Comparative Genomics Points to Tandem Duplications ofSADGene Clusters as Drivers of Increased ω-3 Content inS. hispanicaSeeds

Abstract

ABSTRACTA high-quality chromosome-level reference genome ofS. hispanicawas assembled and analysed.Ancestral whole-genome duplication events have not promoted the high α-linolenic acid content inS. hispanicaseedsTandem duplication of six stearoyl-ACP desaturase genes is a plausible cause for high ω-3 content in chia seeds.Salvia hispanicaL. (chia) is an abundant source of ω-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 forS. 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 theS. hispanicalineage. However, these WGD events could not be linked to the high α-linolenic acid (ALA, ω-3) accumulation inS. hispanicaseeds 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 ω-3 PUFAs inS. hispanicaseeds. The insights gained from the genomic analysis ofS. hispanicawill help leveraging advanced genome editing techniques and will greatly support breeding efforts for improving ω-3 content in other oil crops.