Conifers are of enormous ecological and economic importance and improved understanding of conifer genomics, genetics and evolution is crucial for questions related to climate change, biodiversity and for sustainable and efficient forestry.  

We have produced chromosome-scale, high-quality reference genomes of Norway spruce (Picea abies) and Scots pine (Pinus sylvestris), the two most ecologically important conifers in Europe. Our annotation of the genome included identification of pseudogenes and long non-caoding RNAs, both of which are highly abundant. There are many protein coding genes with very long introns as a result of transposable element (TE) insertions. Despite the prevalence of TEs, there is striking macro-synteny between the two genomes across all chromosomes. Contrary to expectations, we found that genetic innovation by novel coding gene copies is laregly driven by local segmental or tandem duplications rather than new genes arising from retrotransposition. We additionally explored the role of chromatin conformation and associated epigenetic signals to increase understanding of transcriptional control in these giant genomes, finding that protein coding genes are largely located at the borders of intergenic condensed spacers (ICONS). 

We have complemented the improved Norway spruce genome assembly with short-read whole-genome re-sequencing of more than 1000 trees originating from across Eurasia. Analysis of this resource has identified signals of selection and provided a more detailed view of within-species variation, including larger structural variations. Combined with large-scale genotyping using a newly design SNP chip, these resources are now enabling a new era of breeding using genomic selection.