Picea pan-transcriptomes reveal signatures of complex phylogenetic conflict and adaptation.

Coniferous forests are among the ecosystems most exposed to rapid climate warming, and a well-resolved phylogeny of Picea is essential for understanding the evolutionary processes that have shaped diversification and regional differentiation across the genus. Here, we analysed pan-transcriptomes spanning 37 Picea species from across Northern Hemisphere forests. Our analyses reveal a bipartite pan-transcriptomic architecture in which core genes (9.4%) are associated primarily with fundamental cellular functions, whereas dispensable and private components (90.6% combined) are more strongly associated with ecological differentiation. Species trees inferred from low-copy orthologues resolve four major clades, and approximately 275 loci are sufficient to recover a stable backbone topology. Coalescent analyses indicate pervasive genealogical discordance, with incomplete lineage sorting (ILS) showing the greatest relative importance (27.75%) and gene-flow signals contributing less (7.27%). The most variable gene families (7.4%) further delimit three biogeographically structured regional groups: Qinghai-Tibet Plateau lineages are characterized by genes involved in environmental stress, signalling and low-oxygen responses; East Asian lineages show greater representation of protein metabolism and ubiquitin-mediated regulation; and Holarctic lineages are characterized by photosynthesis, chloroplast function, cell-wall processes and secondary metabolism. Together, these findings link regional gene-family differentiation with the persistence of ancestral polymorphism and provide a phylogenomic framework for understanding spruce diversification and for developing hypotheses relevant to climate-resilient forest conservation.