Chromosome-level assembly and analysis of three hydroxy fatty acid-producing Physaria species

Several Physaria species (Brassicaceae) produce abundant hydroxy fatty acids in their seeds, with industrial applications. Here, we report three chromosome-level genomes of Physaria species: P. lindheimeri, P. pallida and P. fendleri, with sizes of 344 Mb, 329 Mb and 452 Mb, respectively. Comparative genome analysis reveals that these three Physaria species diverged from Arabidopsis thaliana approximately 14.10-14.46 million years ago and underwent two consecutive Physaria-specific whole-genome duplication events. Their centromeres harbor an 111-bp satellite repeat and two retrotransposon classes (Gypsy/CRM, Copia/Ale). Transcriptomic analysis identifies seed-highly expressed lipid synthesis genes potentially underlying unique fatty acid profiles. Furthermore, we pinpoint the two residues in FAH12 variants that cause the disparity in hydroxylation activity among the three Physaria species. Taken together, this study provides important genomic resources for investigating the evolution of Physaria species and developing industrial oil crops for sustainable production of hydroxy fatty acids.