title: Towards unambiguous transcript mapping in the allotetraploid Brassica napus.
abstract: The architecture of the Brassica napus genome is marked by its evolutionary origins. The genome of B. napus was formed from the hybridization of two closely related diploid Brassica species, both of which evolved from an hexaploid ancestor. The extensive whole genome duplication events in its near and distant past result in the allotetraploid genome of B. napus maintaining multiple copies of most genes, which predicts a highly complex and redundant transcriptome that can confound any expression analyses. A stringent assembly of 142,399 B. napus expressed sequence tags allowed the development of a well-differentiated set of reference transcripts, which were used as a foundation to assess the efficacy of available tools for identifying and distinguishing transcripts in B. napus; including microarray hybridization and 3' anchored sequence tag capture. Microarray platforms cannot distinguish transcripts derived from the two progenitors or close homologues, although observed differential expression appeared to be biased towards unique transcripts. The use of 3' capture enhanced the ability to unambiguously identify homologues within the B. napus transcriptome but was limited by tag length. The ability to comprehensively catalogue gene expression in polyploid species could be transformed by the application of cost-efficient next generation sequencing technologies that will capture millions of long sequence tags.
authors.affiliation: Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada. isobel.parkin@agr.gc.ca
authors.forename: Isobel A P
authors.initials: IA
authors.lastname: Parkin
authors.forename: Wayne E
authors.initials: WE
authors.lastname: Clarke
authors.forename: Christine
authors.initials: C
authors.lastname: Sidebottom
authors.forename: Wentao
authors.initials: W
authors.lastname: Zhang
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Robinson
authors.forename: Matthew G
authors.initials: MG
authors.lastname: Links
authors.forename: Steve
authors.initials: S
authors.lastname: Karcz
authors.forename: Erin E
authors.initials: EE
authors.lastname: Higgins
authors.forename: Pierre
authors.initials: P
authors.lastname: Fobert
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Sharpe
mesh_terms: D029688:Brassica napus / Q000235:genetics*; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D020411:Oligonucleotide Array Sequence Analysis; D057891:Tetraploidy