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Series GSE49378 Query DataSets for GSE49378
Status Public on Aug 30, 2013
Title RNA-Seq effectively monitors gene expression in Eutrema salsuginuem plants growing in an extreme natural habitat and in controlled growth cabinet conditions
Organism Eutrema salsugineum
Experiment type Expression profiling by high throughput sequencing
Summary Background: The investigation of extremophile plant species growing in their natural environment offers certain advantages, chiefly that plants adapted to severe habitats have a repertoire of stress tolerance genes that are regulated to maximize plant performance under physiologically challenging conditions. Accordingly, transcriptome sequencing offers a powerful approach to address questions concerning the influence of natural habitat on the physiology of an organism. We used RNA sequencing of Eutrema salsuginuem, an extremophile relative of Arabidopsis thaliana, to investigate the extent to which genetic variation and controlled versus natural environments contribute to differences between transcript profiles.
Results: Using 10 million cDNA reads, we compared transcriptomes from two natural Eutrema accessions (originating from Yukon Territory, Canada and Shandong Province, China) grown under controlled conditions in cabinets and those from Yukon plants collected at a Yukon field site. We assessed the genetic heterogeneity between individuals using single-nucleotide polymorphisms (SNPs) and the expression patterns of 27,016 genes. Over 39,000 SNPs distinguish the Yukon from the Shandong accessions but only 4,475 SNPs differentiated transcriptomes of Yukon field plants from an inbred Yukon line. We found 2,898 genes that were differentially expressed between the three sample groups and multivariate statistical analyses showed that transcriptomes of individual plants from a Yukon field site were as reproducible as those from inbred plants grown under controlled conditions. Predicted functions based upon gene ontology classifications show that the transcriptomes of field plants were enriched by the differential expression of light- and stress-related genes, an observation consistent with the habitat where the plants were found.
Conclusion: Our expectation that comparative RNA-Seq analysis of transcriptomes from plants originating in natural habitats would be confounded by uncontrolled genetic and environmental factors was not borne out. Moreover, the transcriptome data shows little genetic variation between laboratory Yukon Eutrema plants and those found at a field site. Transcriptomes were reproducible and biological associations meaningful whether plants were grown in cabinets or found in the field. Thus RNA-Seq is a valuable approach to study native plants in natural environments and this technology can be exploited to discover new gene targets for improved crop performance under adverse conditions.
Funding Acknowledgement: This work was sponsored by an Ontario Research Fund-Research Excellence award 03-043 to EAW and RKC with support from by Viterra Inc. and Sigma-Aldrich.
 
Overall design The set of nine transcriptomes is 3 repeats of 3 different 'Treatments'. Each transcriptome was obtained from a different plant.
 
Contributor(s) Champigny MJ, Sung WW, Catana V, Salwan R, Summers PS, Dudley SA, Provart NJ, Cameron RK, Golding GB, Weretilnyk EA
Citation(s) 23984645
Submission date Jul 30, 2013
Last update date May 15, 2019
Contact name Elizabeth A Weretilnyk
E-mail(s) weretil@mcmaster.ca
Organization name McMaster University
Department Biology
Street address 1280 Main Street West
City Hamilton
State/province Ontario
ZIP/Postal code L8S4K1
Country Canada
 
Platforms (1)
GPL17514 454 GS FLX Titanium (Eutrema salsugineum)
Samples (10)
GSM1198449 Shandong Cabinet 1
GSM1198450 Shandong Cabinet 2
GSM1198451 Shandong Cabinet 3
Relations
BioProject PRJNA213746
SRA SRP028337

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE49378_RAW.tar 2.3 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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