Multivariate analysis of digital gene expression profiles identifies a xylem signature of the vascular tissue of white spruce (Picea glauca)
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A collection of cDNA libraries from white spruce (Picea glauca) and interior spruce (P. glauca × engelmanii) vascular tissue were analyzed to identify a set of genes that could serve as tissue-related markers within the coniferous vascular system. Multivariate exploratory methods identified up to 128 genes co-expressed similarly among three xylem libraries. The majority (87) of these genes formed three distinctive meta-clusters, denoting putative gene cliques in xylem tissue. Of the selected genes, 33 (25%) exhibited no significant sequence homology in queries against any public databases, indicating the possibility of their unique expression in the xylem tissue of conifers. Another 38 genes (30%) had ambiguous annotation. Validation of the annotated genes with analog data, obtained from a wet-lab study utilizing microarray slides with 18,881 spots, resulted in a screened list of 29 genes as xylem-related markers. Response to stress was the predominant category to which the screened genes corresponded. Among the screened genes, elements of the phenolics biosynthesis, cinnamyl alcohol dehydrogenase and laccase, together with the fundamental enzyme of the cell wall biosynthesis, cellulose synthase, prominently delineated characteristics of the wood-forming tissue, xylem.
KeywordsConifer EST Digital gene expression Spruce Vascular tissue Xylem
This work was supported by Genome British Columbia, Genome Canada, and the Province of British Columbia (Treenomix Conifer Forest Health grant to J.B. and K.R.), by a Natural Science and Engineering Research Council of Canada (NSERC) grant to K.R., and UBC Faculty of Graduate Studies award to R.A. The authors thank Rick White, Department of Statistics, UBC for his assistance with cluster analysis, and Nancy Liao at the Vancouver Genome Sciences Centre for retrieving the spruce EST data.
- Miller B, Madilao LL, Ralph S, Bohlmann J (2005) Insect-induced conifer defense: white pine weevil and methyl jasmonate induce traumatic resinosis, de novo formed volatile emissions, and accumulation of terpenoid synthase and putative octadecanoid pathway transcripts in Sitka spruce. Plant Physiol 137:369–382PubMedCrossRefGoogle Scholar
- Pittelkow YR, Wilson S (2003) Visualisation of gene expression data—the GE-biplot, the chip-plot and the gene-plot. Stat Appl Genet Mol Biol 2(article 6):1–17Google Scholar
- Ralph SG, Yueh H, Friedmann M et al (2006) Conifer defence against insects: microarray gene expression profiling of Sitka spruce (Picea sitchensis) induced by mechanical wounding or feeding by spruce budworms (Choristoneura occidentalis) or white pine weevils (Pissodes strobi) reveals large-scale changes of the host transcriptome. Plant Cell Environ 29:1545–1570PubMedCrossRefGoogle Scholar
- ter Braak CJF (1987) CANOCO—a FORTRAN program for canonical community ordination by correspondence analysis, principal components analysis and redundancy analysis (version 2.1). Agricultural Mathematics Group, Wageningen, p 95Google Scholar
- ter Braak C, Smilauer P (2003) CANOCO 4.5 reference manual. User’s guide to CANOCO for Windows. Centre for Biometry, Wageningen, p 351Google Scholar