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Open Access Highly Accessed Research article

Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression

Elie Raherison1, Philippe Rigault2, Sébastien Caron1, Pier-Luc Poulin1, Brian Boyle1, Jukka-Pekka Verta1, Isabelle Giguère1, Claude Bomal1, Jörg Bohlmann3 and John MacKay1*

Author Affiliations

1 Center for Forest Research and Institute for Integrative and Systems Biology, Université Laval, Québec, QC, Canada, G1V 0A6

2 Gydle Inc., Québec, QC, Canada

3 Michael Smith Laboratories, University of British-Columbia, Vancouver, BC, Canada

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BMC Genomics 2012, 13:434  doi:10.1186/1471-2164-13-434

Published: 29 August 2012

Abstract

Background

Conifers have very large genomes (13 to 30 Gigabases) that are mostly uncharacterized although extensive cDNA resources have recently become available. This report presents a global overview of transcriptome variation in a conifer tree and documents conservation and diversity of gene expression patterns among major vegetative tissues.

Results

An oligonucleotide microarray was developed from Picea glauca and P. sitchensis cDNA datasets. It represents 23,853 unique genes and was shown to be suitable for transcriptome profiling in several species. A comparison of secondary xylem and phelloderm tissues showed that preferential expression in these vascular tissues was highly conserved among Picea spp. RNA-Sequencing strongly confirmed tissue preferential expression and provided a robust validation of the microarray design. A small database of transcription profiles called PiceaGenExpress was developed from over 150 hybridizations spanning eight major tissue types. In total, transcripts were detected for 92% of the genes on the microarray, in at least one tissue. Non-annotated genes were predominantly expressed at low levels in fewer tissues than genes of known or predicted function. Diversity of expression within gene families may be rapidly assessed from PiceaGenExpress. In conifer trees, dehydrins and late embryogenesis abundant (LEA) osmotic regulation proteins occur in large gene families compared to angiosperms. Strong contrasts and low diversity was observed in the dehydrin family, while diverse patterns suggested a greater degree of diversification among LEAs.

Conclusion

Together, the oligonucleotide microarray and the PiceaGenExpress database represent the first resource of this kind for gymnosperm plants. The spruce transcriptome analysis reported here is expected to accelerate genetic studies in the large and important group comprised of conifer trees.