplication in the expansion and diversification of many gene families. However, empirical data and theory suggest that whole-genome and small-scale duplication events differ with respect to the types of genes preserved as duplicate pairs. We compared gene duplicates resulting from a recent whole genome duplication to a set of tandemly duplicated genes in the model forest tree Populus trichocarpa. We used a combination of microarray expression analyses of a diverse set of tissues and functional annotation to assess factors related to the preservation of duplicate genes of both types. Whole genome duplicates are 700 bp longer and are expressed in 20% more tissues than tandem duplicates. Furthermore, certain functional categories are over-represented in each class of duplicates. In particular, disease resistance genes and receptor-like kinases commonly occur in tandem but are significantly under-retained following whole genome duplication, while whole genome duplicate pairs are enriched for members of signal transduction cascades and transcription factors. The shape of the distribution of expression divergence for duplicated pairs suggests that nearly half of the whole genome duplicates have diverged in expression by a random degeneration process. The remaining pairs have more conserved gene expression than expected by chance, consistent with a role for selection under the constraints of gene balance. We hypothesize that duplicate gene preservation in Populus is driven by a combination of subfunctionalization of duplicate pairs and purifying selection favoring retention of genes encoding proteins with large numbers of interactions.
Eli Rodgers-Melnick; Shrinivasrao P Mane; Palitha Dharmawardhana; Gancho T Slavov; Oswald R Crasta; Steven H Strauss; Amy M Brunner; Stephen P Difazio
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Publication Detail:
Type:  Journal Article     Date:  2011-10-05
Journal Detail:
Title:  Genome research     Volume:  22     ISSN:  1549-5469     ISO Abbreviation:  Genome Res.     Publication Date:  2012 Jan 
Date Detail:
Created Date:  2012-01-04     Completed Date:  2012-04-24     Revised Date:  2013-06-27    
Medline Journal Info:
Nlm Unique ID:  9518021     Medline TA:  Genome Res     Country:  United States    
Other Details:
Languages:  eng     Pagination:  95-105     Citation Subset:  IM    
Department of Biology, West Virginia University, Morgantown, West Virginia 26506, USA.
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MeSH Terms
Evolution, Molecular*
Gene Duplication / physiology*
Gene Expression Regulation, Plant / physiology
Genome, Plant / physiology*
Models, Genetic*
Plant Diseases / genetics
Plant Proteins / genetics,  metabolism
Populus / physiology*
Signal Transduction / physiology
Transcription Factors / genetics,  metabolism
Reg. No./Substance:
0/Plant Proteins; 0/Transcription Factors

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