Conifer genomes present challenges for successful sequencing, mainly due to their large size and complexity. The goal of the PineRefSeq project is the development of a high quality reference genome sequence for loblolly pine (Pinus taeda), Douglas-fir (Pseudotsuga menziesii) and sugar pine (Pinus lambertiana) by means that can serve as a model approach for sequencing other large, complex genomes. In addition to the reference sequence, extensive transcriptome sequencing in loblolly pine will provide a basis for gene discovery and aid in the final genome assembly. The results will empower the forest tree biology research community and the broader biological research community in the practical use and application of this resource. A primary tenet of this work is to develop new sequencing approaches that can rapidly and inexpensively sequence genomes exceeding 20Gb. A second tenet is to fully integrate genome sequences into all other existing genomic information resources that can be used by researchers, breeders, and resource managers. The primary vehicle for accomplishing this goal is the Dendrome/TreeGenes databases that have served the forestry community for 20 years. In addition, we are collaborating with the horticultural genomics community through the Genome Database for Rosaceae (GDR) project. Together, we will develop community-based gene annotation and genome database platforms that leverage the strengths of both the forestry and the horticultural community.