Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the .100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (.10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.

The large vascular meristem of poplar trees with its highly organized secondary xylem enables the boundaries between different developmental zones to be easily distinguished. This property of wood-forming tissues allowed us to determine a unique tissuespecific transcript profile for a well defined developmental gradient. RNA was prepared from different developmental stages of xylogenesis for DNA microarray analysis by using a hybrid aspen unigene set consisting of 2,995 expressed sequence tags. The analysis revealed that the genes encoding lignin and cellulose biosynthetic enzymes, as well as a number of transcription factors and other potential regulators of xylogenesis, are under strict developmental stage-specific transcriptional regulation.T ranscript profiling has the potential to reveal transcriptional hierarchy during development for thousands of genes, as well as providing expression data for many genes of unknown function (1, 2). This is especially true when expression patterns can be obtained for well defined tissues at specific developmental stages. However, this is technically demanding and so far there are no reports demonstrating tissue-specific analysis on cell types from a single developmental sequence. We have studied the developing secondary xylem of poplar, which is highly organized with easily recognized and distinct boundaries between the different developmental stages. Wood formation is initiated in the vascular cambium. Cambial derivatives develop into xylem cells through the processes of division, expansion, secondary wall formation, lignification, and finally, programmed cell death. The large physical size of the vascular meristem in trees offers a unique possibility to obtain samples from defined developmental stages by tangential cryo sectioning (3). To determine the steady-state mRNA levels at specific stages during the ontogeny of wood formation in Populus tremula ϫ Populus tremuloides (hybrid aspen) we sampled 30-m-thick sections through the wood development region and subsequently analyzed the samples by using a spotted cDNA-microarray (4) consisting of 2,995 unique ESTs from hybrid aspen. Our study provides a unique global examination of gene expression patterns that encompasses a developmental gradient within a multicellular organism. Materials and MethodsThe Unigene set was selected from the expressed sequence tags (ESTs) presented in ref. 5, using cluster analysis. ESTs were transformed into Escherichia coli by using TSS competent cells (6), plasmids were prepared by using 96-well Multiscreen FB plates (Millipore), inserts were PCR amplified by using vectorspecific primers, and PCR products were purified on Multiscreen PCR filter plates (Millipore) and spotted in duplicate onto CMT GAPS slides (Corning) by using the GMS 417 Arrayer (Affymetrix, Santa Clara, CA) as described (7). All PCR products were checked on ethidium bromide-stained agarose gels. Nine clones giving double PCR bands were excluded from the analysis.A subset of 2,085 of the 2,995 PCR products in the Unigene set...