Expression profiling of the lignin biosynthetic pathway in Norway spruce using EST sequencing and real-time RT-PCR Sanna Koutaniemi Æ Tino Warinowski Æ Anna Ka ¨rko ¨nen Æ Edward Alatalo Æ Carl G. Fossdal Æ Pekka Saranpa ¨a ¨ Æ Tapio Laakso Æ Kurt V. Fagerstedt Æ Liisa K. Simola Æ Lars Paulin Æ Stephen Rudd Æ Teemu H. Teeri Received: 20 November 2006 / Accepted: 2 August 2007 / Published online: 1 September 2007 Ó Springer Science+Business Media B.V. 2007 Abstract Lignin biosynthesis is a major carbon sink in gymnosperms and woody angiosperms. Many of the enzymes involved are encoded for by several genes, some of which are also related to the biosynthesis of other phe- nylpropanoids. In this study, we aimed at the identification of those gene family members that are responsible for developmental lignification in Norway spruce (Picea abies (L.) Karst.). Gene expression across the whole lignin bio- synthetic pathway was profiled using EST sequencing and quantitative real-time RT-PCR. Stress-induced lignification during bending stress and Heterobasidion annosum infec- tion was also studied. Altogether 7,189 ESTs were sequenced from a lignin forming tissue culture and devel- oping xylem of spruce, and clustered into 3,831 unigenes. Several paralogous genes were found for both monolignol biosynthetic and polymerisation-related enzymes. Real- time RT-PCR results highlighted the set of monolignol biosynthetic genes that are likely to be responsible for developmental lignification in Norway spruce. Potential genes for monolignol polymerisation were also identified. In compression wood, mostly the same monolignol bio- synthetic gene set was expressed, but peroxidase expression differed from the vertically grown control. Pathogen infection in phloem resulted in a general up- regulation of the monolignol biosynthetic pathway, and in an induction of a few new gene family members. Based on the up-regulation under both pathogen attack and in com- pression wood, PaPAL2, PaPX2 and PaPX3 appeared to have a general stress-induced function. Keywords Compression wood Á EST Á Heterobasidion annosum Á Lignin biosynthesis Á Picea abies Á Real-time RT-PCR Abbreviations CAD Cinnamyl alcohol dehydrogenase CADL CAD-like CCOMT Caffeoyl-CoA O-methyltransferase CCR Cinnamoyl-CoA reductase COMT Caffeic acid O-methyltransferase CoA Coenzyme A Ct Cycle threshold C3H p-coumarate-3-hydroxylase C4H Cinnamate-4-hydroxylase EST Expressed sequence tag F5H/ CAld5H Ferulate/coniferaldehyde-5-hydroxylase Electronic supplementary material The online version of this article (doi:10.1007/s11103-007-9220-5) contains supplementary material, which is available to authorized users. S. Koutaniemi Á T. Warinowski Á A. Ka ¨rko ¨nen Á T. H. Teeri (&) Department of Applied Biology, University of Helsinki, Latokartanonkaari 7, PO Box 27, Helsinki 00014, Finland e-mail: teemu.teeri@helsinki.fi E. Alatalo Á L. Paulin Institute of Biotechnology, University of Helsinki, Helsinki, Finland C. G. Fossdal Norwegian Forest and Landscape Institute, A ˚ s, Norway P. Saranpa ¨a ¨ Á T. Laakso Finnish Forest Research Institute Metla, Vantaa, Finland K. V. Fagerstedt Á L. K. Simola Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland S. Rudd Centre for Biotechnology, Turku, Finland 123 Plant Mol Biol (2007) 65:311–328 DOI 10.1007/s11103-007-9220-5