Chromosome-scale genome assembly and integrated transcriptomic analysis reveal candidate regulators of omega-3 fatty acid and triacylglycerol biosynthesis in sacha inchi (Plukenetia volubilis)

Sacha inchi ( Plukenetia volubilis L.) is an emerging woody oilseed crop renowned for its exceptionally high alpha-linolenic acid (ALA) content. However, the lack of a chromosome‑scale reference genome has severely limited the dissection of its unique lipid biosynthetic pathways, a key gap beyond existing transcriptome‑only studies in this species. In this study, we report a high-quality, chromosome-scale genome assembly of sacha inchi, spanning 710.62 Mb, with 94.3% BUSCO completeness. The Hi-C scaffolding anchored 86.32% of the assembled sequences onto 29 pseudochromosomes (11.04–35.98 Mb). We annotated 37,570 protein-coding genes and identified 379.86 Mb (53.45%) of repetitive sequences. Phylogenomic analyses show that sacha inchi diverged from its closest sequenced relative, Ricinus communis , approximately 32.6 million years ago, with only ancient whole-genome duplication events. Combined with developmental transcriptome profiling, our analyses suggest that high TAG content may be associated with the sustained expression of biosynthetic genes and low activity of degradation genes during mid-to-late seed development. Notably, while genes encoding stearoyl-ACP desaturases (SADs) may help maintain the precursor pool, the expression of genes encoding fatty-acid desaturase 2 (FAD2) and FAD3 is positively correlated with the final accumulation of C18:2 and C18:3 fatty acids, respectively. We further identified candidate lncRNAs that may modulate core desaturase gene transcription, as inferred from co-expression patterns, although functional validation is still required. Together, this work provides a foundational genomic resource for elucidating lipid metabolism and advancing molecular breeding strategies in this industrially important oilseed crop.