title: Gene expression analysis of flax seed development.
abstract: BACKGROUND
  Flax, Linum usitatissimum L., is an important crop whose seed oil and stem fiber have multiple industrial applications. Flax seeds are also well-known for their nutritional attributes, viz., omega-3 fatty acids in the oil and lignans and mucilage from the seed coat. In spite of the importance of this crop, there are few molecular resources that can be utilized toward improving seed traits. Here, we describe flax embryo and seed development and generation of comprehensive genomic resources for the flax seed.
  
  
  RESULTS
  We describe a large-scale generation and analysis of expressed sequences in various tissues. Collectively, the 13 libraries we have used provide a broad representation of genes active in developing embryos (globular, heart, torpedo, cotyledon and mature stages) seed coats (globular and torpedo stages) and endosperm (pooled globular to torpedo stages) and genes expressed in flowers, etiolated seedlings, leaves, and stem tissue. A total of 261,272 expressed sequence tags (EST) (GenBank accessions LIBEST_026995 to LIBEST_027011) were generated. These EST libraries included transcription factor genes that are typically expressed at low levels, indicating that the depth is adequate for in silico expression analysis. Assembly of the ESTs resulted in 30,640 unigenes and 82% of these could be identified on the basis of homology to known and hypothetical genes from other plants. When compared with fully sequenced plant genomes, the flax unigenes resembled poplar and castor bean more than grape, sorghum, rice or Arabidopsis. Nearly one-fifth of these (5,152) had no homologs in sequences reported for any organism, suggesting that this category represents genes that are likely unique to flax. Digital analyses revealed gene expression dynamics for the biosynthesis of a number of important seed constituents during seed development.
  
  
  CONCLUSIONS
  We have developed a foundational database of expressed sequences and collection of plasmid clones that comprise even low-expressed genes such as those encoding transcription factors. This has allowed us to delineate the spatio-temporal aspects of gene expression underlying the biosynthesis of a number of important seed constituents in flax. Flax belongs to a taxonomic group of diverse plants and the large sequence database will allow for evolutionary studies as well.
authors.affiliation: Plant Biotechnology Institute, NRC, 110 Gymnasium Place, Saskatoon, Saskatchewan, S7N 0W9, Canada.
authors.forename: Prakash
authors.initials: P
authors.lastname: Venglat
authors.forename: Daoquan
authors.initials: D
authors.lastname: Xiang
authors.forename: Shuqing
authors.initials: S
authors.lastname: Qiu
authors.forename: Sandra L
authors.initials: SL
authors.lastname: Stone
authors.forename: Chabane
authors.initials: C
authors.lastname: Tibiche
authors.forename: Dustin
authors.initials: D
authors.lastname: Cram
authors.forename: Michelle
authors.initials: M
authors.lastname: Alting-Mees
authors.forename: Jacek
authors.initials: J
authors.lastname: Nowak
authors.forename: Sylvie
authors.initials: S
authors.lastname: Cloutier
authors.forename: Michael
authors.initials: M
authors.lastname: Deyholos
authors.forename: Faouzi
authors.initials: F
authors.lastname: Bekkaoui
authors.forename: Andrew
authors.initials: A
authors.lastname: Sharpe
authors.forename: Edwin
authors.initials: E
authors.lastname: Wang
authors.forename: Gordon
authors.initials: G
authors.lastname: Rowland
authors.forename: Gopalan
authors.initials: G
authors.lastname: Selvaraj
authors.forename: Raju
authors.initials: R
authors.lastname: Datla
mesh_terms: D000269:Adhesives / Q000378:metabolism; D001483:Base Sequence; D016000:Cluster Analysis; D018556:Crops, Agricultural / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D018076:DNA, Complementary / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D020224:Expressed Sequence Tags; D005419:Flavonoids / Q000378:metabolism; D019597:Flax / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D017705:Lignans / Q000378:metabolism; D012639:Seeds / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism
chemical_list: D000269:Adhesives; D018076:DNA, Complementary; D018744:DNA, Plant; D005419:Flavonoids; D017705:Lignans