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

Authors

Zhaorui Fan, Lian Liu, Liru Ma, Qing Lai, Chaoran Weng, Shengming Lu, Hui Zhu, Jiahui Chen, Yongshuai Sun, Dafu Ru

Published in

Cladistics : the international journal of the Willi Hennig Society. Oct 24, 2026. Epub Oct 24, 2026.

Abstract

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.

PMID:
42920398
Bibliographic data and abstract were imported from PubMed on 24 Oct 2026.

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