Comparative Genomics Points to Tandem Duplications of SAD Gene Clusters as Drivers of Increased ω-3 Content in S. hispanica Seeds

O_LIA high-quality chromosome-level reference genome of S. hispanica was assembled and analysed. C_LIO_LIAncestral whole-genome duplication events have not promoted the high -linolenic acid content in S. hispanica seeds C_LIO_LITandem duplication of six stearoyl-ACP desaturase genes is a plausible cause for high {omega}-3 content in chia seeds. C_LI Salvia hispanica L. (chia) is an abundant source of {omega}-3 polyunsaturated fatty acids (PUFAs) that are highly beneficial to human health. The genomic basis for this accrued PUFA content in this emerging crop was investigated through the assembly and comparative analysis of a chromosome-level reference genome for S. hispanica (321.5 Mbp). The highly contiguous 321.5Mbp genome assembly, which covers all six chromosomes enabled the identification of 32,922 protein coding genes. Two whole-genome duplications (WGD) events were identified in the S. hispanica lineage. However, these WGD events could not be linked to the high -linolenic acid (ALA, {omega}-3) accumulation in S. hispanica seeds based on phylogenomics. Instead, our analysis supports the hypothesis that evolutionary expansion through tandem duplications of specific lipid gene families, particularly the stearoyl-acyl carrier protein (ACP) desaturase (ShSAD) gene family, is the main driver of the abundance of {omega}-3 PUFAs in S. hispanica seeds. The insights gained from the genomic analysis of S. hispanica will help leveraging advanced genome editing techniques and will greatly support breeding efforts for improving {omega}-3 content in other oil crops.