title: Transcriptome analysis based on next-generation sequencing of non-model plants producing specialized metabolites of biotechnological interest.
abstract: Plants produce a vast array of specialized metabolites, many of which are used as pharmaceuticals, flavors, fragrances, and other high-value fine chemicals. However, most of these compounds occur in non-model plants for which genomic sequence information is not yet available. The production of a large amount of nucleotide sequence data using next-generation technologies is now relatively fast and cost-effective, especially when using the latest Roche-454 and Illumina sequencers with enhanced base-calling accuracy. To investigate specialized metabolite biosynthesis in non-model plants we have established a data-mining framework, employing next-generation sequencing and computational algorithms, to construct and analyze the transcriptomes of 75 non-model plants that produce compounds of interest for biotechnological applications. After sequence assembly an extensive annotation approach was applied to assign functional information to over 800,000 putative transcripts. The annotation is based on direct searches against public databases, including RefSeq and InterPro. Gene Ontology (GO), Enzyme Commission (EC) annotations and associated Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway maps are also collected. As a proof-of-concept, the selection of biosynthetic gene candidates associated with six specialized metabolic pathways is described. A web-based BLAST server has been established to allow public access to assembled transcriptome databases for all 75 plant species of the PhytoMetaSyn Project (www.phytometasyn.ca).
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada.
authors.forename: Mei
authors.initials: M
authors.lastname: Xiao
authors.forename: Ye
authors.initials: Y
authors.lastname: Zhang
authors.forename: Xue
authors.initials: X
authors.lastname: Chen
authors.forename: Eun-Jeong
authors.initials: EJ
authors.lastname: Lee
authors.forename: Carla J S
authors.initials: CJ
authors.lastname: Barber
authors.forename: Romit
authors.initials: R
authors.lastname: Chakrabarty
authors.forename: Isabel
authors.initials: I
authors.lastname: Desgagné-Penix
authors.forename: Tegan M
authors.initials: TM
authors.lastname: Haslam
authors.forename: Yeon-Bok
authors.initials: YB
authors.lastname: Kim
authors.forename: Enwu
authors.initials: E
authors.lastname: Liu
authors.forename: Gillian
authors.initials: G
authors.lastname: MacNevin
authors.forename: Sayaka
authors.initials: S
authors.lastname: Masada-Atsumi
authors.forename: Darwin W
authors.initials: DW
authors.lastname: Reed
authors.forename: Jake M
authors.initials: JM
authors.lastname: Stout
authors.forename: Philipp
authors.initials: P
authors.lastname: Zerbe
authors.forename: Yansheng
authors.initials: Y
authors.lastname: Zhang
authors.forename: Joerg
authors.initials: J
authors.lastname: Bohlmann
authors.forename: Patrick S
authors.initials: PS
authors.lastname: Covello
authors.forename: Vincenzo
authors.initials: V
authors.lastname: De Luca
authors.forename: Jonathan E
authors.initials: JE
authors.lastname: Page
authors.forename: Dae-Kyun
authors.initials: DK
authors.lastname: Ro
authors.forename: Vincent J J
authors.initials: VJ
authors.lastname: Martin
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Facchini
authors.forename: Christoph W
authors.initials: CW
authors.lastname: Sensen
mesh_terms: D000465:Algorithms; D001709:Biotechnology / Q000379:methods; D019295:Computational Biology; D057225:Data Mining / Q000379:methods; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D010944:Plants / Q000235:genetics* / Q000378:metabolism*; D016415:Sequence Alignment; D017421:Sequence Analysis; D059467:Transcriptome