title: Comparative exomics of Phalaris cultivars under salt stress.
abstract: BACKGROUND
  Reed canary grass (Phalaris arundinacea) is an economically important forage and bioenergy grass of the temperate regions of the world. Despite its economic importance, it is lacking in public genomic data. We explore comparative exomics of the grass cultivars in the context of response to salt exposure. The limited data set poses challenges to the computational pipeline.
  
  
  METHODS
  As a prerequisite for the comparative study, we generate the Phalaris reference transcriptome sequence, one of the first steps in addressing the issue of paucity of processed genomic data in this species. In addition, the differential expression (DE) and active-but-stable genes for salt stress conditions were analyzed by a novel method that was experimentally verified on human RNA-seq data. For the comparative exomics, we focus on the DE and stable genic regions, with respect to salt stress, of the genome.
  
  
  CONCLUSIONS
  In our comparative study, we find that phylogeny of the DE and stable genic regions of the Phalaris cultivars are distinct. At the same time we find the phylogeny of the entire expressed reference transcriptome matches the phylogeny of only the stable genes. Thus the behavior of the different cultivars is distinguished by the salt stress response. This is also reflected in the genomic distinctions in the DE genic regions. These observations have important implications in the choice of cultivars, and their breeding, for bio-energy fuels. Further, we identified genes that are representative of DE under salt stress and could provide vital clues in our understanding of the stress handling mechanisms in general.
authors.forename: Niina
authors.initials: N
authors.lastname: Haiminen
authors.forename: Manfred
authors.initials: M
authors.lastname: Klaas
authors.forename: Zeyu
authors.initials: Z
authors.lastname: Zhou
authors.forename: Filippo
authors.initials: F
authors.lastname: Utro
authors.forename: Paul
authors.initials: P
authors.lastname: Cormican
authors.forename: Thomas
authors.initials: T
authors.lastname: Didion
authors.forename: Christian
authors.initials: C
authors.lastname: Jensen
authors.forename: Christopher E
authors.initials: CE
authors.lastname: Mason
authors.forename: Susanne
authors.initials: S
authors.lastname: Barth
authors.forename: Laxmi
authors.initials: L
authors.lastname: Parida
mesh_terms: D000465:Algorithms; D059472:Exome; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D031783:Phalaris / Q000235:genetics*; D010641:Phenotype; D055049:Salt Tolerance / Q000235:genetics*; D013312:Stress, Physiological / Q000235:genetics*; D059467:Transcriptome