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Series GSE9513 Query DataSets for GSE9513
Status Public on Nov 20, 2008
Title Duplicate genes increase expression diversity in closely related species and allopolyploids
Platform organism Arabidopsis thaliana
Sample organisms Arabidopsis thaliana; Arabidopsis arenosa; Arabidopsis suecica
Experiment type Expression profiling by array
Genome variation profiling by array
Summary Polyploidy or whole genome duplication (WGD) provides raw genetic materials for sequence and expression evolution of duplicate genes. However, the mode and tempo of expression divergence between WGD duplicate genes in closely relates species and recurrent allopolyploids are poorly understood. Arabidopsis is a suitable system for testing the hypothesis that duplicate genes increase expression diversity and regulatory networks. In Arabidopsis, WGD occurred more than once prior to the split between Arabidopsis thaliana and Arabidopsis arenosa, and both natural and human-made allotetraploids are available. Comparative genomic hybridization analysis indicated that single-copy and duplicate genes after WGD were well preserved in A. thaliana and A. arenosa. Analysis of gene expression microarrays showed that duplicate genes generally had higher levels of expression divergence between two closely related species than single-copy genes. The proportion of the progenitors' duplicate genes that were nonadditively expressed in the resynthesized and natural allotetraploids was significantly higher than that of single-copy genes. Duplicate genes related to environmental stresses tended to be differentially expressed, and multi-copy duplicate genes were likely to diverge expression between progenitors and in the allotetraploids. Compared to single-copy genes, duplicate genes tend to contain TATA boxes and less DNA methylation in the promoter regions, facilitating transcriptional regulation by binding transcription factors and/or cis-and trans- acting proteins. The data suggest an important role of WGD duplicate genes in modulating diverse and novel gene expression changes in response to external environmental cues as well as internal genetic turmoil such as recurrent polyploidy events.
Overall design To analyze expression change of duplicate genes conserved in A.thaliana and A.arenosa, we selected the duplicate genes with the same hybridization intensities in comparative genomic hybridization (CGH) between A. thaliana and A. arenosa.
To test the hypothesis that duplicate genes change expression regulation among different polyploid species, we first compared expression divergences of single-copy and duplicate genes between A. thaliana and A. arenosa. We then examined how duplicate genes affect expression change in new round of polyploidy detecting expression variations of single-copy and duplicate genes between each resynthesized allopolyploid and their progenitors.
Contributor(s) Ha M, Chen J, Wang J, Kim E, Tian L, Lee H, Wei NE, Jiang H, Watson B, Madlung A, Osrborn TC, Doerge RW, Comai L
Citation(s) 19168631
Submission date Nov 05, 2007
Last update date Mar 17, 2012
Contact name Misook Ha
Phone 7732795900
Organization name National Heart Lung Blood Institute
Lab Laboratory of Epigenome Biology
Street address NIH
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (5)
GPL5680 Arabidopsis thaliana 26k 70-mer spotted oligoarray
GPL7498 University of Texas at Austin Arabidopsis thaliana 29k 70-mer spotted oligoarray
GPL7631 Arabidopsis thaliana 11.2k 70-mer spotted oligoprobes
Samples (5)
GSM213692 Comparative genomic hybridization between Arabidopsis thaliana and Arabidopsis arenosa
GSM334287 Gene expression difference between A. suecica and their progenitor species
GSM341923 Expression divergence between Arabidopsis thaliana and Arabidopsis arenosa in leaves
BioProject PRJNA103311

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Supplementary file Size Download File type/resource
GSE9513_RAW.tar 131.1 Mb (http)(custom) TAR (of GPR, TAR)
Processed data included within Sample table

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