Reference genome of the nutrition-rich orphan crop chia (Salvia hispanica) and its implications for future breeding

Abstract

Chia (Salvia hispanica L.) is one of the most popular nutrition-rich foods and pseudocereal crops of the family Lamiaceae. Chia seeds are a rich source of proteins, polyunsaturated fatty acids (PUFAs), dietary fibers, and antioxidants. In this study, we present the assembly of the chia reference genome, which spans 303.6 Mb and encodes 48,090 annotated protein-coding genes. Our analysis revealed that ~42% of the chia genome harbors repetitive content, and identified ~3 million single nucleotide polymorphisms (SNPs) and 15,380 simple sequence repeat (SSR) marker sites. By investigating the chia transcriptome, we discovered that ~44% of the genes undergo alternative splicing with a higher frequency of intron retention events. Additionally, we identified chia genes associated with important nutrient content and quality traits, such as the biosynthesis of PUFAs and seed mucilage fiber (dietary fiber) polysaccharides. Notably, this is the first report of in-silico annotation of a plant genome for protein-derived small bioactive peptides (biopeptides) associated with improving human health. To facilitate further research and translational applications of this valuable orphan crop, we have developed the Salvia genomics database (SalviaGDB), accessible at https://salviagdb.org.

Keywords: Salvia hispanica; biopeptide; chia; lectins; polyunsaturated fatty acid (PUFA); reference genome; seed mucilage; terpene synthase.

Figure 1

Overview of the chia (Salvia hispanica) genome assembly and the annotated features.

Figure 2

Synteny analysis of the chia genome. (A) Chromosome wise colinear genes shared between chia, Arabidopsis and tomato; (B) Chromosome wise collinear gene location; (C) The ratio of non-synonymous (Kn) to synonymous (KS) substitutions per site between syntenic orthologues.

Figure 3

Chia gene family and phylogenetic analysis. (A) Inparanoid-based gene family analysis; (B) Gene family member gain/loss analysis. Gains (blue), conserved (orange), and loss (Grey); (C) Species wise gene distribution in the most significant families.

Figure 4

Chia gene family and expression analysis. (A) Lectin gene family tree with gene expression profiles; (B) terpene synthase (TPS) gene family tree with gene expression profile data.

Figure 5

Chia genes involved in PUFA biosynthesis pathway and their expression across different developmental stages. (A) Biosynthesis of omega-3 and omega-6 fatty acids. LA, Linoleic acid; ALA, α-linolenic acid; GLA, γ‐linolenic acid; SDA, Stearidonic acid; ETA, Eicosatetraenoic acid; DGLA, dihomo-γ-linolenic acid; DHA, Docosahexaenoic acid; DPA, Docosapentaenoic acid. (B) expression of genes involved in omega-3 and omega-6 fatty acids biosynthesis; (C) expression of oleosin, caleosin, and steroleosin genes. The reactions with dashed arrows represent multiple steps. The gene IDs marked with an asterisk (*) represent tandemly duplicated genes. Gene IDs and names in green text are potentially targeted to chloroplast.

Figure 6

Biosynthesis pathways and expression analysis of Chia genes involved in biosynthesis of seed mucilage polysaccharide monomer units. (A) Glucuronate biosynthesis; (B) D-Galacturonate biosynthesis; (C) D-Mannose biosynthesis; (D) D-Xylose biosynthesis; (E) L-Arabinose biosynthesis. The gene IDs marked with an asterisk (*) represent tandemly duplicated genes.