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Series GSE13468 Query DataSets for GSE13468
Status Public on Nov 20, 2008
Title Gene expression change in natural allotetraploid, A.suecica
Platform organism Arabidopsis thaliana
Sample organisms Arabidopsis thaliana; Arabidopsis arenosa; Arabidopsis suecica
Experiment type Expression profiling by array
Summary Arabidopsis is a suitable system for testing the hypothesis that duplicate genes accelerate evolution of expression diversity among species diverged from shared whole genome duplications (WGDs) and recurrent events of WGD. In Arabidopsis, at least 9 species split after WGD of the common ancestor and new allotetraploids were formed in nature and can be resynthesized between closely related species. Using genomic and gene expression microarrays, we detected WGD duplicate and single-copy genes preserved in A.thaliana and A.arenosa in addition to change of gene expression levels among those species. We found that even conserved duplicate genes show 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. This results show that WGD duplicate genes provide expression variegation in response to recurring polyploidy as well as among species diverged from common WGD. Duplicate genes related to external stresses tended to be differentially expressed in allopolyploids and among their progenitors. Moreover, multiple-copy duplicate genes are likely to change expression between species and in the resynthesized and natural allotetraploids. Compared to single-copy genes, duplicate genes are less likely to be methylated in the promoter regions, facilitating transcriptional regulation by binding transcription factors and/or cis-and trans- acting proteins. Our results suggest that highly retained duplicate genes are important source for developing species specific expression level and novel expression regulation to adapt to environmental changes including subsequent polyploidy.
Overall design Microarray data was obtained using a comparison between mRNA from A. suecica and an artificial mRNA mix of two parents. Total 8 hybridization intensity pairs were obtained. two dye swap experiments and four replications of them using different plant populations (biological replications). In one biological replication, 500 ng of mRNA each from about 12 A.suecica plants and from artificial mix of more than 12 A.thaliana plants and 12 A.arenosa plants were used for the labeling reacting using Cy3- or Cy5-dCTP (Amersham Biosciences). For each biological replication, the Cy3-dCTP reaction was mixed with the Cy5-dCTP reaction for one hybridization experiment, and then an equal amount of RNA samples was reversely labeled for another hybridization experiment (dye-swap experiment). Four biological replications were performed. Eventually, 8 replicated measurements were obtained per probe feature. We applied a linear model to exclude technical variation by arrays and dyes and biological variation by different plant populations. The linear model is
Log (Yigkl) = µ + Gi + Tj + Ak + Dl + (G*T)ij + (G*A)ik + (G*D)il + (G*T*D)ijl + ɛijkl
Where Y represents raw intensity after background level is subtracted; G, T, A, and D are main sources of variation from gene (G), treatment (plant species, T), array (A) and dye (D); i = 1,…, 31818; j = 1, 2; k = 1, 2, 3, 4;l = 1,2; µ represents the overall mean. The interaction terms, G*T, G*A, G*D, and G*T*D mean gene-by-species, gene-by-array, gene-by-dye and gene-by-species-by-dye. ɛijkl represents random error.
To test difference of mRNA expression between A.suecica and mid-parent value (MPV), t-tests were employed for individual genes (pergene-variance).
The null hypothesis, H0: TA.suecica + (G*T)i,A.suecica = TMPV + (G*T)i,MPV was examined by p-value. Overall type I error rate of multiple testing was controlled to be below 0.05 employing the false discovery rate of Benjamini and Hotchberg.
Contributor(s) Ha M, Kim E, Chen ZJ
Citation(s) 19168631
Submission date Nov 04, 2008
Last update date Mar 20, 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 (1)
GPL7498 University of Texas at Austin Arabidopsis thaliana 29k 70-mer spotted oligoarray
Samples (1)
GSM334287 Gene expression difference between A. suecica and their progenitor species
BioProject PRJNA109997

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Supplementary file Size Download File type/resource
GSE13468_RAW.tar 25.5 Mb (http)(custom) TAR (of GPR)
Processed data included within Sample table

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