title: De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum.
abstract: BACKGROUND
  Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes of two Triticum monococcum subspecies, the wild winter wheat T. monococcum ssp. aegilopoides (accession G3116) and the domesticated spring wheat T. monococcum ssp. monococcum (accession DV92) by generating de novo assemblies of RNA-Seq data derived from both etiolated and green seedlings.
  
  
  RESULTS
  The de novo transcriptome assemblies of DV92 and G3116 represent 120,911 and 117,969 transcripts, respectively. We successfully mapped ∼90% of these transcripts from each accession to barley and ∼95% of the transcripts to T. urartu genomes. However, only ∼77% transcripts mapped to the annotated barley genes and ∼85% transcripts mapped to the annotated T. urartu genes. Differential gene expression analyses revealed 22% more light up-regulated and 35% more light down-regulated transcripts in the G3116 transcriptome compared to DV92. The DV92 and G3116 mRNA sequence reads aligned against the reference barley genome led to the identification of ∼500,000 single nucleotide polymorphism (SNP) and ∼22,000 simple sequence repeat (SSR) sites.
  
  
  CONCLUSIONS
  De novo transcriptome assemblies of two accessions of the diploid wheat T. monococcum provide new empirical transcriptome references for improving Triticeae genome annotations, and insights into transcriptional programming during photomorphogenesis. The SNP and SSR sites identified in our analysis provide additional resources for the development of molecular markers.
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America.
authors.forename: Samuel E
authors.initials: SE
authors.lastname: Fox
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America; Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, Oregon, United States of America.
authors.forename: Matthew
authors.initials: M
authors.lastname: Geniza
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America.
authors.forename: Mamatha
authors.initials: M
authors.lastname: Hanumappa
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America.
authors.forename: Sushma
authors.initials: S
authors.lastname: Naithani
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America.
authors.forename: Chris
authors.initials: C
authors.lastname: Sullivan
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America.
authors.forename: Justin
authors.initials: J
authors.lastname: Preece
authors.affiliation: Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America.
authors.forename: Vijay K
authors.initials: VK
authors.lastname: Tiwari
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America.
authors.forename: Justin
authors.initials: J
authors.lastname: Elser
authors.affiliation: Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America.
authors.forename: Jeffrey M
authors.initials: JM
authors.lastname: Leonard
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America.
authors.forename: Abigail
authors.initials: A
authors.lastname: Sage
authors.affiliation: Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America.
authors.forename: Cathy
authors.initials: C
authors.lastname: Gresham
authors.affiliation: European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom.
authors.forename: Arnaud
authors.initials: A
authors.lastname: Kerhornou
authors.affiliation: European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom.
authors.forename: Dan
authors.initials: D
authors.lastname: Bolser
authors.affiliation: School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States of America.
authors.forename: Fiona
authors.initials: F
authors.lastname: McCarthy
authors.affiliation: European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom.
authors.forename: Paul
authors.initials: P
authors.lastname: Kersey
authors.affiliation: USDA-ARS, Western Regional Research Center, Albany, California, United States of America.
authors.forename: Gerard R
authors.initials: GR
authors.lastname: Lazo
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America; Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America.
authors.forename: Pankaj
authors.initials: P
authors.lastname: Jaiswal
mesh_terms: D004171:Diploidy; D018745:Genome, Plant / Q000235:genetics; D036226:Seedlings / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*; D014908:Triticum / Q000235:genetics*