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Multivariate analysis of digital gene expression profiles identifies a xylem signature of the vascular tissue of white spruce (Picea glauca)

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Abstract

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.

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References

  • Adams MD, Kellye JM, Gocayne JD et al (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252:1651–1656

    Article  PubMed  CAS  Google Scholar 

  • Allona I, Quinn M, Shoop E et al (1998) Analysis of xylem formation in pine by cDNA sequencing. Proc Nat Acad Sci U S A 95:9693–9698

    Article  CAS  Google Scholar 

  • Brenner S, Johnson M, Bridgham J et al (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18:630–634

    Article  PubMed  CAS  Google Scholar 

  • da Silva FG, Iandolino A, Al-Kayal F et al (2005) Characterizing the grape transcriptome. Analysis of expressed sequence tags from multiple vitis species and development of a compendium of gene expression during berry development. Plant Physiol 139:574–597

    Article  PubMed  Google Scholar 

  • Diatchenko L, Lau Y-FC, Campbell AP et al (1996) Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Nat Acad Sci U S A 93:6025–6030

    Article  CAS  Google Scholar 

  • Ehlting J, Mattheus N, Aeschilman DS et al (2005) Global transcript profiling of primary stems from Arabidopsis thaliana identifies candidate genes for missing links in lignin biosynthesis and transcriptional regulators of fiber differentiation. Plant J 42:618–640

    Article  PubMed  CAS  Google Scholar 

  • Ewing RM, Ben Kahla A, Poirot O et al (1999) Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. Genome Res 9:950–959

    Article  PubMed  CAS  Google Scholar 

  • Foucart C, Paux E, Ladouce N et al (2006) Transcript profiling of a xylem vs phloem cDNA subtractive library identifies new genes expressed during xylogenesis in Eucalyptus. New Phytol 170:739–752

    Article  PubMed  CAS  Google Scholar 

  • Franceschi VR, Krokene P, Christiansen E, Krekling T (2005) Anatomical and chemical defenses of conifer bark against bark beetles and other pests. New Phytol 167:353–376

    Article  PubMed  CAS  Google Scholar 

  • Friedmann M, Ralph SG, Aeschliman D et al (2007) Microarray gene expression profiling of developmental transitions in Sitka spruce (Picea sitchensis) apical shoot. J Exp Bot 58:593–614

    Article  PubMed  CAS  Google Scholar 

  • Gorantla M, Babu PR, Lachagari VBR et al (2007) Identification of stress-responsive genes in an indica rice (Oryza sativa L.) using ESTs generated from drought-stressed seedlings. J Exp Bot 58:253–265

    Article  PubMed  CAS  Google Scholar 

  • Hene L, Sreenu VB, Voung MT et al (2007) Deep analysis of cellular transcriptomes LongSAGE versus classic MPSS. BMC Genomics 8:333

    Article  PubMed  Google Scholar 

  • Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868–877

    Article  PubMed  CAS  Google Scholar 

  • Keeling C, Bohlmann J (2006a) Diterpene resin acids in conifers. Phytochemistry 67:2415–2423

    Article  PubMed  CAS  Google Scholar 

  • Keeling C, Bohlmann J (2006b) Genes, enzymes and chemicals of terpenoid diversity in the constitutive and induced defence of conifers against insects and pathogens. New Phytol 170:657–675

    Article  PubMed  CAS  Google Scholar 

  • Kirst M, Johnson AF, Baucom C, Ulrich E et al (2003) Apparent homology of expressed genes from wood-forming tissues of loblolly pine (Pinus taeda L.) with Arabidopsis thaliana. Proc Nat Acad Sci U S A 100:7383–7388

    Article  Google Scholar 

  • Li LY, Cheng H, Gai JY et al (2007) Genome-wide identification and characterization of putative cytochrome P450 genes in the model legume Medicago truncatula. Planta 226:109–123

    Article  PubMed  CAS  Google Scholar 

  • Lockhart DJ, Dong HL, Byrne MT et al (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotech 14:1675–1680

    Article  CAS  Google Scholar 

  • Martin D, Tholl D, Gershenzon J, Bohlmann J (2002) Methyl jasmonate induces traumatic resin ducts, terpenoid resin biosynthesis, and terpenoid accumulation in developing xylem of Norway spruce stems. Plant Physiol 129:1003–1018

    Article  PubMed  CAS  Google Scholar 

  • 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 137:369–382

    Article  PubMed  CAS  Google Scholar 

  • Omid A, Keilin T, Glass A et al (2007) Characterization of phloem-sap transcription profile in melon plants. J Exp Bot 58:3645–3656

    Article  PubMed  CAS  Google Scholar 

  • Paiva JAP, Garces M, Alves A et al (2008) Molecular and phenotypic profiling from the base to the crown in maritime pine wood-forming tissue. New Phytol 178:283–301

    Article  PubMed  CAS  Google Scholar 

  • Pavy N, Laroche J, Bousquet J et al (2005a) Large-scale statistical analysis of secondary xylem ESTs in pine. Plant Mol Biol 57:203–224

    Article  PubMed  CAS  Google Scholar 

  • Pavy N, Paule C, Parsons L (2005b) Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters. BMC Genomics 6:144

    Article  PubMed  Google Scholar 

  • Peter G, Neale D (2004) Molecular basis for the evolution of xylem lignifications. Curr Opin Plant Biol 7:737–742

    Article  PubMed  CAS  Google 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):1–17

    Google Scholar 

  • Pittelkow Y, Wilson S (2005) Use of principal component analysis and the GE-Biplot for the graphical exploration of gene expression data. Biometrics 61:630–634

    Article  PubMed  Google 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 29:1545–1570

    Article  PubMed  Google Scholar 

  • Ralph SG, Jancsik S, Bohlmann J (2007) Dirigent proteins in conifer defense II: extended gene discovery, phylogeny, and constitutive and stress-induced gene expression in spruce (Picea spp.). Phytochemistry 68:1975–1991

    Article  PubMed  CAS  Google Scholar 

  • Ralph SG, Chun HJE, Kolosova N et al (2008) A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6, 464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis). BMC Genomics 9:484

    Article  PubMed  Google Scholar 

  • Saha S, Sparks AB, Rago C et al (2002) Using the transcriptome to annotate the genome. Nat Biotechnol 20:508–512

    Article  PubMed  CAS  Google Scholar 

  • Schena M, Shalon D, Davis RW, Brown P (1995) Quantitative monitoring of gene-expression patterns with a complementary-DNA microarray. Science 270:467–470

    Article  PubMed  CAS  Google Scholar 

  • Sibout R, Eudes A, Mouille G et al (2005) Cinnamyl alcohol dehydrogenase-C and -D are the primary genes involved in lignin biosynthesis in the floral stem of Arabidopsis. Plant Cell 17:2059–2076

    Article  PubMed  CAS  Google Scholar 

  • Sterkey F, Regan S, Karlsson J et al (1998) Gene discovery in the wood-forming tissues of poplar: analysis of 5,692 expressed sequence tags. PNAS 95:13330–13335

    Article  Google 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 95

    Google Scholar 

  • ter Braak C, Smilauer P (2003) CANOCO 4.5 reference manual. User’s guide to CANOCO for Windows. Centre for Biometry, Wageningen, p 351

    Google Scholar 

  • Udall JA, Swanson JM, Haller K et al (2006) A global assembly of cotton ESTs. Genome Res 16:441–450

    Article  PubMed  Google Scholar 

  • Ukrainetz NK, Kang KY, Aitken SN, Stoehr M, Mansfield SD (2008a) Heritability, phenotypic and genetic correlations of coastal Douglas-fir (Pseudotsuga menziesii) wood quality traits. Can J For Res 38:1536–1546

    Article  CAS  Google Scholar 

  • Ukrainetz NK, Ritland K, Mansfield SD (2008b) Identification of quantitative trait loci for wood quality and growth across eight full-sib coastal Douglas-fir families. Tree Genet Genomics 4:159–170

    Article  Google Scholar 

  • Velculescu VE, Zhang L, Vogelstein B et al (1995) Serial analysis of gene expression. Science 270:484–487

    Article  PubMed  CAS  Google Scholar 

  • Wanderley-Nogueira AC, Soares-Cavalcanti NM, Morais DAL et al (2007) Abundance and diversity of resistance genes in the sugarcane transcriptome revealed by in silico analysis. Genet Mol Res 6:866–889

    PubMed  CAS  Google Scholar 

  • Zhang Y, Sederoff RR, Allona I (2000) Differential expression of genes encoding cell wall proteins in vascular tissues from vertical and bent loblolly pine trees. Tree Physiol 20:457–466

    PubMed  Google Scholar 

  • Zhang Y, Brown G, Whetten R et al (2003) An arabinogalactan protein associated with secondary cell wall formation in differentiating xylem of loblolly pine. Plant Mol Biol 52:91–102

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

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.

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Authors and Affiliations

  1. Department of Forest Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada

    Rokneddin Albouyeh, Nima Farzaneh, Jörg Bohlmann & Kermit Ritland

  2. Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada

    Jörg Bohlmann

  3. Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada

    Jörg Bohlmann

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  1. Rokneddin Albouyeh
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  2. Nima Farzaneh
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  3. Jörg Bohlmann
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  4. Kermit Ritland
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Correspondence to Kermit Ritland.

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Communicated by J. Dean

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Albouyeh, R., Farzaneh, N., Bohlmann, J. et al. Multivariate analysis of digital gene expression profiles identifies a xylem signature of the vascular tissue of white spruce (Picea glauca). Tree Genetics & Genomes 6, 601–611 (2010). https://doi.org/10.1007/s11295-010-0275-0

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