The pan-genome provides insights into evolutionary dynamics and fatty acid metabolism in Aceraceae family

The Aceraceae family has ecological, ornamental and economical importance in plants. However, the genetic variations, evolution, and domestication of Aceraceae species are not well understood. Pan-genomes provide a framework for capturing genetic diversity across a genus and for a comprehensive understanding of genomic variation during evolution. Here, we construct a graph-based pan-genome from 13 Aceraceae species, revealing evolutionary dynamics driven by long-terminal repeat retrotransposons. Sequencing of 134 cultivated Acer palmatum accessions identifies 2,160 single nucleotide polymorphisms associated with 10 fatty acid traits through genome wide association study. We further characterize 1,064,183 structural variation loci impacting fatty acid accumulation. By multi-omics analysis, we also identify ActKCS as a key candidate gene required for nervonic acid biosynthesis. Transgenic overexpression of ActKCS in Arabidopsis thaliana and Brassica napus enhances seed nervonic acid content, with increases ranging from 0.05% to 0.12% and 0.25% to 1.05%, respectively. We find that the transcription factor ActMYB95 directly regulates ActKCS. These findings decipher the genetic architecture underlying fatty acid synthesis and enable sustainable production of high value nervonic acid rich oils for neurological therapeutics and bio industrial applications. This study provides insights into the genetic and molecular mechanisms that underpin fatty acid biosynthesis. The resources and findings will accelerate the utilization and improvement of Aceraceae genetic diversity.