1000 conifer genomes: Genome innovation, organisation and diversity

Norway spruce (Picea abies L. Karst) and Scots pine (Pinus sylvestris L.) are the dominant tree species in northern Eurasia with global importance for carbon sequestration and that are increasingly at risk from climate change. Here, we present chromosome-scale reference genomes for both species and an unprecedented conifer resequencing effort comprising over 1000 Norway spruce trees. We show that, despite diverging ~130 million years ago, and in contrast to angiosperms, the genomes retain remarkable macro-synteny with no signs of major chromosomal rearrangements or recent whole genome duplications. Instead, genetic novelty is primarily fuelled by novel gene copy creation by frequent segmental duplications, independent of retrotransposition, that account for almost 1 Gbp of novel genetic material created since the spruce/pine split. We show that gene accessibility and regulation in these large genomes is facilitated by a highly structured three-dimensional chromatin organisation and epigenetic landscape, with housekeeping genes containing long introns located at the boundaries of topologically associating domains (TADs), with TADs and chromatin loops facilitating gene co-expression. Comparative transcriptome profiling during wood development identified sub- and neo-functionalisation among segmentally duplicated genes, as well as conserved and diverged gene co-expression between species. Population genomics analyses confirmed a recently expanded, largely panmictic population with a latitudinal cline, and identified genes under selection involved in climate adaptation and geographically segregating presence-absence variation of genes.