SummaryMaritime pine (Pinus pinaster Ait.) is a widely distributed conifer species in Southwestern Europe and one of the most advanced models for conifer research. In the current work, comprehensive characterization of the maritime pine transcriptome was performed using a combination of two different next-generation sequencing platforms, 454 and Illumina. De novo assembly of the transcriptome provided a catalogue of 26 020 unique transcripts in maritime pine trees and a collection of 9641 full-length cDNAs. Quality of the transcriptome assembly was validated by RT-PCR amplification of selected transcripts for structural and regulatory genes. Transcription factors and enzyme-encoding transcripts were annotated. Furthermore, the available sequencing data permitted the identification of polymorphisms and the establishment of robust single nucleotide polymorphism (SNP) and simple-sequence repeat (SSR) databases for genotyping applications and integration of translational genomics in maritime pine breeding programmes. All our data are freely available at SustainpineDB, the P. pinaster expressional database. Results reported here on the maritime pine transcriptome represent a valuable resource for future basic and applied studies on this ecological and economically important pine species.

Global transition towards a bioeconomy sets new demands for wood supply (bioenergy, biomaterials, biochemicals, etc.), and the forestry sector is also expected to help mitigate climate change by increasing carbon fixation. For increased biomass production, the use of improved, genetically superior materials becomes a necessity, and vegetative propagation of elite genotypes provides a potential delivery mechanism for this. Vegetative propagation through somatic embryogenesis alone or in combination with rooted cuttings obtained from somatic young trees can facilitate both tree breeding (greater selection accuracy and gains,