Nervonic acid (NA) is a monounsaturated fatty acid (FA) with multiple therapeutic and hygienic benefits, and accumulates in plant seeds. It is essential for developing innovative plant sources of NA to elucidate the molecular regulation mechanisms underlying NA biosynthesis and accumulation. We present high-quality chromosome-level de novo genome assemblies of two contrasting NA-producing plants: high-NA Macaranga indica and low-NA M. denticulata. Both M. indica and M. denticulata retained considerable repetitive sequences, similar chromosome arrangements, and analogous regulation models in capsule maturation. Correlated to faster accumulation of NA, M. indica concentrated genes and regulators of FA biosynthesis, FA elongation and triacylglycerol biosynthesis in three ways: uniform regulators, fewer analogous duplications and higher expression of genes. In contrast, M. denticulata showed a diverse environment response, and had more analogous redundant duplications. Despite their sympatric distribution, the two species showed staggered flowering. Cold, ABA and phosphate starvation were major elicitors in M. indica, and core genes were identified as KCS, PDAT, and DGAT. Further resequencing analysis of M. indica revealed geography-specific gene polymorphisms and migration pathways. Our results unveil the differences in NA biosynthesis and accumulation mechanisms between M. indica and M. denticulata. This understanding, combined with insights into cultivation strategies and regional genetic diversity, provides a basis for the domestication and breeding of Macaranga species toward efficient NA production.

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