title: RNA-Seq effectively monitors gene expression in Eutrema salsugineum plants growing in an extreme natural habitat and in controlled growth cabinet conditions.
abstract: 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 salsugineum, 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 2,989 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada. weretil@mcmaster.ca.
authors.forename: Marc J
authors.initials: MJ
authors.lastname: Champigny
authors.forename: Wilson Wl
authors.initials: WW
authors.lastname: Sung
authors.forename: Vasile
authors.initials: V
authors.lastname: Catana
authors.forename: Rupa
authors.initials: R
authors.lastname: Salwan
authors.forename: Peter S
authors.initials: PS
authors.lastname: Summers
authors.forename: Susan A
authors.initials: SA
authors.lastname: Dudley
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Provart
authors.forename: Robin K
authors.initials: RK
authors.lastname: Cameron
authors.forename: G Brian
authors.initials: GB
authors.lastname: Golding
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Weretilnyk
mesh_terms: D000222:Adaptation, Physiological; D019607:Brassicaceae / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D016000:Cluster Analysis; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D006579:Heterozygote; D058977:Molecular Sequence Annotation; D015999:Multivariate Analysis; D010641:Phenotype; D018515:Plant Leaves / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D012335:RNA, Ribosomal / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D013312:Stress, Physiological / Q000235:genetics*; D059467:Transcriptome
chemical_list: D018749:RNA, Plant; D012335:RNA, Ribosomal