title: Wheat EST resources for functional genomics of abiotic stress.
abstract: BACKGROUND
  Wheat is an excellent species to study freezing tolerance and other abiotic stresses. However, the sequence of the wheat genome has not been completely characterized due to its complexity and large size. To circumvent this obstacle and identify genes involved in cold acclimation and associated stresses, a large scale EST sequencing approach was undertaken by the Functional Genomics of Abiotic Stress (FGAS) project.
  
  
  RESULTS
  We generated 73,521 quality-filtered ESTs from eleven cDNA libraries constructed from wheat plants exposed to various abiotic stresses and at different developmental stages. In addition, 196,041 ESTs for which tracefiles were available from the National Science Foundation wheat EST sequencing program and DuPont were also quality-filtered and used in the analysis. Clustering of the combined ESTs with d2_cluster and TGICL yielded a few large clusters containing several thousand ESTs that were refractory to routine clustering techniques. To resolve this problem, the sequence proximity and "bridges" were identified by an e-value distance graph to manually break clusters into smaller groups. Assembly of the resolved ESTs generated a 75,488 unique sequence set (31,580 contigs and 43,908 singletons/singlets). Digital expression analyses indicated that the FGAS dataset is enriched in stress-regulated genes compared to the other public datasets. Over 43% of the unique sequence set was annotated and classified into functional categories according to Gene Ontology.
  
  
  CONCLUSIONS
  We have annotated 29,556 different sequences, an almost 5-fold increase in annotated sequences compared to the available wheat public databases. Digital expression analysis combined with gene annotation helped in the identification of several pathways associated with abiotic stress. The genomic resources and knowledge developed by this project will contribute to a better understanding of the different mechanisms that govern stress tolerance in wheat and other cereals.
authors.affiliation: Département des Sciences biologiques, Université du Québec à Montréal, Centre-ville, Montréal QC, H3C 3P8, Canada. houde.mario@uqam.ca
authors.forename: Mario
authors.initials: M
authors.lastname: Houde
authors.forename: Mahdi
authors.initials: M
authors.lastname: Belcaid
authors.forename: François
authors.initials: F
authors.lastname: Ouellet
authors.forename: Jean
authors.initials: J
authors.lastname: Danyluk
authors.forename: Antonio F
authors.initials: AF
authors.lastname: Monroy
authors.forename: Ani
authors.initials: A
authors.lastname: Dryanova
authors.forename: Patrick
authors.initials: P
authors.lastname: Gulick
authors.forename: Anne
authors.initials: A
authors.lastname: Bergeron
authors.forename: André
authors.initials: A
authors.lastname: Laroche
authors.forename: Matthew G
authors.initials: MG
authors.lastname: Links
authors.forename: Luke
authors.initials: L
authors.lastname: MacCarthy
authors.forename: William L
authors.initials: WL
authors.lastname: Crosby
authors.forename: Fathey
authors.initials: F
authors.lastname: Sarhan
mesh_terms: D000064:Acclimatization / Q000235:genetics*; D000596:Amino Acids / Q000378:metabolism; D021301:Antifreeze Proteins / Q000235:genetics; D001692:Biological Transport / Q000235:genetics; D016000:Cluster Analysis; D003080:Cold Temperature; D020451:Contig Mapping; D030541:Databases, Genetic / Q000600:supply & distribution*; D020224:Expressed Sequence Tags / Q000378:metabolism; D017343:Genes, Plant; D018745:Genome, Plant; D006295:Health Resources; D050356:Lipid Metabolism / Q000235:genetics; D008954:Models, Biological; D010788:Photosynthesis / Q000235:genetics; D010840:Phytosterols / Q000737:chemistry; D015398:Signal Transduction / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics; D014908:Triticum / Q000235:genetics*
chemical_list: D000596:Amino Acids; D021301:Antifreeze Proteins; D010840:Phytosterols; D014157:Transcription Factors