High-quality genomic data reveal the origin, dispersal, and lipid accumulation mechanisms of the woody oil-bearing species Pistacia chinensis

Pistacia chinensis is an oil-rich tree native to East Asia with considerable potential as a bioenergy species. Here, we present a near-complete genome assembly for P. chinensis , representing a significant improvement over existing genomic resources. We identified chromosome 1 (Chr1) as the ZW sex chromosome and delimited its sex-determining region. Chr1 harbored significantly more and denser transposable elements (TEs) than the autosomes, with TE copy number significantly correlated with chromosome length. Analysis of intact LTR insertion times further revealed an enrichment of recently inserted LTRs on Chr1 relative to the autosomes. Together, these findings suggest that TE accumulation has contributed to the expansion of the sex chromosome in P. chinensis . Phylogenetic analysis revealed three major genetic lineages of P. chinensis in East Asia, closely aligned with its geographic distribution. The P. chinensis germplasm in Yunnan Province likely represents the earliest ancestral lineage of this species, and we propose possible dispersal routes for P. chinensis across East Asia. The demographic history of P. chinensis indicates that temperature may be an important environmental factor affecting the population expansion. Additionally, we found that lipid droplet (LD) protein-encoding genes are critical for lipid accumulation. Transcriptome and regulatory analyses indicate that these LD protein-encoding genes are seed-specific, highly expressed during late development, and regulated by PcLEC2, a transcription factor that governs seed maturation. Our findings provide important genomic resources and mechanistic insights into the biology of P. chinensis , offering valuable guidance for its genetic improvement and breeding.