Chromosome-level genome assembly of Pinus massoniana provides insights into conifer adaptive evolution.

Pinus massoniana, a conifer of significant economic and ecological value in China, is renowned for its wide adaptability and oleoresin production. We sequenced and assembled the chromosomal-level P. massoniana genome, revealing 80,366 protein-coding genes and significant gene family expansions associated with stress response and plant-pathogen interactions. Long-intron genes, which are predominantly presented in low-copy gene families, are strongly linked to the recent long terminal repeat burst in the Pinus genome. By reanalyzing population transcriptomic data, we identified genetic markers linked to oleoresin synthesis, including those within the CYP450 and TPS gene families. The results suggest that the genes of the resin terpene biosynthesis pathway can be activated in several cell types, and the oleoresin yield may depend on the rate-limiting enzymes. Using a multiomics algorithm, we identified several regulatory factors, including PmMYB4 and PmbZIP2, that interact with TPS and CYP450 genes, potentially playing a role in oleoresin production. This was further validated through molecular genetics analyses. We observed signatures of adaptive evolution in dispersed duplicates and horizontal gene transfer events that have contributed to the species adaptation. This study provides insights for further research into the evolutionary biology of conifers and lays the groundwork for genomic-assisted breeding and sustainable management of Masson pine.